Biodiversity and Earth History

Jens Boenigk · Sabina Wodniok
Edvard Glücksman
Biodiversity
and Earth History
Biodiversity and Earth History
Jens Boenigk • Sabina Wodniok • Edvard Glücksman
Biodiversity and Earth History

Jens Boenigk Sabina Wodniok
Faculty of Biology Faculty of Biology
Biodiversity Department Biodiversity Department
University Duisburg-Essen University Duisburg-Essen
Essen, Germany Essen, Germany
Edvard Glücksman
Environment & Sustainability Institute
University of Exeter, Cornwall Campus
Penryn, Cornwall, UK
ISBN 978-3-662-46393-2 ISBN 978-3-662-46394-9 (eBook)

DOI 10.1007/978-3-662-46394-9
Library of Congress Control Number: 2015936446
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Foreword V
Foreword
The detection of biological diversity and the understand- eukaryotes in the context of geological history. The focus
ing of its underlying mechanisms – how it is generated and of this work, therefore, is to address areas not covered by
maintained – has preoccupied humans since antiquity. Snap- conventional textbooks, specifically forging interdisciplinary
shots of information about biodiversity were developed as links to develop new methods of understanding known con-
early as in Ancient Greece, especially by the philosophers cepts. To that end, we address the overall diversity of eukary-
Aristotle and Theophrastus. In the 18th century, Carl Lin- otes, avoiding the standard anthropocentric view of life as
naeus proposed a classification system for plants and ani- mainly comprising animals and plants. We also cover, based
mals, initially to understand the Divine Order of God’s crea- on highly advanced molecular studies, the phylogenetic de-
tion. Roughly a century later, Charles Darwin published his velopment of species in the context of the planet’s geological
canonical ideas about species variability; his theory of evo- development, weaving together the history of the Earth and
lution continues to drive global research into the molecular the evolution of life.
diversity of species, communities, and ecosystems, including We address classical biological and geosciences concepts
the Human Genome Project or the Census of Marine Life. in a fresh and innovative manner. Our approach represents a
Biodiversity is one of the most complex research topics. In definite break from the disciplinary segregation that charac-
order to properly understand the mechanisms underpinning terises conventional textbooks; such a dramatic change could
species distribution patterns, researchers must bring together not be avoided. However, in our opinion, this ‘interdiscipli-
information from a range of different disciplines, mapping narity’ is one of the book’s great strengths, broadening the
the evolution and development of organisms to their ecologi- context of biodiversity studies and presenting new insights
cal adaptations and interactions, and linking physiological across century-old disciplines.
and morphological diversity patterns to the interplay be- This book covers a range of concepts largely underrepre-
tween Earth’s geological development and the evolution of sented in the literature. For example, we describe at length
the planet’s life forms. the geological drivers behind the emergence of biodiversity
Tools from a wide variety of disciplines, especially in the and current global species distribution patterns. We also
life- and geosciences, are needed to address the various com- address in detail the enormous diversity of eukaryotes, em-
ponents relating to biodiversity. Maintaining and developing phasising their massive but often overlooked microscopic
this interdisciplinary framework is the key to understanding component. Therefore, at the very least, the content of this
the emergence and preservation of species. Despite these book draws from geology and palaeontology, morphology
unique advantages of such a broad-based approach, such and physiology, chemistry and physics, biology and ecology,
work continues to face significant opposition, including from as well as from the most cutting-edge biological systematics.
more conventional, single-discipline methods. Although to Our hope is that the truely transdisciplinary focus of this
a certain extent valuable as independent research strands, book will resonate with researchers, teachers, and students
such frameworks restrain and restrict our understanding of alike, as well as with members of the general public curious
the more multifaceted aspects inherent in global biodiversity to learn more about biodiversity – one of nature’s most fun-
studies. damental and awe-inspiring phenomena.
In this book we provide a balancing act between the geo-
sciences and biosciences, aiming to examine the diversity of
VI Acknowledgements
Acknowledgements
We thank Susann Schiwy and Julia Nuy for their great We thank everyone at Springer-Spektrum, in particular
support in all aspects of this book’s design. In particular, we Meike Barth, Merlet Behncke-Braunbeck, Barbara Lühker,
thank Susann for her tremendous effort in compiling and and Andreas Held for the proofreading as well as everyone
managing the image database and Julia for her invaluable at Springer, in particular Stephan Klapp and Ulrike Strick-
contributions to the book’s layout and graphics through her er-Komba. For proofreading and editing, we also thank the
mastery of Adobe InDesign. staff from proof-reading-service.com and Deutsche Hochs-
We also thank Wolfgang Boenigk and Lars Großmann for chulverband, and specifically Frederic Bartlett and Gabriele
their critical comments and editorial help in earlier versions Berberich.
of the manuscript. Finally, we are particularly grateful to our families and
We thank the late Michael Neugebauer and the rest of loved ones. In particular, JB thanks his wife, Stephanie, for
the Boenigk working group for their patience and support, her infinite patience throughout the countless hours of re-
especially during the increasingly stressful periods leading up search, creation of figures, and during the writing process.
to the submission of both manuscripts. Her understanding gave him the time to bring this project
We are also grateful to many colleagues and photogra- to fruition. SW thanks her partner, Thomas, and the rest of
phers for making the many images featured in this book her family for their loving support, patience, and encourage-
available to us. Without them, this project would not have ment. EG thanks his partner, Antonia, for all her love and
been possible. inspiration, and his parents, Jerzy and Soulla, for a lifetime
of support.
Content VII
Table of contents
1 Introduction ..................................................................................................................................... 1
1.1 How do I use this book? .............................................................................................................. 2
1.2 Biodiversity ..................................................................................................................................... 4
1.3 Life .................................................................................................................................................... 6
1.4 Species ............................................................................................................................................. 8
2 Earth‘s History ................................................................................................................................ 11
2.1 Fundamentals of the geosciences ............................................................................................ 12
2.1.1 Construction and formation of the Earth .................................................................................. 14

2.1.1.1 Composition of the Earth’s layers .......................................................................................... 16
2.1.1.2 Plate tectonics ................................................................................................................... 18
2.1.2 Rock-forming processes ............................................................................................................ 20
2.1.2.1 Magmatism and igneous rocks.............................................................................................. 22
2.1.2.2 Weathering, erosion, sedimentation and sedimentary rocks...................................................... 24
2.1.2.3 Carbonate balance and carbonates ....................................................................................... 26
2.1.3 Eons........................................................................................................................................... 28
2.2 The Precambrian ........................................................................................................................... 30
2.2.1 The Archean eon ....................................................................................................................... 32

2.2.1.1 Chemical evolution and origin of life ...................................................................................... 34
2.2.1.2 ‘RNA world hypothesis’ and formation of cells during the Archean ............................................. 36
2.2.1.3 The Archean carbon metabolism: fermentation ....................................................................... 38
2.2.1.4 Evolution of the Archean photoautotrophy:
energetics of the anoxygenic and oxygenic photosynthesis ....................................................... 40
2.2.1.5 Evolution of the Archean photoautotrophy: compartmentalisation ............................................ 42
2.2.2 The Proterozoic eon .................................................................................................................. 44
2.2.2.1 Biogenic and geochemical feedback loops of the Proterozoic oxygen evolution ............................ 46
2.2.2.2 Climatic effects of oxygen evolution: the Huronian glaciation (from 2.4 to 2.1 billion years) ........... 48
2.2.2.3 Metabolic effects of oxygen evolution: cytotoxic effect ............................................................. 50
2.2.2.4 Metabolic consequences of oxygen evolution: aerobic respiration ............................................. 52
2.2.2.5 Evolution of the eukaryotic cell in the Mesoproterozoic ............................................................ 54
2.2.2.6 Evolution of the eukaryotic algae in the Mesoproterozoic ......................................................... 56
2.2.2.7 The ‘boring billion’ years (1.85-0.85 billion years) .................................................................... 58
2.2.2.8 Evolution of complex multi-cellularity in the Neoproterozoic ..................................................... 60
2.2.2.9 Neoproterozoic glaciations (0.85–0.72 billion years)................................................................. 62
VIII Content
2.3 The Phanerozoic eon ................................................................................................................... 64
2.3.1 The Phanerozoic eon: an overview ........................................................................................... 66

2.3.1.1 Plate tectonics and climate evolution during the Phanerozoic .................................................... 68
2.3.1.2 Lagerstätten....................................................................................................................... 70
2.3.1.3 Fossilisation – the formation of fossils.................................................................................... 72
2.3.1.4 Geochronology and stratigraphy ........................................................................................... 74
2.3.1.5 Termination and biostratigraphic definition of the Phanerozoic systems ...................................... 76
2.3.2 Fossil biodiversity ...................................................................................................................... 78
2.3.2.1 Foraminifers ...................................................................................................................... 80
2.3.2.2 Reef-builders ..................................................................................................................... 82
2.3.2.3 Cephalopods ...................................................................................................................... 84
2.3.2.4 Benthic filter-feeders: brachiopods and bivalves ...................................................................... 86
2.3.2.5 Trilobites ........................................................................................................................... 88
2.3.2.6 Echinoderms ...................................................................................................................... 90
2.3.2.7 Graptolites and Conodonts................................................................................................... 92
2.3.2.8 Vertebrates........................................................................................................................ 94
2.3.2.9 Land plants ........................................................................................................................ 96
2.3.3 The Palaeozoic era .................................................................................................................... 98
2.3.3.1 The Ediacaran and Phanerozoic-Precambrian boundary ............................................................ 100
2.3.3.2 Evolution of skeletal elements .............................................................................................. 102
2.3.3.3 The Cambrian period........................................................................................................... 104
2.3.3.4 The Ordovician period ......................................................................................................... 106
2.3.3.5 The Silurian period.............................................................................................................. 108
2.3.3.6 Colonisation of terrestrial environments ................................................................................ 110
2.3.3.7 The Devonian period ........................................................................................................... 112
2.3.3.8 The Carboniferous period .................................................................................................... 114
2.3.3.9 The Permian period ............................................................................................................ 116
2.3.3.10 Development of the cormus ............................................................................................... 118
2.3.3.11 Towards a smaller and shorter-lived haploid generation (gametophyte) .................................... 120
2.3.3.12 Towards an increasingly dominant diploid generation (sporophyte) .......................................... 122
2.3.4 The Mesozoic era ...................................................................................................................... 124
2.3.4.1 The Triassic period .............................................................................................................. 126
2.3.4.2 Reproductive adaptations to terrestrial life ............................................................................. 128
2.3.4.3 The Jurassic period ............................................................................................................. 130
2.3.4.4 Sauria ............................................................................................................................... 132
2.3.4.5 The Cretaceous period ........................................................................................................ 134
2.3.4.6 EEvolution of pollination ...................................................................................................... 136
2.3.5 The Cenozoic era ....................................................................................................................... 138
2.3.5.1 The Palaeogene period ........................................................................................................ 140
2.3.5.2 The Neogene period ........................................................................................................... 142
2.3.5.3 Evolution of C4 photosynthesis .............................................................................................. 144
2.3.5.4 Physiological efficiency of C4 and CAM photosynthesis ............................................................. 146
2.3.5.5 The Quaternary period ........................................................................................................ 148
2.3.5.6 The Cenozoic Ice Age........................................................................................................... 150
Content IX
2.3.5.7 Hominisation ..................................................................................................................... 152

2.3.5.8 The future ......................................................................................................................... 154
3 Distribution of present-day biodiversity ....................................................................... 157
3.1 Basics of the biogeographical distribution of taxa ............................................................... 158
3.1.1 Species descriptions .................................................................................................................. 160

3.1.2 The species concept .................................................................................................................. 162
3.1.3 Molecular diversity and OTUs ................................................................................................... 164
3.1.4 Biodiversity indices ................................................................................................................... 166
3.1.5 Spatial distribution of biodiversity ............................................................................................ 168
3.1.6 Species concept limitations: viruses ......................................................................................... 170
3.1.7 Species concept limitations: lichen ........................................................................................... 172
3.2 Biodiversity distribution .............................................................................................................. 174
3.2.1 Pattern and mechanisms .......................................................................................................... 176

3.2.1.1 Biodiversity hotspots........................................................................................................... 178
3.2.1.2 Ecological niches ................................................................................................................ 180
3.2.1.3 Speciation mechanisms ....................................................................................................... 182
3.2.1.4 Island biogeography ............................................................................................................ 184
3.2.1.5 Global biodiversity gradients ................................................................................................ 186
3.2.1.6 Biogeography of microorganisms .......................................................................................... 188
3.2.1.7 Alien and invasive species .................................................................................................... 190
3.2.1.8 Cenozoic mass extinction ..................................................................................................... 192
3.2.2 Biogeographic regions............................................................................................................... 194
3.2.2.1 Global precipitation and temperature distribution ................................................................... 196
3.2.2.2 Global wind systems and climate zones .................................................................................. 198
3.2.2.3 Tundra .............................................................................................................................. 200
3.2.2.4 Taiga ................................................................................................................................. 202
3.2.2.5 Temperate forests ............................................................................................................... 204
3.2.2.6 Temperate grasslands .......................................................................................................... 206
3.2.2.7 Montane and flooded grasslands .......................................................................................... 208
3.2.2.8 Mediterranean biome ......................................................................................................... 210
3.2.2.9 Hot and temperate deserts .................................................................................................. 212
3.2.2.10 Subtropical and tropical grasslands ...................................................................................... 214
3.2.2.11 Subtropical and tropical arid (xerophytic) forests ................................................................... 216
3.2.2.12 Tropical rainforest ............................................................................................................. 218
3.2.2.13 Lakes .............................................................................................................................. 220
3.2.2.14 Rivers .............................................................................................................................. 222
3.2.2.15 Oceans and seas ............................................................................................................... 224
X Content
4 Megasystematics .......................................................................................................................... 227
4.1 Basics of Megasystematics ......................................................................................................... 228
4.1.1 Historical and philosophical basis of megasystematics ............................................................. 230

4.1.1.1 Carl Linnaeus and the fundamentals of modern systematics ...................................................... 232
4.1.1.2 Basics of modern phylogeny: Darwin and Pasteur .................................................................... 234
4.1.1.3 What is a plant? ................................................................................................................. 236
4.1.1.4 What is an animal? ............................................................................................................. 238
4.1.1.5 What is a fungus? ............................................................................................................... 240
4.1.1.6 Phylogenetic trees .............................................................................................................. 242
4.1.1.7 Cladograms and phylograms................................................................................................. 244
4.1.1.8 Molecular diversity of the eukaryotic supergroups ................................................................... 246
4.1.2 The three domains .................................................................................................................... 248
4.1.2.1 Bacteria ............................................................................................................................ 250
4.2.2.2 Archaea ............................................................................................................................ 252
4.1.2.3 Eukarya ............................................................................................................................. 254
4.1.2.4 Eukarya: Cellular structures .................................................................................................. 256
4.2 Unikonta (= Amorphea) ............................................................................................................... 258
4.2.1 Holozoa ..................................................................................................................................... 260

4.2.1.1 Choanomonada .................................................................................................................. 262
4.2.1.2 Porifera ............................................................................................................................. 264
4.2.1.3 Placozoa, Cnidaria, Ctenophora............................................................................................. 266
4.2.1.4 Protostomia ....................................................................................................................... 268
4.1.2.5 Ecdysozoa.......................................................................................................................... 270
4.2.1.6 Spiralia.............................................................................................................................. 272
4.2.1.7 Deuterostomia ................................................................................................................... 274
4.2.1.6 Gnathostomata .................................................................................................................. 276
4.2.1.9 Amniota ............................................................................................................................ 278
4.2.2 Holomycota ............................................................................................................................... 280
4.2.2.1 Microsporidia and Chytridiomycota ....................................................................................... 282
4.2.2.2 Glomeromycota: arbuscular mycorrhizal fungi ........................................................................ 284
4.2.2.3 Zygospore-forming fungi ...................................................................................................... 286
4.2.2.4 Ascomycota ....................................................................................................................... 288
4.2.2.5 Basidiomycota.................................................................................................................... 290
4.2.3 Amoebozoa ............................................................................................................................... 292
4.2.3.1 Conosa.............................................................................................................................. 294
4.3 Excavata ........................................................................................................................................... 296
4.3.1 Metamonada ............................................................................................................................ 298

4.3.2 Discoba...................................................................................................................................... 300
4.3.2.1 Euglenozoa: Euglenida......................................................................................................... 302
4.3.2.2 Euglenozoa: Kinetoplastea ................................................................................................... 304
Content XI
4.4 Archaeplastida ............................................................................................................................... 306
4.4.1 Glaucocystophyta ...................................................................................................................... 308

4.4.2 Rhodophyta............................................................................................................................... 310
4.4.3 Viridiplantae .............................................................................................................................. 312
4.4.3.1 Streptophyta...................................................................................................................... 314
4.4.3.2 Basale embryophytes: bryophytes ......................................................................................... 316
4.4.3.3 Rhyniophytina and Lycopodiophytina .................................................................................... 318
4.4.3.4 Monilophyta (Ferns)............................................................................................................ 320
4.4.3.5 Gymnosperms.................................................................................................................... 322
4.4.3.6 Magnoliopsida I: Overview ................................................................................................... 324
4.4.3.7 Basal Magnoliopsida and Monocotyledons ............................................................................. 326
4.4.3.8 Eudicotyledons I: Rosids ...................................................................................................... 328
4.4.3.9 Eudicotyledons II: Asterids ................................................................................................... 330
4.5 Rhizaria ............................................................................................................................................ 332
4.5.1 Cercozoa.................................................................................................................................... 334

4.5.2 Retaria ....................................................................................................................................... 336
4.5.2.1 Foraminifera ...................................................................................................................... 338
4.6 Alveolata and Stramenopiles ..................................................................................................... 340
4.6.1 Alveolata ................................................................................................................................... 342

4.6.1.1 Ciliophora.......................................................................................................................... 344
4.6.1.2 Dinophyta ......................................................................................................................... 346
4.6.1.3 Apicomplexa ...................................................................................................................... 348
4.6.2 Stramenopiles ........................................................................................................................... 350
4.6.2.1 Peronosporomycetes (Oomycetes) ........................................................................................ 352
4.6.2.2 Phaeophyceae ................................................................................................................... 354
4.6.2.3 Chrysophyceae ................................................................................................................... 356
4.6.2.4 Bacillariophyceae ............................................................................................................... 358
4.7 Hacrobia and eukaryotes of uncertain placement (incertae sedis) ................................ 360
4.7.1 Haptophyta ............................................................................................................................... 362
4.7.2 Cryptophyta .............................................................................................................................. 364
Glossary ................................................................................................................................................... 367
References ............................................................................................................................................. 379
Index .......................................................................................................................................................... 387

XII List of subject boxes
List of subject boxes
Cilium/Flagellum ............................................................................................................................................... 259
Protection from predation ................................................................................................................................ 261
Predator-prey size relationships ........................................................................................................................ 263
Motile and sessile lifestyles ............................................................................................................................... 265
Symmetry and body structure ........................................................................................................................... 267
Segmentation .................................................................................................................................................... 269
Freezing and thawing ........................................................................................................................................ 271
Why can some fossils not be found? ................................................................................................................. 273
Protection from UV radiation ............................................................................................................................ 275
The development of dinosaurs and angiosperms ............................................................................................. 277
Size and dimensions .......................................................................................................................................... 279
Cell wall materials ............................................................................................................................................. 281
Generational shift in parasites .......................................................................................................................... 283
Mycorrhiza......................................................................................................................................................... 285
Organisational morphology and phylogeny....................................................................................................... 287
Multinucleate cells ............................................................................................................................................ 289
Symbiosis / mutualism ...................................................................................................................................... 291
Pseudopodia ...................................................................................................................................................... 293
Chemical communication and semiochemicals................................................................................................. 295
Phagocytosis ...................................................................................................................................................... 297
Hydrogenosomes............................................................................................................................................... 299
Reducing of genome size in parasites................................................................................................................ 301
Perception of light ............................................................................................................................................. 303
Position of the kinetoplast-kinetosome-flagellar pocket complex .................................................................... 305
Chlorophyll ........................................................................................................................................................ 307
Are higher-level organisms evolutionarily better-adapted? .............................................................................. 309

List of subject boxes XIII
Photo pigments and vertical ecological niches.................................................................................................. 311
Multicellularity .................................................................................................................................................. 313
Shape as protection against predation .............................................................................................................. 315
Cell wall and cuticula ......................................................................................................................................... 317
Alternation of generations – meiosis ................................................................................................................ 319
Vascular bundles ............................................................................................................................................... 321
Origin, radiation, and dominance of taxa .......................................................................................................... 323
Ancestry of the Magnoliopsida lineage ............................................................................................................. 325
Carnivory in plants and fungi............................................................................................................................. 327
Distribution mechanisms (wind and animal) ..................................................................................................... 329
Coevolution within pollination biology ............................................................................................................. 331
Nucleomorph .................................................................................................................................................... 333
Paulinella: a model for the emergence of plastids ............................................................................................ 335
Biogenic minerals .............................................................................................................................................. 337
Biomineralisation .............................................................................................................................................. 339
Organelles.......................................................................................................................................................... 341
Model organisms ............................................................................................................................................... 343
Endosymbiotic algae.......................................................................................................................................... 345
Bioluminescence ............................................................................................................................................... 347
Compartmentalisation ...................................................................................................................................... 349
Osmoregulation ................................................................................................................................................. 351
The chemical basis for life ................................................................................................................................. 353
Buoyancy ........................................................................................................................................................... 355
Phototrophy, mixotrophy, heterotrophy ........................................................................................................... 357
Locomotion by gliding ....................................................................................................................................... 359
Eukaryotic biocenosis and the ‘microbial loop’ ................................................................................................. 361
Algal blooms ...................................................................................................................................................... 363
Surface scales .................................................................................................................................................... 365

XIV Biographies
Professor Jens Boenigk is head of the Biodiversity Department at the University of Duis-
burg-Essen. His broad research interests include the many different facets of molecular
and organismal biology and how they relate to biodiversity, specifically focusing on the
mechanisms of speciation, evolution, phylogenetics, population biology, and biogeography.
Professor Boenigk also teaches general botany and biodiversty to undergraduate students at
all levels. His previous postdoctoral work, carried out at the Austrian Academy of Sciences,
focused on the diversity and feeding ecology of protists, specifically on the functional dif-
ferentiation between phototrophic and heterotrophic flagellates. He has also held a Marie
Curie Fellowship at the Natural History Museum in London, where he investigated effects
of suspended sediments on the microbial food web. Professor Boenigk holds a PhD in Zool-
ogy from the University of Cologne, where his doctoral work focused on feeding interac-
tions within the microbial food web. He studied biology and geology at the University of
Cologne and holds a Diploma in Biology, which included a research project on the impact
of livestock on the vegetation of semiarid areas within the southern Namib desert.
Dr Sabina Wodniok is a researcher in the Biodiversity Department at the University

of Duisburg-Essen, where she is currently exploring the evolution and ecological signifi-
cance of plastid reduction in algae, their molecular evolution and phylogeny, as well as the
biodiversity and distribution patterns of protists more generally. She teaches biodiversity,
molecular evolution, and different aspects of botany to undergraduate students and coor-
dinates the faculty’s study courses. Dr Wodniok previously studied the genome evolution
of Viridiplantae, which formed the bulk of her doctoral work, carried out at the University
of Cologne. She also holds a Diploma from the University of Bielefeld, which included a
research project on establishment of genetic transformation in green algae.
Dr Edvard Glücksman is a scientist based at the University of Exeter’s Environment and

Sustainability Institute, where he is currently researching strategies for responsible mining.
He has previously worked both as a postdoctoral fellow in microbial ecology at the Uni-
versity of Duisburg-Essen and as a professional science communicator with the European
Geosciences Union, Europe’s largest organisation in the Earth and planetary sciences. In
addition, Dr Glücksman has served as an advisor to the UK Parliamentary Office of Sci-
ence & Technology, where he wrote a briefing on market-based biodiversity conservation
schemes. He is also an active member of the transatlantic Emerging Leaders in Environ-
mental and Energy Policy (ELEEP) network, jointly coordinated by the Atlantic Council
and Ecologic Institute think tanks. Dr Glücksman holds a DPhil and MSc in Zoology from
the University of Oxford, a BSc from the University of St Andrews, and a BA from McGill
University.
1
1. Introduction

J. Boenigk et al., Biodiversity and Earth History, DOI 10.1007/978-3-662-46394-9_1
2 Introduction
1.1
How do I use this book?

This book is aimed at students of the Life and Earth Sci- palaeontology, geology, and geography. Due to the breadth
ences as well as to all those interested in biodiversity and of the subject matter of this book, sections differ in their level
its development. Beyond the fragmented view of animal and of difficulty in accordance with the educational background
plant diversity it focusses on the total diversity of eukaryotes: of the reader.
their diversity and distribution on Earth as well as the geolo- Each topic is presented in the same way across a two-page
gical development of present-day biodiversity. spread, including one page of text and one with explanatory
This book aims to link geoscientific concepts, such as figures. The text is further divided into an introductory sec-
Earth’s history and macroevolution, to topics in the biosci- tion, featuring general principles, and a section building on
ences, including biodiversity and its distribution in the natu- the basics, showing selected aspects in depth.
ral environment. The text is intentionally oriented at the in- The figure pages contain explanatory text boxes emphasi-
terface of both disciplines, in order to illustrate correlations zing distinct aspects in order to clarify and link content to the
between the development of the planet and the evolution of main text. In addition to providing content relating directly
life: the effects of geological and climatic development on to the text, the the figure pages often put subject matter in a
the evolution of life and, conversely, the effects of the origin greater context or offer starting points for further study.
and evolution of life on the geological and climatic evolution As a result of its rigid structure, the book invites readers
of the Earth. either to work through its content chapter by chapter – par-
The book is divided into three main subject areas: the first ticularly applicable to material in the geosciences – or to na-
section deals with the geological development of the Earth vigate through thematically, moving between related aspects
and biodiversity, the second illustrates the current distributi- by way of the cross references.
on of Earth’s diversity, and the third provides an overview of With this distinctively theme-based approach, we hope
the diversity of eukaryotic organisms. Each of these topics is that this book closes gaps in the textbook landscape and fa-
preceded by an introductory chapter, providing background cilitates learning.
and an explanation of basic concepts on aspects of biology,
Introduction 3
Textbook structure:
This book is built around a double-page concept, where the left page
shows text and the right side displays figures and annotations.
Text pages are generally divided into an introductory (1) and an advan-
ced section (2). In addition, important terms are explained in a glossary
at the bottom of the page (3). Cross references to other chapters (4), lo-
cated at the bottom of each page, facilitate thematically-driven reading.
The book can therefore be used both for chapter-by-chapter learning
and for studying by theme. Figure pages (5) complement the main text
1: A green square indicates introductory text, providing a 5: Figure pages illustrate selected topics. Although comple-
broad overview of a topic mentary to the main text, in most cases figures are inde-
pendent and can be understood on their own. Figure leg-
ends are available wherever additional information, beyond
2: A blue square indicates text offering a deeper understan- what is provided in the main text, seems necessary
ding of selected topics
3: The thematic glossary explains the most important tech-

nical terms used on each page. An overview of all glossary
terms can be found at the end of the book
6: A box at the bottom of figure pages (only in the systemat-
ics chapter) provides additional general information about
the organisms in question. These facts are usually relevant
to many different groups of organisms or explain general
4: An orange square thematically links topics on each page principles relating to a particular organismic group
to other sections in the book
4 Introduction
1.2
Biodiversity
Life can be found everywhere on Earth, from the deepest tinct, total diversity counts are estimated to comprise over 5
oceanic valley to the highest mountain peaks and from the million animal species and over 400,000 plant species. The
coldest polar ice deserts to the hottest deserts and hydro- diversity of microorganisms, which has been far less inten-
thermal vents. Present-day biodiversity and its distribution sively studied, is probably much greater: the ‘tree of life’,
on Earth is the result of over 4 billion years of evolution. based on the analysis of species at the genetic level, reflects
Since the origin of life, biodiversity levels on the planet have this vast microbial diversity and confines multicellular life
experienced several sharp fluctuations. Five major and many to a few barely noticeable side branches. A quote from the
smaller extinction events have been recorded since the emer- journal Nature (2004) highlights this point: „It is now time for
gence of complex multicellular life forms, causing sudden biologists to cease presenting to their students and the public
sharp declines in global biodiversity. Today, primarily as a re- a perspective of life on Earth that is so biased towards the
sult of human activity, rates of biodiversity loss have reached visible. This will not be easy. The first part of the challenge is
or even exceed rates of the other five major extinction events. accepting that the contribution of visible life to biodiversity
Even though over 99 % of Earth’s total species have gone ex- is very small indeed.“
Why is life on Earth so successful? What adjustments do most common measure of biodiversity. Only a fraction of
most life forms have in common, that have made it possible living species has so far been scientifically described. Of the-
for them to inhabit the planet? Which characteristics and ad- se, fewer than 1 % have been described in greater depth than
aptations vary between different life forms, that has brought merely confirming their existence. However, the species level
about such a great variety of species? How did the current is only one of many possible approaches to biodiversity, and
biodiversity arise and how did the geological development of we know that differences between organisms play an impor-
Earth influence the evolution of life? What, exactly, is meant tant role in ecological systems even below the species level
by the term ‘biodiversity’? (intra-specific or micro-diversity).
Although the term ‘biodiversity’ seems intuitively clear, Biodiversity is an essential prerequisite for human life and
it is difficult to define it precisely. A number of definitions the survival of humanity itself forms a part of biodiversity
exist, of which only the one put forth by the UN Conven- studies. Biodiversity is also of fundamental importance for
tion on Biological Diversity is provided here: ‚The varia- ecosystem services such as regulating climate, soil fertility,
bility among living organisms from all sources, including, the water cycle, agriculture and fisheries, fossil fuels and re-
inter alia‘, terrestrial, marine, and other aquatic ecosystems, newable energies, pharmaceuticals, medicine, and quality of
and the ecological complexes of which they are part: this life economies. In practice, biodiversity is never completely
includes diversity within species, between species and of recorded in environmental studies, with the majority of work
ecosystems.”‘Biodiversity is distributed unevenly on Earth, focusing on a handful of organismal groups, often plants,
with terrestrial diversity highest in the lower latitudes, i.e., vertebrates, and a number of invertebrates. Many other
near the equator. In the ocean, biodiversity among coastal groups of organisms, especially more common microorga-
taxa is highest in the Western Pacific and in the mid-latitudes nisms, are rarely taken into account. Even within established
of the open sea. organismal groups, studies often focus on model species or a
The species is the most commonly used unit of biologi- specific size range of individuals.
cal diversity; therefore, the number of species is probably the
biodiversity: (definition given by the UN Convention on Bio- a part; this includes diversity within species (genetic diversity),
logical Diversity) the variability among living organisms from all between species (diversity of species) and of ecosystems (and the
sources including, inter alia, terrestrial, marine and other aqua- interactions contained within them)
tic ecosystems and the ecological complexes of which they are
Introduction 5
C C TAG CG
ATG GA
AT
C G G AT C G AG
TA CC
T T C TAT
AT CA
CG
ATA
GT
Different levels of resolution when measuring biodiversity: genes, individuals, populations, and ecosystems
Biodiversity below the species level: Brassica oleracea var. gemmifera (Brussels sprouts), Brassica oleracea var. italica (broccoli), Brassica oleracea var.
botrytis (cauliflower), Brassica oleracea var. sabellica (kale)
Krautschicht
Biodiversity at the community level at different spatial scales using the example of the deciduous forest: microbial diversity, lichen and moss layers, herb
layers, and tree layers
Biodiversity at the level of habitats and biomes: rape monoculture, desert, temperate beech forest, tropical rainforest
Temporal dimension of biodiversity: in the case of microorganisms, the diversity often may change within just a few hours (here: Euglena gracilis);
speciation is also a good example of the temporal dimension of biodiversity (here: Corvus corone [the carrion crow], Corvus cornix [hooded crow]);
around 99 % of species that have existed on Earth are extinct (here: Coelonautilus planotergatus)
6 Introduction
1.3
Life
The question of what exactly constitutes life initially ap- ‘foreign’, mainly prokaryotes (especially the intestinal flora).
pears to be easy to answer. However, it is very difficult or even Likewise, most higher plants live in symbiosis with mycor-
impossible to provide a clear definition of life, and those that rhizal fungi and parasites about in nature, living in narrowly-
exist are surprisingly different from each other. Among the defined interdependencies with their hosts. Many free-living
frequently mentioned criteria for life are movement, self-sus- organisms also live in close reciprocal relationships with
tainment, reproduction, self-organisation, and metabolism. other lifeforms; their viability therefore depends on other
If we restrict ourselves to defining life according to what is free-living organisms. In this sense, the inclusion of viruses
already known on Earth, we can narrow the definition down within the definition of life is justified: their dependence on
further. In this case, all life is made of highly developed cells other lifeforms is only more pronounced. However, including
(or is at least highly dependent on the reproduction of cells the need to interact with or to depend on other life into the
– as is the case with viruses) dependent on nucleic acids and definition of life would even cover the properties of biomole-
proteins. cules. Thus, excluding biomoleculaes from the definition of
Another key feature of life is self-sufficiency. Although life will become problematic. Furthermore, autonomous ro-
this seems self-evident, this view is problematic: most living bots with artificial intelligence, also challenge conventional
organisms are in the very least strongly dependent on other definitions of life. It is therefore relatively easy to recognise
lifeforms. For example, only around 10 % of cells within the life – at least life on Earth – yet, it remains difficult, if not
human body are human, whereas the remaining 90 % are impossible, to provide a unique and striking definition of life.
A comprehensive attempt to define life was undertaken Another example of a non-living system that bears a strong
by a panel of NASA experts: they defined life as a chemical resemblance to life is the growth of crystals: errors occur,
system capable of Darwinian evolution. This definition is though these are not passed on in the formation of other
focused, in particular, on reproduction and the appearance crystals; as a result, crystal growth is not subjected to Darwi-
and passing on of mutations. Precisely this inheritance of nian evolution. On the other hand, NASA’s definition of life
mutations differentiates living organisms and systems from includes viruses, often considered non-living by other defini-
their non-living counterparts. tions. In particular, viruses do not arise from cells and have
Fire is an oft-cited example of a non-living system mee- no independent metabolism.
ting most of the criteria for life. Fire is separate from its en- NASA’s definition also relates particularly to humans:
vironment and has a metabolism: it breaks complex, com- through tool use and progress in medicine, humanity is no
bustible materials into simple carbon dioxide and water. It longer exclusively surviving and reproducing by way of Dar-
can also grow and multiply. ‘Errors’ certainly occur during winian evolution, further complicating the above definition.
a fire’s combustion process, though these are not inherited.
life: life is a self-sustaining system capable of Darwinian evoluti-

on (working definition used by NASA)
Introduction 7
An apple tree is clearly considered to be alive, even though the bulk of its biomass consists of dead tissue. The seeds enclosed within each apple can
grow into a new generation of trees; thus, the apple, too, is alive. Freshly squeezed apple juice, on the other hand, is non-living, even though it com-
prises many of life’s processes
Many life forms cannot survive without interaction with other living beings. Viruses and bacteriophages, if classified as living, are dependent on host
cells for their reproduction. Similarly, most higher-level animals would cease to live without the diversity of bacteria found within their intestinal flora.
Parasitic and parasitoid organisms are also dependent on other things. Independent viability is therefore not an essential criterion for life
Even non-living systems possess many features of life. Particularly good examples are crystals and fire: both can grow and multiply
8 Introduction
1.4
Species
The most commonly used unit of biodiversity is the spe- ly that a single universal definition will ever be found. Bio-
cies. Around 1.6 million species have been described so logical diversity is simply too diverse to allow for a unified
far. However, the total number of living eukaryotic species approach to the species concept.
is estimated to be around 9 million, of which 5 million are The most widely used approach for defining a species is
animals and 400,000 are plants. The number of prokaryotic using the biological species concept, which postulates that
species is difficult to estimate. The vast majority of species each species exists in reproductive isolation. In practice, eu-
that once existed over the course of Earth’s history are now karyotic species are mainly distinguished based on morpho-
extinct: the total number of species thought to have evolved logical similarities. To what extent these morphologically
during the Phanerozoic alone (i.e. during the past 542 my) is differentiated species differ from the true biological species
thought to be around one billion. concept definitions remains unclear.
However, what is a species? Which individuals belong to- The variability of species and the splitting of existing
gether within such a grouping? And which level of ranking species into new ones has other problems: cryptic species,
do we refer to, when we speak of a species? Even though the species complexes, and ring species represent just some
answers to these questions seem obvious, they become more examples of ways by which the species concept, simple to
difficult – even impossible – to solve upon closer inspection. grasp on first thought, is in fact complex and highly difficult
As a result, there currently exists no species definition that to interpret.
can be applied across all organismal groups, and it is unlike-
The definition of the species concept is related to the un- concept, which can be applied to multicellular and sexually
derstanding of species variability. Before the advent of the reproducing eukaryotes: species are reproductively isolated
theory of evolution, the species was considered to be an im- when the descendants of two paired species are sterile. The
mutable unit, with intraspecific variability considered a de- biological species concept thereby brings together the his-
viation from the norm. The theory of evolution then shifted torical understanding of species, as clearly separated units,
the focus to the variability of species, challenging the idea with the modern understanding of evolution and heredity.
that species are immutable. However, the idea that species Unfortunately, these ideas remain idealistic: in asexual spe-
can be clearly demarcated from one another remained. As cies, for example, which include many microorganisms as
the understanding of inheritance grew, these considerations well as some metazoan plants, the biological species concept
developed further into notions of a separate gene pool wit- cannot be fully applied. Moreover, the prerequisite state of
hout gene exchange across species boundaries. These con- reproductive isolation is often not even available in sexually
siderations are formulated within the biological species reproducing species.
species complex: the idea of categorising living organisms into morphological species concept (as per Darwin): varieties with a
small, formal groups, usually based on a specific definition; ex- lack of or total absence of transitional forms between them;
amples are: ecological species complex: a lineage occupying an adaptive
biological species complex: taxa which are reproductively isola- zone differing minimally from others of similar lineages
ted from other species;
evolutionary species complex: a lineage that evolves indepen-
dently from other lineages;
Introduction 9
Brown bears (Ursus arctos) and polar bears (Ursus maritimus) can pro- Lions and tigers can form fertile hybrids (centre). Since the distribution
duce fertile hybrids, which sometimes happens in nature wherever their areas of these species do not overlap, such hybrids are only known in
distribution areas overlap. Nevertheless, they are described as separate captivity
species because of their differing morphology, ecology, and behavior
Heliconius erato (top row) and Heliconius melpomene (bottom) are an example of Müllerian mimicry. Both species benefit from the unpalatability of
the other, and both display a large morphological variability within a distribution area, with the colour variations of both species each having a similar
distribution
11
2. Earth‘s History
This chapter focuses on the development of the Earth quent exposure of fossils. Plate tectonics and the position of
since its formation, roughly 4.6 billion years ago. The plan- continents during different geological periods impact climate
et’s geological development is closely linked to the evolution and, therefore, the development of life.
of life, which evolved approximately 4 billion years ago on The chapters that follow deal with the evolution of life,
Earth. essential metabolic pathways, and their feedback with geo-
This introductory chapter explains the precise nature of chemical and climatic processes.
the relationship between biological evolution and the devel- Of particular importance for the evolution of life is the
opment of Earth. It opens with a survey of the composition evolution of atmospheric composition: the availability of
of the planet’s oceanic and continental crust, their inter- free oxygen, but also the concentrations of greenhouse gases
action within plate tectonic processes, and their behaviour such as carbon dioxide and methane: the increase in oxygen
during weathering, erosion, and sedimentation, vital in un- concentration creates the preconditions for the emergence
derstanding geochemical flows of material across the planet. of eukaryotic cells. A billion years ago the oxygen concen-
Igneous rock formation processes play a role in the absolute tration exceeded 1 %, which led to the formation of a first
age determination of material (geochronology), based on ozone layer a few hundred million years later. Thereby, the
the decay of radioactive elements incorporated into the rock colonisation of the Earth‘s surface was facilitated or even
crystals. Sedimentation, weathering, and erosion processes made possible. The current oxygen content of nearly 21 %
are also significant, as they drive the formation and subse- was finally achieved some 350 million years ago.
2.1 Basics of the Geosciences

This chapter covers the basics for understanding the development and distribution of biodiversity (for example,
plate tectonics) and climatic development (for example, the rock cycle or carbonate balance)
2.2 The Precambrian eon

This chapter broadly discusses the development of Earth from its creation until the beginning of the Phanerozoic,
with a particular focus on the importance of the carbon cycle on the evolution of climate and the history of life
2.3 The Phanerozoic eon
2.3.1 Overview
This chapter provides an overview of the development of Earth and of life in the Phanerozoic, with a focus on the
stratigraphic distribution of fossils and palaeo-ecologically significant group of organisms
2.3.2 Fossil Biodiversity

This chapter focuses on the stratigraphic distribution of fossils and on palaeo-ecologically significant groups
2.3.3 The Palaeozoic era

This chapter focuses on the stratigraphic distribution of fossils and on palaeo-ecologically significant groups
2.3.4 The Mesozoic era

This chapter describes the evolution of Earth and life from the Permian-Triassic boundary mass extinction event to
the mass extinction at the end of the Cretaceous
2.3.5 The Cenozoic era

This chapter deals with the youngest section of Earth’s history. It focuses on the relationships between climate
change, evolution of photosynthesis and the evolution of humans

12 Earth‘s history
2.1
Fundamentals of the geosciences

The biodiversity, distribution, and phylogenetic develop- For an understanding of the feedback loops between the
ment of life on Earth are closely linked with the formation origin and development of life, on the one hand, and the for-
and evolution of the planet. Earth’s climatic and geochemical mation and development of Earth on the other, knowledge
cycles have, thus, been vital for the origin and development regarding some of the fundamentals of the geosciences is
of life. Conversely, the activity of living organisms affects the necessary. These include the formation of Earth, aspects of
planet’s atmospheric composition (and thus the climate) and rock formation, and plate tectonics, as well as an overview of
erosion processes. In addition, its biogenic sedimentation en- the temporal structure of Earth’s history.
abled the formation of rock in many geologic settings.
The Earth’s atmospheric composition as well as the avail- In addition, the colonisation of terrestrial habitats by
ability of nutrients are both heavily influenced by geological living organisms affects weathering processes; for example,
and geochemical processes. For example, volcanic activity plant roots penetrating soils and sediment or burrowing an-
produces large amounts of lava and significant amounts of imals can change mechanical stress and physical weather-
carbon dioxide. Lava production can locally and, after large ing. Living organisms also influence chemical weathering
eruptions, also supra-regionally impact the availability of through their uptake of nutrients and excretion of organic
ions. Erupted carbon dioxide, a greenhouse gas, influences and inorganic substances.
Earth’s climate. These prevailing circumstances strongly in- Thick sediments are formed by bio-mineralisation and
fluence the evolution of life. biogenic sedimentation; for example, reef limestone and de-
At the same time, living organisms directly influence the posits of planktonic organisms (chalk, radiolarite) and the
planet’s climate. formation of coal and crude oil. This biogenic sedimentation
For example, basic metabolic processes of life, such as res- is also connected with Earth’s climatic history, since many
piration and photosynthesis, directly impact the gas balance of these formations (limestone, coal, and crude oil) are asso-
of the Earth’s atmosphere. Furthermore, biogenic formation ciated with a reduction in atmospheric carbon dioxide con-
of oxygen has an impact on the concentration of greenhouse centrations.
gases like carbon dioxide and methane.
erosion: exogenic processes leading to the removal of soil and sediments: deposits of material on the Earth’s surface, trans-
rock from the Earth’s surface and its transportation from one ported by wind, water or ice
location to another weathering: the breaking down of rocks in mechanical or
chemical processes
See also
also: Respiration: 2.2.2.4; Photosynthesis: 2.2.1.4, 2.2.1.5; Biomineralisation: 4.5.2, 4.5.2.1
Fundamentals of the geosciences 13
Satellite image of the Earth
Orthoklase (Potash feldspar), Epidote,

a tectosilicate a sorosilicate
Fern frond of
Lonchopteris rugoso
2.1.1
Construction and formation of the Earth

The universe began with the Big Bang roughly 13.7 billion (rock-loving) elements were pushed to the planet’s outer ar-
years ago and it continues to expand until today. Our solar eas. As a result, the Earth comprises an iron-rich core and a
system was formed around 4.7 billion years ago from the silicate-rich mantle and crust.
centre of a solar nebula. The accumulated mass in the centre The mantle and the heavy oceanic crust are richer in iron
of the solar nebula was so large that nuclear fusion processes and magnesium than the lighter continental crust. The latter
were initiated. floats as slabs on the heavier, partially molten, material of
Matter located furthest away began to concentrate along the upper mantle, known as the asthenosphere.
elliptical orbits, forming proto-planets. Like other planets, The time since the formation of the Earth is divided
Earth was initially formed as a protoplanet by an accu- into the Phanerozoic and Precambrian. The Phanerozoic
mulation of dust and larger-sized material. Due to further includes the last approximately 541 million years. The Pre-
collisions with other debris Earth’ mass increased and the cambrian encompasses the time since the formation of Earth
released gravitational energy increasingly heated the Earth. until the beginning of the Phanerozoic. The Precambrian is
Earth became a liquid planet on which subsequently in turn divided into the Hadean, the Archean and Proterozo-
melted rock rich in silicates and melted metals rich in iron ic. The first life arose in the Archaean some 3.8 billion years
split. The denser siderophiles (iron-loving elements) were ago, after the Earth‘s surface had cooled enough to allow for
enriched in the Earth’s core, whereas the lighter lithophilic the existence of liquid water.
The Hadean was the first stage of Earth’s development, concentrated across the planet’s mantle, crust, and atmos-
covering a period from 4.7 to 4 billion years ago. In this phere. The primordial atmosphere consisted mainly of water
phase the Earth was subjected to frequent collisions with vapour (H2O, up to 80 %), carbon dioxide (CO2, up to 20 %),
meteorites. hydrogen sulfide (H2S), ammonia (NH3), and methane (CH4).
The moon was formed approximately 4.5 billion years Prior to around 4.2 billion years ago, the surface tempera-
ago, probably due to a collision of the Earth with a very large ture of the Earth sank below 100 °C. The Earth’s crust subse-
body. Since then, the moon’s mass slows down the Earth’s quently solidified and liquid water first appeared.
speed of rotation. A day on Earth in the in early Precam- The ensuing period of 4–2.5 billion years ago is known as
brian lasted only around eight hours. Consequences of this the Archean. With the onset of the formation of the oceans,
rapid day-night-change were strong storms with wind speeds atmospheric water vapour levels dropped and, by UV radia-
well over 500 km/h. To the present-day, the moon slowed tion from the sun, water, methane, and ammonia molecules
down the Earth‘s rotation by ocean tides up to the pres- were photochemically disassembled partially. Lighter gases,
ent day length of 24 hours. In addition, the rotation of the such as hydrogen and helium, volatilised for the most part
Moon around the Earth contributes to the stabilisation of into space, leaving behind nitrogen to make up the largest
the Earth‘s axis and thereby maintaining long-term climatic constituent of the atmosphere over the past 3.4 billion years.
stability: without a stable earth‘s axis, the Earth’s alignment The resulting carbon dioxide was for the most part dissolved
with the sun would fluctuate greatly, as would the position into the oceans, acidifying them to around pH 4. Subsequent-
of the Equator and polar regions. In short, the moon creates ly, chemical and later biogenic precipitation of carbonates
the preconditions for a consistent seasonal climate and the (limestone, dolomite, etc.) decreased the concentration of
occurrence of stable climate zones on Earth. dissolved CO2, causing oceanic pH to slowly rise again.
Initially, the Earth had no solid surface. High-density el- Chemical evolution started in the Archean, through
ements, in particular iron, were concentrated within the the abiotic formation of organic molecules. Life appeared
Earth’s core. Elements with lower density were subsequently around 3.8 billion, but at the latest 3.6 billion years ago.
protoplanet: (Grk.: protos = first) large body of matter in orbit ultraviolet: radiation having a wavelength shorter than that of
around a star and thought to be developing into a planet the violet end of the visible spectrum but longer than that of
solar nebula: thick clouds of interstellar matter remaining fol- X-rays (100–380 nm)
lowing the explosion of a supernova
See also: Composition of the Earth’s layers: 2.1.1.1

inner earth-like planets asteroids belt gas planets
Neptune
Uranus
Mercury
Venus Saturn
Earth
Mars
Jupiter
Life relies on liquid water, which is only available on planets or- The outermost layer of the Earth is the hydrosphere, comprising the
biting at a certain distance from the sun, known as the ‘habitable oceans, and the atmosphere. The atmosphere consists of about 78 % ni-
zone’. In the solar system, Earth is in this zone and, according to trogen and 21 % oxygen, along with various trace gases, including carbon
some models, so is Mars. If the Earth’s orbit around the sun were dioxide (0.04 %)
shifted just a few percent closer to the sun, the higher temper-
atures would not allow oceans with liquid water; on the other The Earth’s crust is divided into the basalt-rich oceanic crust,
hand, a shift of only a few percent away from the sun would send and the continental crust consisting mainly of quartz and feld-
Earth into a permanent global glaciation spar. The oceanic crust has a thickness of 5–10 km. It is con-
tinuously formed at mid-ocean ridges and subducted into the
mantle at subduction zones. The continental crust consists of
individual slabs (continents) floating on the asthenosphere,
with an average thickness of 35 km, though it can reach as
much as 60 km at the site of mountain ranges
In the Archean, 3.8 million years ago the Earth‘s surface temperature
sank below 100 °C and oceans were formed. Over the next 100–200 mil-
lion years, life appeared on Earth
The Earth’s mantle consists mainly of minerals. In contrast

with the crust, the mantle has elevated quantities of iron
and magnesium but a lower proportion of silicon and al-
uminium. The lower mantle has a thickness of around
2,250 km and is composed mainly of heavy silicates and
metal oxides. The outer mantle is separated from the inner
mantle by a 250 km-thick transitional zone and itself has
a thickness of around 400 km. It consists primarily of the
magnesium- and iron-rich silicate peridotite. The dominant
mineral within peridotite is olivine
Earth’s core consists mainly of metal and, in particular, iron. The Earth’s
inner core is composed of a solid iron-nickel alloy and has a radius of
The first free oxygen was chemically bound and deposited in iron oxides around 1,250 km. The liquid outer core surrounds the solid inner core,
(left: magnetite; right: red iron ore) which consists mainly of iron and has a thickness of around 2,200 km
2.1.1.1
Composition of the Earth’s layers

The Earth’s diameter is around 12,740 km, excluding ivine finally decomposes into perovskite and ferropericlase.
the atmosphere. The planet is divided into the core, mantle, Therefore, no olivine is found in the lower mantle (at a depth
crust, hydrosphere, and atmosphere. Heavier elements, such of 660–2,900 km). Due to the high pressure and despite the
as iron, nickel, and magnesium, are concentrated in the in- high temperatures (about 1,000–4,200 °C), the Earth‘s man-
ner layers, whereas lighter elements, like silicon or oxygen, tle is mainly solid.
are found mostly in the outer layers. The Earth’s crust, at a depth of 0–35 km, is mostly made
The Earth’s core consists mainly of iron and is divided out of oxygen, silicon, and other light metals. It is divided
into an outer and an inner core. The Earth’s core has an av- into a magnesium-rich oceanic crust and an aluminium-rich
erage density of 11 g/cm3, the inner one has a density of continental crust. Oceanic crust has an average density of 3 g/
12.5–13 g/cm3. Due to the high pressure of the inner core cm3 and is mostly comprised of mafic minerals. Its dominant
(at a depth of 5,150–6,371 km) and despite the high temper- rock is gabbro. The continental crust with an average density
atures of about 5,500° C the core is solid, the outer core (at a of 2.7 g/cm3 is predominantly made of felsic rocks such as
depth of 2,900–5,150 km) is liquid. granite.
The mantle is mainly composed of magnesium, silicon The hydrosphere mostly comprises the planet’s oceans
and oxygen and is divided into the lower mantle, a transition and has an average density of 1 g/cm3. It is mostly made
zone and the upper mantle. The mantle has a mean density of water (oxygen and hydrogen). The atmosphere is mostly
of 4.5 g/cm3 and consists predominantly of mafic rocks. Ne- made of oxygen and nitrogen and is approximately 0.0012 g/
sosilicates such as olivine and inosilicates as pyroxene dom- cm3 in density at the Earth’s surface, becoming decreasingly
inate. Olivine of the upper mantle (at a depth of 35–660 km) dense as altitude increases towards space. The atmosphere’s
is transformed into the high-pressure modification wadsley- transition towards space is continuous and is defined differ-
ite within the transition zone (at a depth of 410–660 km), entially according to the source. For example, NASA defines
which still belongs to the upper mantle. This mineral trans- space as starting at 80 km in height whereas the Fédération
formation marks the boundary between the upper mantle Aéronautique Internationale defines it at 100 km.
and transition zone. At the border of the lower mantle, ol-
The composition of rock in the Earth’s crust is dependent Rich silicate melts arise from molten earth‘s crust within the
on the chemical composition of the magma (molten rock) subduction zones.
in the crust and the upper mantle. The dominant minerals The magma‘s composition determines which minerals are
in the crust and mantle are silicates, therefore silicon oxide formed. This simple relationship is varied by magmatic dif-
compounds. ferentiation, i.e. a change in the magmatic melt composition
Magma from the continental crust tends to form different during the crystallisation process: different minerals crys-
crystals and rocks as magma from oceanic crust and the up- tallise at different temperatures. Mafic crystals are already
per mantle. formed at higher temperatures, the chemical composition of
Magnesium- and iron-rich magma (mafic material) main- the residual melt changes; it becomes increasingly felsic. By
ly produces metal-rich but silicon-poor minerals. The silicate this magmatic differentiation process felsic melts may arise
tetrahedra of these minerals are either isolated (nesosilicates) from originally mafic magmas, from which silicate-rich alka-
or formed in chains or bands (inosilicates). Such melts oc- li feldspar and quartz may crystallize, for example.
cur mainly at mid ocean ridges, where plate boundaries drift As the magmas and rocks contain varying amounts of
apart and material of the upper mantle is included in these metal ions according to their origin, an altered volcanic activ-
melts. ity also affects the composition of the surface rocks. In par-
From more silicate-rich melts, silicates with a higher de- ticular, an increased volcanism at divergent plate boundaries
gree of crosslinking and a correspondingly lower proportion leads to increased formation of iron- and magnesium-rich
of metal ions are formed: phyllosilicates such as mica, tecto- rocks. As a result, the bioavailability of these elements is in-
silicates such as feldspars and quartz (pure silicon dioxide). creased in the ocean by weathering and erosion processes.
felsic: coinage from feldspar and quartz (silicate); light coloured, mafic: dark, rock-forming minerals which are rich in magnesium
igneous minerals rich in silicic acid and iron (Lat.: ferrum)
See also: Magmatic rocks: 2.1.2.1; Subduction: 2.1.1.2, 2.1.2

Chemical composition of the Earth‘s crust, mantle and core
magnesium
aluminium
potassium
sodium
calcium
silicon
oxygen
iron
crust
upper
mantle
transiti
on zon
e
lower mantle
mantle
magnesium
silicon
oxygen
iron
outer
core
core
residue
nickel
iron
inner core
Rock melts of the Earth‘s crust are silicate-rich and in-

clude higher proportions of lighter elements, especially silicate-rich
calcium, sodium and potassium, compared to the mantle.
To that effect, the resulting rocks are usually silicate-rich.
Rocks with a silicate content of more than 63 % are re-
ferred to as felsic (feldspar-silicate). Felsic rocks are
Tectosilicates such as potassium feldspar (KAlSi3O8) consist of
characterised by tectosilicates, i.e. three-dimensionally
three-dimensionally combined silicate tetrahedra
combined silicates such as quartz and feldspar, and phyl-
losilicates, i.e. two-dimensional combined silicates such
as mica.
Felsic rocks are often light; its chemical composition in-
dicate the formation by melting of crustal material (felsic
magmas can also be formed out of mafic magmas by dif-
ferential crystallisation processes of mafic and ultramafic
crystals)
Clay minerals and micas, such as muscovite (KAl2(OH)2AlSi3O10),
are phyllosilicates. In phyllosilicates the silicate tetrahedra are
linked at the corners forming layers. The individual layers are
not mutually connected
Rock melts of the upper mantle are poorer in silicate, but

richer in magnesium than the melts of the Earth‘s crust.
The resulting rocks are therefore usually very poor in sil-
icate. Rocks with a silicate content of less than 52 % are
considered as mafic (magnesium-ferric, i.e. magnesium
and iron rich); rocks with less than 45 % of silicate are ad-
dressed as ultramafic. Mafic rocks are dominated by iron Pyroxene (Mg/Fe)2 Si2O6 is a inosilicate. In inosilicates the sili-
and magnesium silicates. Common minerals are nesosil- cates consist of linear chains of silicate tetrahedra. The crystal
icates such as olivine and inosilicates such as pyroxene shape is often prismatic or acicularily stretched
and silicate-poor feldspars as plagioclase. Mafic rocks are
often dark, their chemical composition indicates their
formation within the upper mantle. The Earth‘s mantle
mostly consists of peridotite, an ultramafic rock with at
least 40 % olivine, but also of orthopyroxene, clinopyrox-
ene and – depending on the pressure in the zone of for-
mation – garnet, spinel or plagioclase poor in
silicate
Olivine (Mg/Fe)2SiO4 is a nesosilicate. Silicates of nesosilicates
consist of isolated silicate tetrahedra. They are not connected
to each other via Si–O–Si bonds
2.1.1.2
Plate tectonics
Plate tectonics, on the one hand, is important to explain African plate) with the Eurasian plate. The Rocky Moun-
the distribution and exchange of species between conti- tains were formed by the collision and subduction of the Pa-
nents, on the other hand it is based on orogeny and the car- cific plate beneath the North American Plate and the Andes
bonate-silicate-cycle and thus has a climatically effect. resulted by the subduction of the Nazca plate beneath the
Although the rocks of the mantle are mostly solid, there South American Plate.
is also a plastic flow, as it occurs also in glass, salt or gla- The oceanic crust formed from mantle material has a high
cial ice. The mantle‘s convection is driven by differences in density, since it is rich in iron and magnesium. The conti-
temperature and density between upper and lower mantle. nental crust, however, is poorer in iron and magnesium; it
This convection drives the movement of the Earth‘s crust. consists of lighter silicates and has a lower density. At con-
The different plates are displaced in relation to one anoth- vergent plate boundaries, therefore the heavy oceanic crust is
er. New crust is formed by ascending mantle material where usually subducted underneath the lighter continental crust.
the plates drift apart. When the plates are compressed, the The cycle of crust formation – especially at oceanic ridges
Earth‘s crust is either subducted or its collision leads to the – and subduction takes approximately 200 million years.
uplift of mountains. Therefore and as a rule, oceanic crust is younger. Only in a
The Himalayas are the result of the collision of the Indian few marine basins, such as in the Mediterranean, older oce-
plate with the Eurasian one. The Alps arose as a result of the anic crust is sporadically found.
collision of the Adriatic (as an offshore micro-plate of the
The oldest parts of the Earth‘s crust are approximately 4.2 the oceans, the late Precambrian glaciations and the evolu-
billion years old. The formation of most cratons was com- tion of the diversity of multicellular eukaryotes.
pleted 2.5 billion years ago. The nuclei of the continents that The present-day northern continents were merged into the
had been formed in the early Precambrian are called cratons. large continent Laurasia covering a long period of time, just
Since the Middle Precambrian, the cratons had not been tec- as today‘s southern continents were unified as Gondwana
tonically shaped anymore and are the cores of the present super continent. In the late Palaeozoic and early Mesozoic
continents. The continents are usually made up of several Laurasia and Gondwana were merged into the super conti-
cratons and other, younger parts. In particular, at their edges, nent Pangaea, that comprised all major land masses.
the continents – in contrast to the cratons – are folded and The position of the continents and especially the aggrega-
restructured. Driven by plate tectonics, the cratons but also tion as super continents affects the climate and the evolution
the continents were shifted against each other over and over of life. Super continents are characterised by a few coasts
again. In Earth‘s history, they aggregated several times form- with high precipitation and large arid regions in the inland.
ing large land masses, the super continents. As a result of climate change, the weathering of rocks and
Probably in the early Proterozoic, supercontinents already thus the release of nutrient ions and carbonates (and thus
existed. However their existence is not secured (Ur, Kenor- carbon dioxide) decreases, which in turn acts on the cli-
land, Columbia). The aggregation leading to the super con- mate – and leading to global coolings. The position of the
tinent Kenorland is associated with the Huron glaciation, continents plays a decisive role also for the distribution and
the oldest secured global glaciation. Approximately 1 billion evolution of life: the connection of continental masses sup-
years ago the supercontinent Rodinia existed, a unification ports the spread of organisms. The separation of individual
of all known landmasses. The increased mafic volcanism of continents during the break-up of a supercontinent leads to
the Rodinia’s break-up is associated with the oxygenation of isolation and (often) adaptive radiations of organisms.
adaptive radiation: the emergence of a multitude of new life converge: (Lat.: convergere = incline towards) to move togeth-
forms from a single ancestor as the result of adaptation to differ- er, to herd, to rally
ent ecological environments oxygenation: provision of oxygen; oxidation where the electron
convection: circular movement within fluids due to differences acceptor is oxygen
in density subduction zone: convergent boundary between one tectonic
plate of the lithosphere and another on the Earth’s upper crust
See also: Gondwana: 2.3.4.3; Huron glaciation: 2.2.2.2; Laurasia: 2.3.4.3; Composition of the Earth’s layers: 2.1.1.1
2.1.2
Rock-forming processes
The evolution of life and rock-forming processes are in- as plate tectonics. This leads to the subduction of usually
terrelated. Biogenic sediments, particularly limestone, are oceanic plates at one hand and on the other hand, to the for-
of key importance to the global carbonate-silicate cycle. The mation of new crust, mainly along mid-ocean ridges.
volcanic eruption of plutonic rocks (with a higher proportion On the Earth‘s surface weathering of rocks takes place
of calcium and magnesium) leads to a higher input of these due to the influence of temperature fluctuations and wind,
ions into the sea and thus affects the precipitation of lime. water and ice. These weathered rock fragments are eroded
Due to diffusion equilibria the atmospheric carbon dioxide and deposited again as clastic sediments. In addition to the
concentrations are reduced. As a consequence, this process clastic sediments, chemical sediments (i.e. rock salt) and bio-
acts on the climate and on the evolution of life. genic sediments (i.e. coral limestone, coal) play an important
The various rock-forming processes are closely interre- role. The sediments are solidified by increasing pressure and
lated: the formation of igneous rocks from rock melts, the solution processes within the pore water, a process called di-
formation of sedimentary rocks from weathered and eroded agenesis. Due to increasing temperature and pressure con-
rock fragments, the formation of metamorphic rocks under ditions, some minerals start transformation processes, also
high temperatures and pressures in deeper regions of the known as rock metamorphism. If temperatures rise more
Earth‘s crust and the anatexis, the (partial) re-melting of and more, the rocks are partially (anatexis) or completely
rocks. (igneous rocks) re-melt again. Such re-molten rocks can be
The convection of mantle rock driven by thermal gradi- transported as plutonic or volcanic rocks by uplift processes
ents leads to movements of the Earth‘s crust, also addressed in higher regions of the Earth‘s crust.
The cyclic process of subduction of rocks, especially of pheric carbon dioxide dissolves in water. Dissolved in water,
the oceanic crust along plate boundaries, and rock formation carbon dioxide reacts to form carbonic acid. Silicate bear-
from (partially) molten material is summarised as rock cycle. ing rocks are weathered and eroded by dissolution process-
It takes approximately 200 million years. Therefore, oceanic es caused by carbonic acid. Metal ions (including calcium
crust is not older than that. Exceptions can be found in a few and magnesium) are released. These ions are finally washed
marine sub-basins such as the Mediterranean with oceanic into the sea, where they are (mostly) bound due to biogenic
crust aged up to 270 million years. Continental crust may be carbonate precipitation as calcite, aragonite or dolomite and
significantly older. The oldest rocks exposed at the Earth‘s deposited on the sea floor. Due to subduction processes, car-
surface are 4.3 billion years old. bonates get into the Earth‘s mantle, where high pressures and
The carbonate-silicate cycle is significant for the devel- high temperatures lead to the formation of silicates through
opment of climate and the evolution of life. This refers to the release of carbon dioxide. Via volcanic eruptions carbon
the mutual influence of carbonic acid and carbonate on one dioxide finally re-enters the atmosphere.
hand and silicic acid and silicate on the other hand: atmos-
anatexis: partial melting of rocks in the continental crust dur- erosion: exogenic processes leading to the removal of soil and
ing high-grade regional metamorphism rock from the Earth’s surface and its transportation from one
burial metamorphism: metamorphism caused when rocks location to another
are buried at great depth in the ground mineral: homogeneous, naturally-occurring solid, usually anor-
contact metamorphism: metamorphism caused by tempera- ganic with a crystal structure
ture increases due to hot magma rock: mixture of minerals occurring in solid form
diagenesis: compression of sediments by lithification; chemi- rock metamorphism: changes in rocks under high pressure
cal, physical or biological change at relatively low temperatures and temperatures without them melting into liquid magma
See also: Magmatic rocks: 2.1.2.1; Sedimentary rocks: 2.1.2.2; Chemical evolution, Origin of life: 2.2.1.1; Subduction: 2.1.1.2
Magmatic rocks are formed by cooling and crystallisation of molten Rock fragments removed by weathering and erosion are deposited
rock. Igneous rocks (plutonic rocks) formed in deeper crustal regions, mainly in the sea and in lakes. Initially loose sediments as clay, sand and
slowly cool down and are characterised by large crystals. Magmatic rocks gravel are formed. The grain size depends on flow conditions. The lower
formed at or near the Earth‘s surface (volcanic rocks), quickly cool down the flow velocity, the more fine-grained the sediments are
and are characterised by small crystals
we
athe
rin
g
lift
up
ero
sio
n
sediment (loose rocks)

magmatite dia
gen
uplift e sis
up
me
sediment (solid rock)
lift
tam
orp
his
m ism
rph
amo
met
up
metamorphite
lift
s
texi
magma ana
Metamorphic rocks are formed under higher pressure and temperature Under increasing pressure, for example by further superimposed loads
conditions compared to weathering and diagenesis processes. Differ- of sediments, the loose sediments solidify and are transformed into hard
ent minerals are formed that can be parallelly aligned under a domi- sediments such as sandstone. Due to exchange and solution processes,
nant pressure direction. Examples of metamorphic rocks are schist and the sediments are thereby chemically solidified. Dissolution and precipi-
gneiss. Even higher temperatures lead to melting of rocks (anatexis) tation of carbonates and silicates play a decisive role
2.1.2.1
Magmatism and igneous rocks

Magmatism refers to processes that affect the rock melt, volcanic activity, also significantly influence the atmospheric
the magma. A differentiation is made between near-surface composition.
processes – volcanism – and processes occurring in deeper Especially carbon dioxide can be released by volcanic
regions of the crust – plutonism. activity in large quantities and thus contribute to climate
Plutonic rocks stay at greater depths and therefore cool down change. Due to volcanism hot rock melts are transported to
very slowly. Since the melts slowly cool down, there is a very or near the Earth‘s surface. Ascending magmas reaching the
long periods of time for crystal growth. Plutonites are there- Earth‘s surface are also referred to as lava. Here, the melts
fore characterised by larger crystals. cool down quickly. Therefore, crystallisation time of miner-
Volcanism is usually found in tectonically active regions, als is short and the crystals in the resulting rocks are usually
in particular at the divergent plate boundaries such as mid- small.
ocean ridges and subduction zones of converging plate Magmas, rich in silicate (felsic) usually solidify as light
boundaries. Rocks and gases are transported from the lower rocks: close to the surface, for example, as fine crystalline
crust and upper mantle to the Earth‘s surface. The hot source rhyolite, at greater depths as coarsely crystallised granite.
rock melts mostly by pressure release during its ascent and Magmas, poorer in silicate but iron- and magnesium-rich
concentrates in magma chambers. From there, it ascends (mafic) mostly solidify as dark rocks – close to the surface,
via narrow vents towards the volcanoes. The released gases for example, as fine crystalline basalt, at greater depths as
can, in particular in geological periods of time of increased coarsely crystallised gabbro.
Due to mantle convection and ascending magmas rock melts quickly ascend from the upper mantle, those minerals
fragments are delivered from greater depths. Those rock frag- will not be molten and can be found in the corresponding
ments do not always melt completely, so that rock fragments igneous rocks. Well-known examples are the diamond- and
and minerals of the Earth‘s mantle reach the surface. The garnet-bearing kimberlites of South Africa. Magmas consist-
mantle mainly consists of the ultramafic peridotite, a coarse ing of mantle material and cooled down in volcanic vents are
crystalline rock consisting mainly of the nesosilicate olivine, referred to as kimberlites.
besides pyroxene and to a smaller proportion of the alumin- The dissolved gases in the magma, especially water, are
ium silicates garnet or spinel. At low pressures (correspond- retained at greater depths in the magma by high pressures.
ing to approximately the upper 30 km of the Earth‘s crust) Near the surface, the gases can explosively expand due to de-
plagioclase, as an aluminium silicate, generally forms in maf- creasing pressure, releasing lava as well as surrounding rocks
ic rocks. At the higher pressures spinel or garnet are formed in pyroclastic clouds or flows. These pyroclasts are often de-
in the mantle. Depending on the chemical conditions amphi- tectable at a great distance to the volcano and can be used as
boles or graphite respectively diamond can also be formed. If a stratigraphic marker.
igneous rock: rock formed by the solidification of lava rhyolite: acid igneous rock
plutonism: geological process in which a pluton develops as volcanism: geological processes connected to volcanoes; mag-
the result of magma crystalising under the Earth’s surface matic processes near the Earth’s surface
pyroclasts: fragmented material consisting of volcanic (erup-
tive) clasts to a degree of more than 75 % (e.g. ash)
See also: Silicates: 2.1.1.1

Rock fragments, which are ejected during an explosive vol-

canic eruption are summarised as pyroclasts. Fine-grained
volcanic ashes can be widespread. The deposited ashes
(tuffs) are useful as stratigraphic calibration horizons
Volcanoes are mountains that are Magmatic rocks close to the surface (volcanites) cool down quickly.
formed by rock melts transported to the Thus, no or only small crystals can form. Silicate-rich (felsic) magmas, for example,
surface produce rhyolite (left). Rhyolites are common volcanic rocks of continental plates
and emerge as the corresponding plutonic rocks (granites) from molten material of
the lower crust and at subduction zones.
Basalt (right) is formed out of silicate-poor (mafic) magmas. Basalts emerge, as well
as the corresponding plutonic rock (gabbro), from magmas influenced by mantle
material. Such magmas are especially found at mid-ocean ridges
Igneous rocks (plutonites) slowly cool down. Thus large crystals can develop. These
are usually visible to the naked eye.
From silicate-rich (felsic) magmas granites (left) are formed. These consist mainly
Magmatic rock bodies crystallised within the Earth‘s of quartz, feldspar and mica. Granites are common plutonic rocks of continental
crust are called plutons. plates and emerge for example from molten material of the lower crust at sub-
duction zones.
Gabbro (right) develops from silicate-poor (mafic) magmas. Gabbro forms primar-
ily out of mantle influenced magmas at mid-ocean ridges. Gabbro is the dominant
rock of the oceanic crust
Mafic rocks are rocks with silicate content less than 52 %;

rocks with less than 45 % silicate are referred to as ultra maf-
ic rocks. The mafic rocks are dominated by iron and magne-
sium silicates. Common minerals are olivine, pyroxene and
silicate-poor feldspars as plagioclase. Mafic rocks are often
dark; their chemical composition indicates the formation in
the upper mantle. Such magmas especially reach the sur-
face at divergent plate boundaries (i.e. mid-ocean ridges). Garnet peridotide (left) is formed only under high pressures and in depths larg-
Felsic rocks show a silicate proportion of over 63 %. Felsic er than 30 km. Due to mantle convection and volcanism, minerals such as garnet
magmas are often created by subduction processes and par- (right) can be transported to higher regions. Garnets can be found in rocks – mainly
tial melting of continental crust at convergent plate bound- of mafic and ultramafic composition
aries
2.1.2.2
Weathering, erosion, sedimentation and sedimentary rocks

During weathering rocks are decomposed by chemical, as feldspars are converted by hydrolytic weathering into clay
physical and biogenic processes. During physical weather- minerals (i.e. illite, kaolinite). Of particularly significance are
ing, the minerals are preserved, whereas, during chemical the dissolution of salts and carbonates and the weathering of
weathering, substances are released or integrated into the carbonates by carbonic acid.
mineral constituents. The weathering products are removed by erosion process-
Physical weathering acts mainly by temperature changes and deposited as sediments. Here, the most significant are
es. Frost wedging is of particular importance in temperate marine sediments, but also in lakes (lacustrine sediments)
and cold climates: the repeated growth and melting of ice and rivers (fluvial sediments) sedimentation processes take
crystals and the associated volume changes of freezing and place. Fine sediments, for example Loess, can be transported
thawing water of up to 9 % in the rock voids contribute to the by air (aeolian sediments) and deposited afterwards.
decomposition of rock blocks. The formation of salt crystals If sediments are exposed to higher pressures and higher
acts in a similar way (salt weathering). temperatures (for example, as a consequence of further in-
Chemical weathering attacks mainly silicates with a high creasing sedimentation load), they are diagenetically solidi-
proportion of metal ions, especially neso- and inosilicates fied. In that case, chemical transformations take place. These
such as olivine, pyroxene and amphibole. Silicates with a low are also important for fossilisation processes, in particular
content of metal ions, mainly tectosilicates such as feldspar, the exchange of carbonates (bones, shells) by silicates. This
weather more slowly. Quartz withstands weathering espe- process of mineral exchange by preserving the outer shape is
cially well. Via hydrolysis cations such as potassium, sodium, referred to as fossilisation.
magnesium, calcium and iron are dissolved. Silicates such
Sediments, which consist of deposited mineral and rock Of particular importance for the reconstruction of the
particles are called clastic sediments. Clastic sediments usu- Earth‘s palaeoclimate are tillites, that are solidified glacial
ally show a very high proportion of quartz, since this mineral till, of side, end or ground moraines of glaciers. Tillites are
withstands chemical weathering much better than feldspars therefore geological evidence of glaciations, such as the Per-
and ino- and nesosilicates. In contrast, sediments resulting mo-Carboniferous glaciation of Gondwana. When glaciers
from the precipitation of salts are referred as to chemical sed- transport sediments they are not sorted according to grain
iments. These include, for example, rock salt, limestone and size. Sorting according to grain size requires a transport in
dolomite. Are these precipitates attributed to the activity of gases or liquids. In glacial tills and tillites formed by (sol-
living organisms, those sediments called biogenic sediments. id) ice there is no such sorting processes. Glacial sediments,
Examples are coral reefs or the deposits of the remains of therefore, consist of various classes of grain sizes (clay, sand,
coralline algae (chalk), diatoms (kieselguhr, diatomaceous gravel, stones).
earth) and Radiolaria (radiolarite). Coal and peat are bio-
genic sediments as well.
clastische sediments: rock fragments consisting of other rocks Loess: aeolian sediment (without layers) consisting of silt
and minerals which have been subject to mechanical destruction moraine: accumulation of debris transported and deposited by
conglomerate: hardened clastic sediment with clasts >2 mm, glaciers
fragments usually rounded Nagelfluh: (regional Germanism) geologically recent conglom-
fluviates: stones carried downriver by currents erate consisting of compacted pebbles
flysch: sequence of claystone and sandstone formed during sedimentes: deposits of material on the Earth’s surface, trans-
orogenesis in a deep marine facies ported by wind, water or ice
glacial till: heterogeneous glacial sediment which has been tillite: sedimentary rock composed of compacted glacial till
abraded and deposited by a glacier (rock material deposited by glacial ice)
hydrolysis: (Grk.: hydro = water, lysis = separation) cleavage of
molecules through a reaction with water
See also: Climate zones: 3.2.2.2; Silicates: 2.1.1.1

Frost wedging Salt weathering

The weathering (top) includes the physical disintegration and chemical
and biogenic decomposition of rocks. In particular, the effect of tem-
perature and water contributes to weathering processes. During phys-
ical weathering, the minerals are preserved, whereas during chemical
weathering minerals are converted or newly formed (for example, the
weathering of feldspars to clay minerals). Due to erosion (right) the re-
sulting loose materials are removed. Erosion is caused by flowing media,
mostly by water, but also by wind or ice
Due to erosion exposed rock formations
Sedimentation refers to the deposition of particles (usually from liquids

or gases). Depending on their origin, a distinction is made between
clastic, chemical and biogenic sediments and after their deposition site, erosion
marine lacustrine, fluvial, aeolian, pyroclastic and glacial sediments. 100
The consolidation process of loose sediments is known as diagenesis.
Increasing sedimentation load of upper layers lead to compaction of
flow velocity [cm/s]
sediments. Dissolution and crystallisation processes, especially of car- 10

bonates, promote cementation. Examples of diagenesis are the forma- transport
tion of sandstone from loose sand or recrystallisation during the fossil-
isation process 1,0 sedimentation
0,1
0,001 0,01 0,1 1,0 10 100
grain size [mm]
Clastic sediments are caused by physical deposition of rock fragments.

Sedimentation process depends, as well as the erosion, on flow velocity.
This relationship is represented by the Hjulström curve (top): larger grain
sizes are already deposited at higher flow velocities, small grain sizes only
at low velocities. Therefore, river deposits are coarse-grained (gravel,
sand) compared to those of shallow marine areas (e.g. sands). Latter are,
in turn, more coarse-grained compared to those of deep marine regions
Nagelfluh (Carpathians) Flysch (Carpathians) (clays)
Tillit oder Moräne
Salt mining at Uyuni, Bolivia Salt precipitation at the Dead Sea, Earth pyramids made of moraine Tillite (compacted till)
Israel till at Serfaus
Salt precipitations are chemical sediments. They are caused by desicca- Large amounts of rocks are eroded by glaciers. Those rocks are partly de-
tion of waters. Carbonates can be chemically precipitated. Frequently posited beneath the glacier (moraine), at the side or front of the glacier
carbonate rocks (limestone, dolomite) are of biogenic origin as reefs or (terminal moraine). If these original loose sediments are diagenetically
deposits by planktonic organisms solidified, they are called tillites. Glacial transported sediments are poor-
ly sorted according to grain size. Therefore moraine till and tillites consist
of very different sised rock fragments
2.1.2.3
Carbonate balance and carbonates

Carbonates and carbon dioxide play an important role carbonic acid, hydrogen carbonate and carbonate via reac-
both for the evolution of life on Earth and for geochemical tive balances. Reversely, the concentration of dissolved car-
processes. Carbon dioxide is also relevant to the climate, bonates is in solution equilibrium with (precipitated) calcium
since the short-wave solar radiation penetrates to the Earth‘s and magnesium carbonates. Carbonate forms slightly solu-
surface largely unhindered, the long-wave thermal radiation ble salts with calcium and magnesium. An increase in the
from the Earth‘s surface is absorbed by carbon dioxide and is carbonate, or magnesium and calcium concentration beyond
partly reflected to Earth (the greenhouse effect). the solubility product results in the precipitation of calcium
Since 1950, the carbon dioxide concentration of the at- carbonate (calcite, aragonite) and calcium-magnesium car-
mosphere is increased from 0.03 % to approximately 0.04 %. bonate (dolomite).
In the Earth‘s history, the carbon dioxide concentration, Moreover, in water, the solubility of carbon dioxide is
however, was significantly higher – at the beginning of the temperature dependent. The heating of carbon dioxide-rich
Cambrian period about ten times higher at 0.45 %. The high- water induces degassing: carbonic acid is formed out of
er carbon dioxide concentrations caused climatic conditions hydrogen carbonate and hydronium ions. According to the
similar to the ones of present-day, despite the still weaker decrease of hydronium ions, the pH rises and carbonates
solar radiation. precipitate. Such temperature-induced carbonate precip-
In water, the atmospheric carbon dioxide concentration itations can be found at springs, for example, where cool,
is in equilibrium with the concentration of dissolved carbon carbonate-rich deep water is heated during discharge. Lime
dioxide (imbalances can occur in the short-term). The car- formed in such a way is referred to as sinter.
bon dioxide concentration in the water is in balance with
At an increase of calcium or magnesium ion concentra- Since the dissociation of carbonic acid results in hydrogen
tion in water, for example as a result of reinforced volcanism carbonate, carbonate and hydronium ions, this dissociation
or enhanced terrestrial weathering, the corresponding car- changes the concentration of hydronium ions (pH value): An
bonates precipitate. This process leads to a further dissoci- increase of the dissociation of carbonic acid determines an
ation of carbonic acid via the reaction equilibrium. Due to increase in the hydronium ions. The dissociation equilibrium
the so-related decrease in carbonic acid, and thus the carbon shifts to hydrogen carbonate. Despite the increasing dissolu-
dioxide concentration, carbon dioxide diffusion from the at- tion and dissociation of carbonic acid, there is no increase of
mosphere into the water takes place. Consequently, the at- carbonate ions. On the contrary, even the concentration of
mospheric carbon dioxide concentration decreases. carbonate ions decreases and carbonates are dissolved. This
An increase in atmospheric carbon dioxide concentra- effect is also responsible for the increasing solubility of car-
tion causes an increase in carbon dioxide concentration in bonates by depth in waters: while carbon dioxide is bound by
water. Via the equilibrium reactions more carbonates are photosynthesis at the surface, respiration processes are pre-
formed. However, there is no (or only under certain condi- dominant at increasing depths. At increasing water depths
tions) increased precipitation of carbonates: the carbonic ac- the concentration of carbon dioxide increases in the oceans.
id-carbonate equilibrium is pH-dependent. Lowering the pH Thus there is a shift in the equilibrium solution by formation
(increase of hydronium ion concentration) shifts the equi- and dissociation of carbonic acid. Below the depth of com-
librium toward hydrogen carbonate and carbonic acid – car- pensation (for aragonite it is 3,000–3,500 m, for calcite at
bonates are increasingly dissolving. Conversely, an increase 3,500–5,000 m) there will be no lime precipitation anymore,
in the pH shifts (decrease in hydronium ion concentration) carbonates are mainly found as completely dissolved hydro-
the balance towards the carbonate – carbonates are increas- gen carbonates.
ingly precipitating.
dissociation: separation of salts into ions, or of a molecule into hydronium ion: positively charged water molecule (H3O+)
its constituent elements
See also: Carboniferous: 2.3.3.8; Late-Proterozoic glaciation: 2.2.2.9

An increase in the concentration of carbon dioxide lead, via the reaction equilibrium, to the formation of hydronium ions and thus a decrease in pH
value. As a result of the lowering pH the solubility of carbonates increases and carbonates are dissolved
H₂O H₂O H₂O
CO₂ H₂CO₃ HCO₃ ‐ C O₃² ‐
H₃O + H₃O +
+ + +
‐ ‐ ‐
carbon dioxide
carbonic acid hydrogen carbonate carbonate
+ +
H₃O H₃O
CO₂ H₂CO₃ HCO₃ ‐ C O₃² ‐
H₂O H₂O H₂O
high pH – alkaline acidic – low pH
low dissolution of carbonates high dissolution of carbonates
A decrease in the concentration of carbon dioxide, for example, by photosynthesis, leads via the equilibrium reactions to an increase in pH. This reduces
the solubility of carbonates and they precipitate
Ca Ca Ca Ca
Ca Ca Ca Ca
Ca Ca
Dolomit Mg Mg
Ca Ca Mg Mg
Ca Ca Ca Ca
Ca Ca Ca Ca
Calcite (CaCO3) and its crystal lattice Dolomite (CaMg(CO3)2) and its crystal lattice
Carbonates are slightly soluble salts. At high carbonate concentrations or high calcium and magnesium concentrations, they precipitate. An increased
entry of calcium and magnesium ions, for example, as a result of increased erosion after an orogeny (bottom left: Dachstein) or by strong volcanic ac-
tivity (bottom centre left and centre right), in particular by eruption of mafic (magnesium and iron rich) magma and erosion of mafic rocks (e.g. basalt:
bottom right) results in the precipitation of carbonates. Via the balance between aqueous and atmospheric carbon dioxide concentration, carbon diox-
ide is removed from the atmosphere by increased carbonate precipitation
Increasing temperature of carbonate bearing water leads to

a decrease of the solubility of carbon dioxide. Carbon dioxide
then migrates into the atmosphere. The pH value increases,
the solubility of these carbonates decreases and they precipi-
tate. Similarly, the solubility of carbon dioxide decreases with
decreasing pressure. Where carbon dioxide-saturated water
enters the surface via springs, the pressure release and tem-
perature rise of the water lead to a decrease in carbon diox-
ide concentration and thus to an increase of the pH and the
precipitation of carbonates. These sinters are found at springs
(left). Precipitation of carbonates is enhanced, when carbon
dioxide is removed by photosynthesis in the water (right: trav-
ertine at mosses)
2.1.3
Eons
The time since the formation of Earth is geologically di- The eons are generally divided into eras, only the Hadean
vided into four periods of time, the eons. The oldest eon, is not further subdivided. The Archean is divided into sec-
the Hadean, roughly covers the period from the formation tions of 400 million years, the Eoarchean, Palaeoarchean,
of the Earth to the formation of a solid Earth‘s crust and the the Mesoarchean and the ‘only’ 300 million years lasting
formation of the primaeval oceans. Neoarchean. These sections are geochronologically defined
The Hadean is followed by the Archean. In this eon according to the absolute geological age. Also, the Proterozo-
prokaryotes already existed, but no eukaryotes. In Prote- ic is geochronologically divided into the Palaeoproterozoic,
rozoic eukaryotes finally emerged, but they had been uni- Mesoproterozoic and Neoproterozoic. The recent geological
cellular or sparse cellular organisms due to the low oxygen sections are, however, globally defined by a defined bound-
availability. Only at the beginning of the most recent eon, ary stratotype, i.e., a point within a particular geologic out-
the Phanerozoic, the oxygen concentrations reached values crop. This applies to the transition to the Phanerozoic and
that favoured the evolution of complex multicellular organ- the subdivision of the Phanerozoic into the Palaeozoic, Mes-
isms. Hardly any fossils are passed on from the first three ozoic and Cenozoic eras.
eons. However, from the Phanerozoic, a variety of fossils are The eras are further divided into geologic periods (or sys-
known. tems), epochs (or series) and age (or stages).
The units determined by the geochronology and stratigra- absolute age. The younger sections of Earth‘s history, how-
phy correspond roughly, but in detail there are deviations due ever, are stratigraphically determined, in connection with the
to different approaches. This is reflected in the naming of the occurrence of index fossils. This definition of the (young-
different geologic units. In stratigraphic terminology the eo- er) sections of Earth‘s history implies that these are indeed
nothem corresponds to the geochronologic eon, the erathem precisely defined by the stratotype at a lithologic boundary.
to the geochronologic era, the system to the geochronologic On the other hand the exact age cannot often be exactly
period, the series to the geochronologic epochs and to the specified. The absolute chronology of the transition from a
stage the geochronologic age. The older sections of Earth‘s stratigraphic unit to the next one can therefore be minimally
history, especially the ones of the Hadean, the Archaean and displaced by new scientific findings.
early Proterozoic are geochronologically defined, i.e. by an
geochronology: the science of dating the absolute temporal primaeval ocean: generic term referring to Earth’s first oceans,
age of rock layers which formed around 4 billion years ago; the Panthalassic Ocean
index fossils: fossil types and species which are particularly in the Paleozoic is often referred to as the primeval ocean
well-suited to correlating different sediments; they can be easily stratigraphy: branch of geology which studies the relative ages
identified at the species level, have a broad geographical distri- of rock layers and strata
bution, are widespread and existed within a narrow time period stratotype: layer of rock in a particular location on the basis of
isotope: different variants of an element which have the same which a stratigraphic unit is defined
number of protons in each atom but which differ in neutron
number
See also: Stratigraphy: 2.3.1.4, 2.3.1.5

In the Cenozoic, vertebrate fauna is domi-

Cenozoic nated by birds and mammals. The beginning
of the Cenozoic is marked by a mass extinc-
The Phanerozoic includes the last 541 million
66 Ma tion event and an anomaly of iridium con-
Phanerozoic years and is characterised by the mass occur-
centration in rock strata
rence of macroscopic organisms
541 Ma In the Mesozoic vertebrate fauna is domi-

The Proterozoic geochronologically started 2.5
Mesozoic nated by reptiles. The start of the Mesozo-
billion years ago. The end of the Proterozoic is
ic is defined by the occurrence of the fossil
biostratigraphically marked by the appearance
Hindeodus parvus (a conodont)
Neoproterozoic of the trace fossil Trichophycus pedum dating
back to approximately 541 million years
1,000 Ma The Neoproterozoic geochronologically started 252 Ma

1 billion years ago. The time is stratigraphically
correlated with the end of the Marinoan glaci-
ation. The rocks, stratigraphically located above
the last tillite bearing layers, are put at the be-
Mesoproterozoic ginning of the Neoproterozoic
The Mesoproterozoic geochronologically start- In the Palaeozoic vertebrate fauna is domi-

ed 1.6 billion and ended 1 billion years ago. This nated by fish and amphibians. Towards the
Palaeozoic end of the Palaeozoic, the largest mass ex-
1,600 Ma period of time comprised the formation and
break-up of the super continent Rodinia tinction event in the Earth‘s history occurred
The Palaeoproterozoic geochronologically start-

ed 2.5 billion and ended 1.6 billion years ago.
This period of time covered the radiation of the
large eukaryotic groups. Since the early Prote-
Palaeoproterozoic rozoic there are eukaryotic cells and the atmos-
phere of the Proterozoic contains free oxygen
P
R
E
C
A 2,500 Ma
M
B
R
I
A
N
The Archean geochronologically extends from 4
to 2.5 billion years ago. During this eon, large
parts of continental plates and first continents
Archean were formed. The atmosphere was free of ox-
ygen, until the end of the Archean, when the
oxygen concentration increased
4,000 Ma
The Hadean is the first eon of Earth‘s history. It
begins with the formation of the proto-Earth.
The Hadean geochronologically ends 4 billion
Hadean years ago. In the Hadean, the basic structure
of the Earth – core, mantle, crust, hydrosphere
and atmosphere – is emerging. The crust is
largely oceanic
The stratigraphically defined reference point (‘Golden
4,600 Ma
Spike’) for the beginning of the Ediacaran worldwide, the
youngest period of the Neoproterozoic
30 Earth's history
2.2
The Precambrian
The Precambrian, which covers the period of time from oxygen was geochemically bound. The first sharp increase
Earth’s creation to the beginning of the Phanerozoic eon, in its atmospheric levels only occurred a few hundred mil-
comprises the three oldest eons in Earth’s history: the Ha- lion years later. The availability of free oxygen affected via
dean, Archean, and Proterozoic. a reduction in greenhouse gases (methane and carbon di-
The development of Earth and the evolution of life are oxide) the climate. A drastically cooling of the planet, the
reciprocal processes. To that end, the evolution of oxygen, Huron glaciation, was the consequence. On the other hand,
hence, the formation of free oxygen played a key role. There oxygen served a prerequisite for the emergence of eukaryotic
was no free oxygen in the Hadean and Archean, whereas cells. After oxygenation of the atmosphere eukaryotes, ex-
in the Lower Proterozoic oxygen levels reached values of isting in the shallower depths of already-oxygenated oceans,
around 0.2 %. It was only in the Upper Neoproterozoic, at could survive. However, eukaryotes remained insignificant
the Phanerozoic boundary, that oxygen concentrations be- in the nutrient-poorer oceans. With increasing oxygenation
gan to increase up to present-day values. of deep ocean waters that was accompanied by an increase
Within the geochemical balance and without the activity of nutrients 700 million years ago, eukaryotic algae became
of living organisms, free oxygen would only be available in more important. Oxygen levels therefore rose alongside an
trace amounts; the atmosphere nearly oxygen-free. Higher increase in global primary production. The oxygenation of
oxygen concentrations can be maintained only by continu- Earth’s atmosphere also had an effect on climate patterns,
ous biogenic formation, through oxygenic photosynthesis, causing extensive glaciations; ultimately, the rise in atmos-
a process originating in cyanobacteria at least 2.5 billion pheric oxygen levels were a prerequisite for the development
years ago (but likely earlier than that). Initially, originating of complex multicellular organisms.
Atmospheric concentrations of oxygen, carbon diox- Sulphur also played a key role in the evolution of oxygen.
ide, and methane played a central role in the development Sulphide dissolved in oxygen-free, anoxic environments of
of the Earth, climatic patterns, and the origin of life. Free the oceans formed low soluble salts with metal ions. Metal
oxygen reacts with methane and also interacts with carbon ions, such as iron, manganese, and molybdenum, were there-
dioxide concentration. Overall, the concentration levels of fore hardly available for living organisms in sulphide-rich
both greenhouse gases are reduced by free oxygen. As a re- waters. The primordial ocean was oxygen-free and iron-rich
sult, increasing oxygen concentrations led to cooling of the from its formation over 4 billion years ago until about 1.8
planet and, ultimately, to the onset of global ice ages. These billion years ago. Even after the oxygenation of the atmos-
extensive glaciations reduced levels of terrestrial weathering phere, the oceans remained oxygen-free for a long time. Until
and erosion, and therefore the release of nutrients into the around 700 million years ago, oceans maintaining anoxic,
oceans. Secondly, global cooling, and, additionally a lack of and in large parts sulphidic conditions, and therefore had
light in icy regions, severely limited primary production. The been iron-poor. Shallow waters already had been partially
growth of cyanobacteria and eukaryotic algae as well as bio- oxic, but the low availability of nutrients limited the growth
genic evolution of oxygen therefore had an impact on Earth’s and evolution of eukaryotes. A period of 100 million years
climate. In turn, climatic changes affected theses organisms. followed, in which the ocean still remained anoxic but now
Climatic change and the evolution of life are therefore mutu- iron-rich and low in sulphides. Oxygenation of the deep
ally dependent processes. oceans started roughly 600 million years ago.
banded iron: (mainly Precambrian) marine sedimentary rock greenhouse gases: gaseous matter which absorbs infrared
containing iron-rich layers radiation emitted from the Earth, thereby contributing to the
biogenic: (Grk.: bios = life) of biological or organic origin warming of the atmosphere
erosion: exogenic processes leading to the removal of soil and oxygenation: provision of oxygen; oxidation where the elec-
rock from the Earth’s surface and its transportation from one tron acceptor is oxygen
location to another primary production: the synthesis of biomas from inorganic
Great Oxidation Event: great oxygen crisis 2.45 billion years compounds
ago caused by the appearance of dioxygen
See also: Huron glaciation: 2.2.2.2; Oxygenic photosynthesis: 2.2.1.4, 2.2.1.5

The Precambrian eon: the Archaean eon 31
Important Precambrian events

Origin of life Formation of Earth
550 million years: Ediacaran fauna

541 Ma 0.7 billion years: widespread glaciations; the Stuart glaci-
ation was the most widespread event
Neoproterozoic
0.8 billion years: break apart of the super continent Rod-

1.2–1.0 billion years: first verified eukaryotic fresh-wa- inia that leads to intensified weathering and to a release
ter fossils. Within this period of time, radiation of eukar- of metal ions into the oceans
1.0 Ba
yotic organism as documented in fossil record
'Boring billion years' (1.85–0.85 billion years) – period of
1.2 billion years: first verified fossils of eukaryotic algae time with an evolutionary stasis: no big changes, evolu-
(red algae) and of terrestrial cyanobacteria mats tionary innovations are of no significance
Mesoproterozoic
1.8 billion years: radiation of eukaryotes likely started 1.6 Ba

immediately after their origin. Fossil records are mark- 1.8 billion years: red sediments indicate the start of the
edly younger. Eukaryotic lineages became important terrestrial oxidation of iron compounds and thus free
only roughly 1.2–0.9 billion years ago atmospheric oxygen. Decrease in formation of marine
banded iron ores
1.8 billion years: Acritarchs are first verified eukaryotic
Paleoproterozoic
fossils in the fossil record. Molecular analyses indicate 2.2 billion years: Huron glaciation as a result of increase
the origin of mitochondria 1.8 billion years ago of atmospheric oxygen and decrease in greenhouse gas
methane
2.3 billion years: large dispersal of stromatolites at shal-
low-marine continentals shelves
2.45 billion years: 'Great Oxidation Event'
2.45 billion years: geochemical evidence of a possible
existence of eukaryotic organisms 2.5 Ba 2.7–2.3 billion years: formation of the large continen-
tal plates – roughly 60 % of the continental plates were
2.45 billion years: colonization of tide areas and successively
formed during this period of time
terrestrial environments by cyanobacteria and microbial mats
2.7–2.4 billion years: main time frame for formation of
2.7–2.5 billion years: evolution of oxygen photosynthe- banded iron ores
sis and cyanobacteria, geochemical analyses indicate an
earlier evolution 2.7 billion years: fossil soils indicate a first colonization of
terrestrial environments by microorganisms
3.3–2.8 billion years: sharp increase of gene families

('Archaic genetic expansion')
Archean
3.5 billion years: first evidence of continental plates

3.5 billion years: oldest stromatolites
above sea level
4.0–3.5 billion years: sodium-carbonate rich soda oceans

change into sodium-chloride- and calcium-rich oceans
4.2–3.8 billion years: origin of life, first evolution of an-
aerobic heterotrophic metabolic pathways, shortly after- 4.0 Ba
4.4–4.0 billion years: cooling of Earth's surface below
wards evolution of anoxygenic photosynthesis
100 °C and formation of oceans
Hadean 4.4 billion years: solidification of Earth's crust and start

of plate tectonics
4.5 billion years: formation of moon
4.6 Ba 4.56 billion years: formation of Earth
4.8–4.6 billion years: formation of solar system and the

protostar sun out of an interstellar cloud
32 Earth's history
2.2.1
The Archean eon

The earliest eons in Earth’s history are the Hadean and in Greenland, dating back to around 3.8 billion years, though
the Archean. individual rock findings from northern Canada date back
The Hadean is geologically defined as the period since the even further to around 4.3 and 4 billion years. Single zircon
formation of the Earth until the start of the Archean roughly minerals from the Australian Yilgam craton can be dated
4 billion years ago. It is not further subdivided. back to 4.4 billion years.
The Archean, on the other hand, is geochronologically It is likely, however, that a continuous solid crust and the
defined as the period between the end of the Hadean (4 bil- formation of the first oceans took place near the end of the
lion years ago) and the start of the Proterozoic (2.5 billion Hadean, when the temperature of the Earth's surface cooled
years ago). It is divided into the Eoarchean (4–3.6 billion to below 100 °C.
years ago), Paleoarchean (3.6–3.2 billion years ago), Mesoar- The Archean is therefore characterized by the further dif-
chean (3.2–2.8 billion years ago), and Neoarchean (2.8–2.5 ferentiation of the Earth’s crust, the formation of cratons,
billion years ago). and by the origin and evolution of life.
In the Archean, Earth’s atmosphere was entirely oxy-
gen-free. The oldest known rock formation is the Isua Gneiss
The proto-Earth was formed during the Hadean. Its formation of continental crust increased; life evolved in the
mass subsequently increased through collisions with mete- oceans.
orites and other protoplanets. Around 4.5 billion years ago, In the Eoarchean, the Earth had a solid crust, leading to
the moon formed as a result of a collision between the pro- the formation of the oceans. In the Lower to Middle Eo-
to-Earth and another protoplanet. archean, Earth’s surface was exposed to a huge number of
In the Lower Hadean, differentiation processes of the asteroid impacts until impacts died down after roughly 3.8
mostly liquid melt of the proto-Earth started. Heavy chem- billion years. The atmosphere remained anoxic and reduc-
ical elements, especially iron and nickel, sank to form the ing environmental conditions prevailed. Early life probably
Earth’s core. Lighter elements, including silicon and oxy- already existed in the Eoarchean, continuing to develop dur-
gen, formed the Earth's mantle. In the early Hadean, Earth’s ing the Paleoarchean. The oldest stromatolites date back to
mantle started to solidify, launching the process of plate tec- the Mesoarchean. A widespread glaciation of the Earth oc-
tonics. Initially, the crust was exclusively oceanic, forming its curred roughly 2.9 billion years ago (the Pongola glaciation).
first continental blocks near the end of the Hadean. In the Neoarchean, the continental crust reached a thick-
In the Archean, Earth possessed a crust. This was initial- ness allowing for the formation of higher mountains for the
ly oceanic and was, like today's oceanic crust, subducted at first time. The end of the Archean eon is characterized by the
plate boundaries again and again. During the Archean the evolution of oxygen (the Great Oxidation Event) due to the
increasing prevalence of photosynthesis.
craton: continental shield; central region of a continent which Great Oxidation Event: great oxygen crisis 2.45 billion years
was formed in the Lower Precambrian and which has suffered no ago caused by the appearance of dioxygen
tectonic deformation since the Precambrian
See also: Geochronology: 2.3.1.4, 2.3.1.5

2.5 Ba
Neoarchean
2.8 Ba
A
Mesoarchean
R
C
H
3.2 Ba
E
A
N
Paleoarchean
3.6 Ba
Eoarchean
4.0 Ba
Hadean
4.6 Ba Stratigraphic time scale of the Hadean and Archean

34 Earth's history
2.2.1.1
Chemical evolution and origin of life

Prebiotic chemical evolution, i.e. the abiotic origin of or- monomers. In nature, theses geothermal and geochemical
ganic molecules, occurred during the first few hundred mil- gradients could be supplied in the vicinity of volcanic hydro-
lion years of Earth's history, in the Hadean. First life then thermal vents. Terrestrial hydrothermal fields, but also the
arose roughly 4 billion years ago. submarine "black smokers" are discussed as locations of for-
Hypotheses on the process of the chemical evolution mation of complex organic molecules and life. Here, chem-
of life are based on experiments, though fossil evidence is ical energy could be provided by the reduction in iron with-
lacking. One of the first pieces of evidence for the forma- in iron-sulphur bearing minerals, such as pyrite (FeS2) with
tion of organic from inorganic molecules was provided in elemental hydrogen (H2) through the reaction FeS2 + H2 ⇌
an experiment by Harold C. Urley and Stanley L. Miller in FeS + H2S. Additionally, the partly high temperatures could
1953. They showed that, in a closed loop, more complex or- have favoured the origin of life, though lower temperatures
ganic compounds, such as amino acids and lower carbonic are required after the emergence of temperature-sensitive en-
and fatty acids, could be formed from inorganic compounds zymes and vitamins. An indicator for the origin of life in
with a supply of energy in form of electrical discharges. In these iron-sulphur reducing environments is, among other
subsequent experiments, additionally amino acids, lipids, pu- things, the prevalence of iron-sulphur centres within many
rines and sugars, as well as the more complex porphyrins and enzymes. It is also likely that minerals (clay minerals, pyrite)
isoprene could be produced. catalysed the formation of biomolecules and self-replicating
It is thought that geochemical energy gradients allowed systems. So far, the emergence of self-replicating systems is
the formation of complex organic molecules from organic hypothetical.
Since the first cells are likely to have possessed only sim- hence a stabilization of the cell environment, played an im-
ple ion-permeable membranes, intracellular ratios of these portant role for the formation of the cells and especially for
cells should have corresponded to those of the external me- their survival.
dium. The potassium/sodium concentration ratios and the Oxygen was formed since approximately 3.5 billion years
high concentrations of zinc and phosphate in today's cells by the oxygenic photosynthesis of cyanobacteria. However,
are more in line with ratios in terrestrial hydrothermal fields the released oxygen was immediately consumed by oxida-
than with conditions in the primordial ocean. The ionic com- tion of, in particular, dissolved sulphides and divalent iron
position of the cytoplasm, therefore, suggests an origin of ions in the oceans. The oceans and the atmosphere therefore
life in terrestrial hydrothermal fields. In the early phase of initially remained nearly free of oxygen only roughly 2.3 bil-
the origin of life, the Earth, however, was repeatedly subject- lion years ago.
ed to severe and frequent meteorite impacts. Their impact Various geochemical factors contributed to this increase:
energy sterilized the Earth's surface, and, also, leading to the continental plates raised above the sea level. The newly
heating and sometimes even to an evaporation of the oceans. starting terrestrial volcanism changed the atmospheric and
Although the origin of life on the Earth's surface appears to marine chemistry. Organic material was subducted by plate
be possible, the colonization of more stable habitats with a tectonic processes on a small scale and parts of the carbon
better protection from meteorite impacts was important to were fixed within the Earth's crust in the long term. Meth-
ensure the further survival. Therefore, deep sea waters near ane released by methanogenic archaea escaped into space re-
hydrothermal vents (black smokers) are likely to have played moving hydrogen from the geochemical cycles. This reduced
a major role. Since the physiological processes were attuned availability of carbon and hydrogen contributed to the estab-
to a cytoplasm composition evolved in a different environ- lishment of free oxygen. However, bioavailability of trace
ment, these habitats could only be colonized after the evolu- elements, such as the reduction in nickel important for the
tion of ion-arresting membranes and their corresponding ion methanogenesis, indirectly promoted the increase of free ox-
pumps. The development of modern membranes equipped ygen (less oxygen was used for the oxidation of the methane
with ion pumps, in particular a sodium-potassium pump and now formed in a lesser extent).
hydrothermal: relating to the action of heated water in the monomers: (Grk.: monos = single, meros = part) individual
Earth’s crust (under pressure to temperatures above 100 °C) molecules which can bind together to make polymers (macro-
molecular bonds)
See also: Plate tectonics: 2.1.1.2; Evolution of oxygen: 2.2.2.1

Urey's and Miller's experiment (right) proofed the possibility that all
necessary organic molecules could have evolved from simple inorgan-
ic molecules in a reducing environment. In the meantime, emerging
doubts with regard to reducing conditions of the primordial atmos-
phere made the atmosphere as a location of organic molecules synthe- electrods
sis less likely. New models again suggest a carbon- and hydrogen-rich
reducing primordial atmosphere. sparking
Geochemical gradients near the black smokers in deep sea waters (bot-
tom), but also terrestrial geothermal fields are discussed as locations
for the origin of life
H2O, CH4, NH3, H2, CO2
cooling coil
heating
Photosynthesis emerged presumably shortly after the origin The evolution of eukaryotic algae roughly 1.2 billion years ago led
of life. Formed oxygen was directly consumed by oxidation of to the formation of larger-sized primary producers. These larger
iron and other compounds. A first increase of oxygen concen- cells sank faster and accelerated the export of organic carbon via
tration occurred 2.4 billion years ago sedimentation. The evolution of eukaryotic algae required a second
sharp increase of oxygen concentration and facilitated the evolution
of complex multi-cellular organisms and colonization of terrestrial
environments
atmosphere 20 %
oxygen concentration
2 %
0.2 %
0.02 %
anoxic oxic
oceans
time [billion years]

Origin of life is connected to the formation of Earth. The interac-
tion of plate tectonics and biogeochemical cycles provided the
prerequisites for the origin of life, in particular for the evolution
of eukaryotes, multi-cellular organisms and for the colonization of
terrestrial environments. High oxygen concentration could only be
fixation of carbon via photosynthesis
provided because organic carbon was permanently removed from
geochemical cycles. This is facilitated – in geological periods of sedimentation of organic
time – by subduction of oceanic crust including all organic depo- matter on the sea floor
sitions. Less than 0.1 % of primary production is released to the
lithosphere in this way. Although, an oxygen concentration of far subduction
below 1 % would be adjusted without this process driven by plate
tectonics
36 Earth's history
2.2.1.2
'RNA world hypothesis' and formation of cells during the Archean

In addition to the abiogenic formation of the essential or- recent cells have formed by the merge of multiple interact-
ganic molecules, the origin of life requires the formation of ing hypercycles that had been less complex each. Instead of
self-replicating systems. Both, protein and lipid macromole- complex interactions between proteins and DNA, structures,
cules can assemble into microspheres that are closed reaction in which a molecule acted as an information storage as wells
chambers with a few microns in diameter. By uptake of new as a catalyst, could have probably developed at first. It is like-
molecules from the solution, these structures can grow and ly that it had been RNA.
divide into smaller microspheres. It is incontestable that all extant living beings go back to
These microspheres can embed DNA or RNA polymers. a common origin of life. This is evidenced by a number of
Furthermore, a reproduction of the nucleic acids in the in- findings. These include the construction of nucleic acids
terior of such microspheres (or proto-cells) had been exper- from the same five nucleic bases (adenine, thymine, cytosine,
imentally demonstrated. It is quite possible that such pro- guanine, and uracil) and the universal genetic code as well
to-cells and life-like structures had independently developed as the correspondence of 20 amino acids in all known forms
multiple times during the Archean. Moreover, it is likely that of life.
There are many indications that during the origin of life Such ribozymes are also known in today's organisms. Thom-
the genetic material was RNA at first. These so-called 'RNA as R. Czech and Sidney Altman received the Nobel Prize in
world hypothesis' is a possible link between chemical evolu- Chemistry in 1989, for the first evidence of such a ribozyme
tion and the origin of cells in their today's shape. (self-splicing RNA in the ciliate Tetrahymena thermophila).
This hypothesis is based on two fundamental characteris- But also the catalytic centres of the ribosomes are made
tics of the RNA: first it can store genetic information, as well of ribosomal RNA (rRNA) and not of proteins. Therefore,
as the DNA. On the other hand RNA can catalyse chemical the rRNA within the ribosomes could potentially be an evo-
reactions as well as proteins. lutionary relic of this phase of the origin of life.
In principle, both DNA and RNA can store genetic infor- It was significant for the evolution of life that a molecule
mation. Although RNA occurs in all organisms, RNA as the combined the two functions of storage of genetic informa-
main genetic material can only be found in small genomes of tion and catalysis. It is likely that RNA trapped in micro-
some viruses today, while other viruses and all other living spheres catalysed its own synthesis in so-called hypercycles.
beings use DNA. One explanation for this fact is the low sta- It is also conceivable that double-stranded RNA, occurring
bility of the usually single-stranded RNA. Although RNA, in warm to hot waters of the young Earth, was melted dur-
as the DNA, can be double-stranded it is more error-prone ing the day and again complemented in the cooler night by
due to its molecular structure compared to DNA. The large monomers within the day-night cycle.
genomes of present-days organisms are only possible due to Since the RNA was error-prone with regard to the stor-
the lower error rate of DNA replication. age of genetic information and proteins in catalytic ways are
RNA can also take over catalytic functions in addition to much more diverse than RNA, the RNA world hypothesis
the storage of genetic information. Single-stranded RNA can assumes that the RNA was replaced in the course of evolu-
fold into complex three-dimensional structures by mating of tion by the more stable DNA with respect to the information
bases of the same RNA strand with complementary bases in storage and catalytic functions taken over by proteins.
some sections. These molecules can be catalytically active.
catalysis: (Grk.: katalysis = dissolution) bringing about, acceler- splicing: modification of the pre-mRNA by removing introns
ating or decelerating a chemical reaction using a catalyst during transcription
See also: Domain of life: from 4.1.2 to 4.1.2.3; Viruses: 3.1.6

O
O O
- P O
O - P
O O
O
H2C O
H2C O
O cytosine
O
O O CH2
OH cytosine guanine
- P O
O - P
O O
O
H2C O
H2C O
adenine
adenine thymine
O
O CH2
O OH O
- P O
O - P
O O
O
H2C O
H2C O
uracil O
thymine adenine CH2
O OH
O OH
O
- P H
O
O
H2C O Deoxyribonucleic acid (DNA) is made up from nucleotides hat are linked
guanine via phosphate groups. They are made up from the sugar deoxyribose
and the bases guanine, thymine, adenine and cytosine. Deoxyribose is
OH OH lacking of an OH-group at the 2'-position, however deoxyribose is more
Ribonucleic acid (RNA) consists of nucleotides that are linked via phos- stable compared to RNA. Normally, DNA is double-stranded. Hydrogen
phate groups. They are made up from the sugar ribose and the bases bonds connect the complementary bases thymine (T) with adenine
guanine, uracil, adenine and cytosine. In contrast to the deoxyribose of (A) as well as cytosine (C) with guanine (G). Complementary bases are
the DNA, the RNA ribose has an OH-group at the 2'-position (red). This equally shared within the DNA, however, the ratio of (A and T) to (G and
results in low RNA stability compared to DNA: in an alkaline solution the C) is variable and can differ hugely between different organismal groups.
OH-group dissociates and the oxygen atom and the phosphate group For G and C are connected via three hydrogen bonds, whereas A and
are bond in a ring structure. With that the connection to the next nucle- T show only two hydrogen bonds, DNA, with a higher proportion of G
otide is unfixed. Normally, RNA is single-stranded, leading to a reduced and C, has a higher melting temperature (its single strands unfix only at
stability on one hand, but having the ability to fold itself into complex higher temperatures)
three-dimensional structures on the other hand
Simple microspheres made of proteins or, as illustrated, of a lipid bilayer

can be spontaneously formed from dissolved monomers. Autocatalyt-
Single-stranded RNA is able to fold itself into complex three-dimension- ic molecules (e.g. RNA) trapped in such microspheres can form simple
al structures. These structures can have catalytic properties and can be self-replicating systems. Such proto-cells are the hypothetical precursor
referred to as ribozymes of today's cells
38 Earth's history
2.2.1.3
The Archean carbon metabolism: fermentation

Life evolved roughly 4.2–3.8 billion years ago. The first of substances. NADH provides electrons as reducing equiv-
cells were heterotrophic, taking up organic material by diffu- alents. On the one hand, the electrons are used to reduce
sion processes through still simple-constructed membranes. various molecules; on the other hand a proton gradient is
During glycolysis monosaccharides such as glucose are de- built up across a membrane by both, the electron transport of
graded to pyruvate. This oxygen-independent pathway could photosynthesis and respiration. This proton gradient is used
even take place under the anoxic conditions of the Archean. by ATPase to synthesize ATP from ADP and phosphate.
First the glucose is converted to fructose-1.6-bisphosphate Both ATP and NADH are composed of simple compounds
by the consumption of two ATP. During further degradation (ribose, phosphate residues, organic bases), which probably
to pyruvate, the so-called amortization phase, four ATP and already being formed by abiogenic processes early in Earth's
two NADH are formed. Since NADH is usually present only history.
in low concentrations in cells, the reduced NADH must be Phylogenetic analyses of organisms from all three do-
re-oxidized to NAD. Under the anoxic conditions during the mains (Eukarya, Bacteria, Archaea) suggest that roughly 2.8
Archean the electrons were transferred to organic molecules. billion years ago, 27 % all major modern gene families (genes
These so-called fermentation pathways are distinguished ac- which code for structurally similar proteins) had been creat-
cording to the target molecule and product. ed. This mainly includes genes for electron transport, respi-
The most important molecules of energy metabolism are ration and coenzyme metabolism, while genes for metabolic
adenosine triphosphate (ATP) and nicotinamide dinucleo- pathways using redox-sensitive metals or oxygen arose later.
tide (NADH). ATP provides chemically bound energy ready This early evolution of gene families is known as 'archaic
for the basic energy consuming processes of all living beings, genetic expansion'.
such as the synthesis of organic molecules or active transport
The climate of the Archean was largely temperate to warm anaerobic microbial degradation of biomass. The feedback
despite an initially weak solar radiation. In the Hadean the in atmospheric greenhouse gas concentrations with biogenic
sun radiated only 70 % of today's energy (at end of the Ar- and geochemical processes caused a relatively stable climate.
chean roughly 80 %). Since its formation radiation energy of Since the heterotrophic lifestyle would have rapidly con-
the sun increased steadily. This is due to a shift of the sun's sumed the organic molecules which have been built by abi-
elemental composition by power generating nuclear fusion ogenic processes, a rapid emergence of (chemo-)autotrophic
processes. In the Archean, a permanent glaciation of the pathways is likely. Additionally, photosynthesis, at least the
Earth was prevented only by high concentrations of green- anoxygenic photosynthesis, must have been evolved soon.
house gases: short-wave radiation from the sun was partially All major metabolic pathways were developed until approx-
reflected from the Earth as thermal radiation. Greenhouse imately 3.5 billion years ago. From this point of time fossils
gases absorbed this thermal radiation, thereby contributing are proved in the fossil record as well as fossil organic mat-
to warming of the atmosphere. In the Archean, the most im- ter and biogenic sediments. Since oxygen was still missing,
portant greenhouse gas was, however, not carbon dioxide. metabolic pathways which did not require oxygen developed
High concentrations of carbon dioxide should have led to first. This evolutionary development is also reflected in the
the formation of the mineral siderite (FeCO3) in iron-rich metabolic pathways of modern organisms: basal reactions
oceans, which is not detectable in the Archean rock record. are often independent of oxygen, while only the terminal
The greenhouse effect of the Archean must therefore be a re- reactions are oxygen-dependent. One example is the energy
sult of methane concentrations of about 0.1 %; methane was metabolism of the early evolved oxygen-independent glycol-
released by anaerobic methanogenic prokaryotes. This for- ysis and the oxygen-dependent respiratory chain of terminal
mation of methane (methanogenesis) is the last stage of the oxidation that developed later.
domain: the highest classification of an organism: Eukarya, Bac- reduction: gain of electrons or a decrease in oxidation state by
teria and Archaea a molecular, atom, or ion
oxidation: the loss of electrons siderite: (Grk.: sideros = iron) mineral composed of iron car-
redox reaction: reduction-oxidation-reaction; chemical reac- bonate (FeCO3)
tion in which electrons are transferred between species
See also: Anoxygenic photosynthesis: 2.2.1.4, 2.2.1.5

NH 2 Adenosine triphosphate (ATP) provides energy for energy-consuming NH 2

processes. ATP is made up by the nucleoside adenosine, consisting of
C C
N adenine and ribose, and phosphate residues. By separation of a phos- N
N C N C
phate residue roughly 32.3 kJ per mol are released CH
CH
HC C HC C N O O
N O O O H2O N
N
adenine H2C O P O P O P O‐ H2C O P O P O‐
O O O
O‐ O‐ O‐ O‐ O‐
HC HC HC HC
H H phosphate residues HO P O ‐ + H+ H H
C C ribose C C
O‐
OH OH OH OH
Adenosine triphosphate (ATP) Adenosine diphosphate (ADP)
Nicotinamide adeninedinucleotide (NAD)

NH 2 NAD+ NADH NH 2
O C CH (oxidised form) H+ 2 e‐ (reduced form) CH2
O C
C CH C CH
O‐ NAD provides reducing equivalents and serves for the con- O‐
HC + CH trolled transfer of electrons. NAD, as well, is composed of
HC CH
N H2C O P O N H2C O P O
nicotinamide O two nucleotides. One nucleotide consists of the compounds O
HC HC adenine, ribose, and phosphate – similar to ATP. The second HC HC
H H nucleotide is made up of nicotinamide, ribose and phos- H H
C C Ribose phate C C
NH 2 NH 2
HO HO O HO HO O
C C
N C N N C N
CH CH
HC C N HC C N
N N
adenine H2C O P O H2C O P O
O O
O‐ phosphate residues O‐
HC HC HC HC
H H H H
C C ribose C C
OH OH OH OH
Glycolysis
glucose Metabolism pathways for the composition and degradation of simple sugars have
2 ATP emerged early in Earth's history. Reversible occurring metabolism pathways of the
2 ADP amortization phase (conversion of glycerinaldehyde-3-phosphate into pyruvate)
are largely preserved across all three domains and are likely developed before
the separation of the domains. The conversion of glucose into fructose-1.6-bis-
phosphate is catalysed in Archaea by different enzymes compared to bacteria and
fructose-1.6-bisphosphate
eukaryotes and is therefore likely to have emerged after the separation of the do-
mains
Fermentation
2 glycerinaldehyde-3-phosphate 2 lactate 2 ethanol With only two ATP per molecule of glucose there is a low gain of ener-
gy of the glycolysis. Since under anoxic conditions of the early Earth a
2 NAD+ terminal oxidation of the resulting NADH/H+ was not possible, it had to
2 NADH/H+ be re-oxidized to NAD+ by fermentation processes. During fermentation,
4 ADP this is done after the glycolysis using the resulting pyruvate. In the lactic
4 ATP acid fermentation lactate is formed from pyruvate; during the alcoholic
2 H2O
fermentation of lactic acid fermentation ethanol is formed after separation of carbon dioxide
2 pyruvate alcoholic fermentation

2 acetaldehyde
2 CO2
40 Earth's history
2.2.1.4
Evolution of the Archean photoautotrophy:

energetics of the anoxygenic and oxygenic photosynthesis
Shortly after the origin of life also autotrophic metabolic Photosystem II may have originated either by an extensive
pathways evolved. In the Lower Archean (besides chemoau- gene duplication of the genes required for photosynthesis or
totrophic metabolic pathways) the anoxygenic photosynthe- by extensive lateral gene transfer. Afterwards it evolved fur-
sis developed at first. Photosynthesis refers to the production ther.
of high-energy organic compounds using light energy. The In the oxygenic photosynthesis the photosystems of type
anoxygenic photosynthesis uses various electron donors II and I then are connected in series. This combination of
such as hydrogen sulphide, ferrous ions, nitrite or elemen- both photosystems and thus the more efficient energetic use
tal hydrogen and requires only one photosystem, either one of water as an electron donor for oxygenic photosynthesis
with a reaction centre type I within the photosystem I (PS I) evolved later. Photosynthetic cyanobacteria probably exist
or of type II within the photosystem II (PS II). It is assumed since roughly 3.5 billion years, they have been proven since
that a photosystem of type I evolved first and that hydrogen 2.45 million years. The oxygenic photosynthesis had proba-
was used by the anoxygenic photosynthesis initially in the bly emerged approximately 3 billion years ago.
Lower Archean.
Today, anoxygenic photosynthesis of type I is still being anoxygenic photosynthesis by using hydrogen sulphide and
used, for example, by green sulphur bacteria (e.g. Chlorobi- other compounds as electron source. It is likely that the pri-
um) and Heliobacteria (Heliobacterium). The anoxygenic pho- meval proto-cyanobacteria only used the photosystem II. It is
tosynthesis has spread across different bacterial groups by further likely, that the possession of two different photosys-
horizontal gene transfer. Today, anoxygenic photosynthesis tems initially may have been beneficial to organisms living
of type II is still being used by green non-sulphur bacteria under changing environmental conditions and either using
(Chloroflexi) and purple bacteria (purple sulphur bacteria photosystem I or photosystem II for the anoxygenic photo-
and purple sulphur bacteria). In general, bacteria have only synthesis.
one of the two photosystems (except for Cyanobacteria). The original advantage of the second photosystem may
In the anoxygenic photosynthesis the first stable elec- have come into play only under certain environmental con-
tron acceptor, depending on the photosystem, is either an ditions: when the proto-cyanobacterium got into a manga-
iron-sulphur protein (PS I), or a quinone (PS II). From there, nese-containing environment, manganese would have re-
the electron is finally led back via a PQ-cycle to the reaction leased electrons via photo-oxidation, which could have been
centre (cyclic electron transport). In this operation, a pro- transferred to photosystem II resulting in an electron accu-
ton gradient is established by which an ATPase is operated. mulation. Through photosystem I, these excess electrons
ATP is formed during the cyclic electron transport, but no could be removed.
reducing equivalents, they have to be formed from external In the course of evolution this originally accidental use
electron donors (inorganic or organic compounds). In addi- of manganese ions of the manganese-rich sea water led to
tion to this cyclic electron transport, there is also a non-cyclic a manganese complex bound to the photosystem II. At this
electron transport, by which reducing equivalents are direct- manganese complex water is split during the oxygenic pho-
ly formed. tosynthesis. During oxygenic photosynthesis, molecular ox-
Unlike to other bacteria cyanobacteria have two photosys- ygen is produced from water; the transfer of electrons from
tems. The precursors of cyanobacteria may have practised water to NAD requires two serial photosystems.
convection: circular movement of molecules within fluids due PQ-Cycle: the result of redox reactions influenced by plastoqui-
to differences in density none (PQ)
molecular oxygen: molecule consisting of two oxygen atoms
(O2)
See also: Bacteria: 4.1.2.1

In PSII, the excited chlorophyll electron is first

–1.25 transferred to a primary electron acceptor (a phe- An electron is transferred through several intermedi-
P700*
ophytin) and finally to a plastoquinone, which can ate steps (via iron-sulphur centres) to ferredoxin from
diffuse within the membrane to a cytochrome- the chlorophyll of the reaction centre of PS I. This
–1.0 b6f-complex connects ferredoxine-NADP reductase and reduces
NADP+ to NADPH
P680*
–0.75
FeS protein
–0.5 ferredoxine
NADP+
NADPH/H +
–0.25
quinone pool
E0' (V) 0.0 The electrons can be transferred alternatively to the cy-
tochrome-b6f-complex from the ferredoxin. This electron flow is
cyt-b6f-complex referred to as cyclic electron transport. There will be no reducing
+0.25 equivalents
plastocyanine
+0.5
PS I
+0.75 From the cytochrome-b6f-complex, the electron is transferred to
2 H20 - plastocyanine, which diffuses to the reaction centre of PS I and
e
here it transfers the electron to the oxidized chlorophyll of PS I
+1.0
O2 + 4 H +
PS II
The oxidized chlorophyll radical of PS II is regener-
ated via the manganese cluster of the water-split-
ting complex cyanobacteria and phototrophic eukaryotes
oxygenic photosynthesis
anoxygenic photosynthesis
The anoxygenic photosynthesis is based on a photosystem. This is
similar to either PS I or PS II of oxygenic photosynthesis. Electron
transport in bacterial anoxygenic photosynthesis is usually cyclical
–1.25 – the electrons flow back to the chlorophyll – and it is used to build P840*
a proton gradient and thus used for the production of ATP
–1.0
P870*
–0.75
FeS-Protein
Ferredoxin
–0.5
NADP+
NADPH/H+
–0.25
quinone pool
quinone pool
E0' (V) 0.0
H2S H2S
e-
e- Cyt bc1
+0.25
S + 2 H+ S + 2 H+ Cyt c553
Cyt bc1
+0.5 In the anoxygenic photosynthesis of type I, the electron is
Cyt c2 transferred to ferredoxin and can either flow back to bac-
During the type II photosynthesis, the quinone pool is the teriochlorophyll via the cyclic electron transport or being
+0.75 first stable electron acceptor. Reducing equivalents (NADPH) transferred to NADP+ via a non-cyclic electron transport. The
can therefore be only formed by expending extra energy. The formation of reducing equivalents is possible without addi-
energy for this reverse non-cyclic electron flow from the qui- tional energy
+1.0 none pool to NAD(P)+ is obtained from the proton gradient
anoxygenic photosynthesis of type II (purple bacteria) anoxygenic photosynthesis of type I (green sulphur bacteria)
42 Earth's history
2.2.1.5
Evolution of the Archean photoautotrophy:

compartmentalisation
Oxygenic photosynthesis became significant only with A structural requirement for energy metabolism is a com-
the development of shallow marine shelf areas – the uplift partmentalization of the cell by membranes. This applies to
and enlargement of the cratons (continental plates) roughly the anoxygenic as well as the oxygenic photosynthesis: Dur-
2.5–2.3 million years ago. As a result, the shallow marine ing the so-called light reaction ATP and reducing equivalents
shelf areas were inhabited by stromatolithes and thus the (NADPH) arise. Both are formed via membrane-bound en-
photosynthesis was greatly promoted on a global scale. In zymes. In the formation of ATP the proton gradient between
addition to habitat availability photosynthesis was also lim- the compartments is utilized. During the bacterial anoxy-
ited by nutrient availability: the archaic ocean was stratified, genic photosynthesis this proton gradient is established via
there was non exchange between the anoxic hydrothermally the plasmalemma, that is, between the cytoplasm on the one
influenced deep waters and the atmospherically affected sur- hand and the intermembrane space, that is located between
face waters. A convection only started with the formation of both bacterial envelope membranes on the other hand. Dur-
large cratons. The availability of nutrients and in particular ing the oxygenic photosynthesis of both, the cyanobacteria
of phosphate was therefore generally low. In addition, phos- and the plastids of the eukaryotes, a proton gradient is devel-
phate was precipitated by adsorption to iron oxides. There- oped at the thylakoid-membranes, between thylakoid lumen
fore, low phosphate concentrations limited photosynthesis. and cytoplasm (in the case of the cyanobacteria) and the
stroma of the plastids (in eukaryotes) respectively.
Only one photosystem is involved in bacterial anoxygen- In the so-called dark reaction reducing equivalents and
ic photosynthesis. In oxygenic photosynthesis two spatially ATP are required for carbon fixation: in the Calvin cycle,
separated photosystems are involved: photosystem I is lo- two molecules of phosphoglycerate are initially formed from
cated in the non-stacked areas of thylakoids. This allows carbon dioxide and ribulose-1.5-bisphosphate, a C5 sugar.
an unhindered electron flow towards ferredoxin and NADP The primary product of carbon fixation is therefore a C3-sug-
reduction. Likewise, the ATP synthase is located in the un- ar. This type of photosynthesis, in which the first product
stacked areas. In contrast, the photosystem II is located in of carbon fixation is a C3-body, is therefore also known as
the stacked thylakoid areas. This arrangement is advanta- C3-photosynthesis. From the resulting 3-phosphoglycerate
geous for the interaction with the light-harvesting complexes. glyceraldehyde-3-phosphate, also a C3-body, is formed by
The spatial separation of the photosystems also prevents an consumption of ATP and NADPH/H. Later in the Calvin
uncontrolled skipping of electrons from photosystem II to cycle three ribulose-1,5-bisphosphate arise from five mole-
photosystem I. cules of glyceraldehyde-3-phosphate by consumption of a
further three ATP molecules.
abiotic: (Grk.: a = not, bios = life) not living lent corresponds to one mole of electrons (due to the transfer of
C5-sugar: sugar molecule with five carbon atoms electrons and oxygen atoms, one mole of NADH corresponds to
photo-oxidation: oxidation caused by the action of light two reducing equivalents)
protocyanobacteria: extinct ancestors of current cyanobacteria thylakoids: (Grk.: thylakoeides = sack-like) systems of mem-
reducing equivalent: unit of measurement used to quantify branes in chloroplasts
the reduction capacity by reducing agents; one reducing equiva-
See also: Evolution of plastids: 2.2.2.5; Organelles: 4.6.1.3; Cyanobacteria: 4.1.2.1

PS I is located in the area of the free thylakoids. Electrons are transferred to NADP
The contact with the stroma is necessary for at the stroma side of the thylakoids
the electron flow towards the ferredoxin
PS II is located in the area of the grana. The spa-
tial separation of the photosystems prevents an 2 NADP+
uncontrolled reflux of electrons 2 NADPH/H+
2.6 ADP + 2,6 Pi

12 H+
4 e-
2.6 ATP
PS II Cyt b6f PS I
2 H20 O2
4 H+ 8 H+
Protons released into the thylakoid lumen

are used by the ATPase for ATP synthesis
Carbon dioxide fixation via the Calvin cycle takes 6 ATP

place in the stroma of the plastids. The enzyme
RubisCO catalyses the reaction of a C5-sugars (rib- 3 CO2 6 ADP + 6 Pi
ulose-1,5-bisphosphate) with carbon dioxide to 6 3-phosphoglycerate
two C3-sugars (phosphoglycerate) 6 NADPH/H+
Carbon fixation via the Calvin cycle arose under 3 ribulose-1.5-bisphosphate

6 NADP+
anoxic conditions, i.e. in the absence of oxygen.
The oxygenase activity of RubisCO (the use of ox- 3 ADP + 3 Pi
ygen as a substrate) and the related photorespira-
tion therefore played no role. Only with increas-
ing oxygen concentrations photorespiration was 3 ATP 6 glycerinaldehyde-3-phosphate
quantitatively significant and started to limit the
efficiency of photosynthesis
3 ribulose-5-phosphate
glycerinaldehyde-3-phosphate
Pi
H2O 5 glycerinaldehyde-3-phosphate
oxygenic photosynthesis
anoxygenic photosynthesis (green sulphur bacteria) Carbon fixation occurs via the Calvin cycle in oxygen-
ic photosynthesis; in the anoxygenic photosynthesis
carbon fixation occurs via various metabolic path-
ways, such as the reverse citric acid cycle
Light energy is collected in a carbon fixation
chlorosome, that is surrounded (inverted citric acid cycles)
by a monolayer of a lipid
H+ ADP + Pi
Gram-negative bacteria are sur-
ATP rounded by two membranes. The
NADPH/H+ proton gradient between the in-
H+
NADP+ ter-membrane space and cytosol is
used by ATPase to produce ATP
ferredoxin
H2S
S 2 H+ e
-
H+
Anoxygenic photosynthesis only uses one photosystem. In the green sulphur
Electron donors are organic molecules, hydrobacteria and the heliobacteria this corresponds to the photosystem I of oxygen-
gen sulphide and hydrogen. There will be no ic photosynthesis; in the green non-sulphur bacteria and the purple bacteria it
oxygen formation corresponds photosystem II of oxygenic photosynthesis
44 Earth's history
2.2.2
The Proterozoic eon

The Proterozoic eon extends from the Archaean (2.5 bil- The eukaryotes developed throughout the Proterozoic
lion years ago) until the start of the Phanerozoic eon (541 so that almost all known major groups existed by the eon’s
million years ago). The start of the Proterozoic is geochron- end. However, the fossil record from this time period only
ologically fixed, whereas its end, and beginning of the Phan- improved near the end of the Proterozoic, with the develop-
erozoic respectively, is stratigraphically defined by the first ment of multicellular life forms and, in particular, with the
appearance of the index fossil Trichophycus pedum. appearance of hard skeletal elements in many organismal
During the Proterozoic the atmosphere contained oxygen, groups.
which changed the climate and erosion patterns in terrestrial
environments.
Atmospheric oxygen concentrations began to rise in the a number of narrow mountain belts in the Upper Ectasian
Upper Neoarchean and the Lower Paleoproterozoic. Simul- and Stenian.
taneously, atmospheric carbon dioxide and methane levels Multicellular eukaryotes appeared for the first time dur-
decreased. This reduction in greenhouse gases led to a long ing the Neoproterozoic. Most major continental masses were
and severe period of global cooling, known as the Huroni- unified at the beginning of the Neoproterozoic era, forming
an glaciation, which extended throughout the Siderian and the super continent Rodinia. However, this super continent
Rhyacian periods. The Orosirian period, which followed, began to break apart into smaller continents in the Upper To-
was characterized by increased orogeny, whereas the subse- nian and during the subsequent Cryogenian. The planet was
quent Statherian period featured the stabilization of cratons. covered by huge glaciers as a result of extensive glaciations.
Many of those central continental areas suffered no tectonic Contrary to earlier theories (known as 'Snowball Earth'), at
deformation since that time. least the planet’s equatorial areas remained ice-free. The eu-
The super continent Rodinia emerged during the Meso- karyotes subsequently spread and radiated during the warm-
proterozoic. At the same time, the eukaryotes emerged. Dur- er phases of the Cryogenian and throughout the Ediacaran
ing the Calymmian and Ectasian periods, extensive sediment period. This phase was characterized by the radiation of ma-
basins formed around the cratons, subsequently forming jor eukaryotic groups.
the super continent Rodinia accompanied by the uplift of
craton: continental shield; central region of a continent which supercontinent: large landmass formed from several conti-
was formed in the early Precambrian and which has suffered no nents or cratons
tectonic deformation since the Precambrian
See also: Cambrian explosion: 2.3.3.1

541 Ma
Ediacaran
635 Ma
Cryogenian
Neoproterozoic
850 Ma
Tonian
1,000 Ma
Stenian
1,200 Ma
P
R
O Mesoproterozoic Ectasian
T
E 1,400 Ma
R
O
Calymmian
Z
O
I 1,600 Ma
C
Statherian
1,800 Ma
Orosirian
Paleoproterozoic 2,050 Ma
Rhyacian
2,300 Ma
Siderian
2,500 Ma Stratigraphic time scale of the Proterozoic

46 Earth's history
2.2.2.1
Biogenic and geochemical feedback loops

of the Proterozoic oxygen evolution
In general, the energy efficiency of fermentation is low. there was a strong selection pressure on the development of
Additionally, the availability of dissolved organic molecules appropriate detoxification mechanisms, such as oxidases.
in the primeval ocean must have been very low. As a result, Anaerobic organisms without proper detoxification
autotrophic metabolic pathways must have originated soon mechanisms could only survive through colonization of an-
after the origin of life. In addition to chemoautotrophy, anoxic habitats, such as the deeper regions of the oceans or
oxic photosynthesis emerged. Therefore, the synthesis of anoxic sediments. However, the colonization of new habitats
porphyrins and chlorophyll must have evolved shortly after required at least a short-term tolerance of low oxygen con-
the origin of life. centrations. The ancestors of today’s anaerobic organisms
With the emergence of oxygenic photosynthesis the de- were therefore – though perhaps to a lesser degree – exposed
pendence on abiotic sources of reduction (hydrothermal to this evolutionary pressure: extant anaerobic organisms are
vents, weathering products) was terminated. On the other therefore only partly suitable as models for life forms of the
hand, organic productivity increased significantly. However, early Precambrian. Oxidases, likely developed as part of the
the resulting atmospheric oxygen caused problems for life oxygen detoxification mechanisms, form the basis for the
forms adapted to Earth’s oxygen-free conditions. Since ox- evolution of the respiratory chain.
ygen reacts with organic molecules, acting as a cytotoxin,
The formation of biotic oxygen is linked to the develop- minerals, such as kaolinite. As a result, ions, such as calci-
ment of Earth’s climate and geochemical cycles. Here, the um and magnesium are released. In the oceans, these ions
natural greenhouse effect plays a key role. In particular, the are biogenically or chemically deposited as carbonates. This
gases methane and carbon dioxide were available at higher removal of carbonates from the water finally leads to a low-
concentrations within the planet’s early atmosphere. As the ering in dissolved carbon dioxide concentrations by way of
relative proportion of atmospheric oxygen rose, greenhouse equilibrium reactions with hydrogen carbonate and carbonic
gas concentrations fell, thus restricting the activity of anaer- acid. Carbon dioxide is therefore removed from the water
obic methanogenic Archaea. These atmospheric changes led and finally from the atmosphere. Carbonates deposited on
to a global cooling which, in turn, limited primary produc- the sea floor are subducted at subduction zones. Under in-
tion and also the release of further oxygen. Biotic oxygen creasing pressure and temperature conditions, the carbonates
production and the global climate were therefore tightly con- react with siliceous melts. Through this process, carbonate
nected within a feedback loop, the one strongly influencing cations are incorporated within the silicates and carbon di-
the other. oxide is released. By way of volcanism, the carbon dioxide
Another global feedback mechanism is the global car- is finally released back into the atmosphere. As carbonate
bonate-silicate cycle, where carbon dioxide reacts with water formation is stronger in higher temperatures than in cooler
to form carbonic acid. This affects silicate minerals, such as ones, this geochemical cycle is also tightly connected within
feldspars, which subsequently weather into, for example, clay a feedback loop with climatic development.
abiotic: (Grk.: a = not, bios = life) not living biotic: (Grk.: bios = life) living
See also: Respiratory chain: 2.2.2.4; Evolution of multi-cellularity: 2.2.2.8; Fermentation: 2.2.1.3; Subduction zone: 2.1.1.2
Evolutionary significance of oxygen

increase of Compared with fermentation, aerobic respiration produced relatively high energy
globale levels and therefore allowed for a comparatively more efficient use of resources.
photosynthesis Life and evolutionary processes could take place much faster now. This energy effi-
ciency was also a prerequisite for the formation of more complex life forms, such as
increase of increase of eukaryotic cells and, ultimately, more complex multicellular eukaryotes
temperature O2-concentration
increase of decrease in
greenhouse gases greenhouse gases
Respiratory chain
The availability of oxygen was also a prerequisite for the evolution of the respira-
tory chain. Oxidases had already formed as detoxification enzymes, but were later
decrease in decrease in integrated into the respiratory chain. In aerobic respiration, around 28 ATP mole-
O2-concentration temperature cules are formed from one molecule of glucose
decrease in
globale
photosynthesis
Climatic relevance of oxygen

Oxygen is one of the most abundant elements on Earth, yet it Oxygen detoxification
mostly remains chemically bound. At equilibrium, the atmos- Oxygen reacts with organic compounds. Oxygen radicals, by way of chain reactions,
phere would contain far below 1 % oxygen. Higher concen- can destroy organic molecules and thus cause massive cellular damage. The emer-
trations of atmospheric oxygen are maintained as a result of gence of free oxygen therefore likely led to a global mass extinction, whereas the
biogenic processes. The Earth’s climate and the oxygen con- surviving species, all possessing detoxification systems to decompose free oxygen
centration of the atmosphere are thus reciprocally fed back to
geochemical and biogenic factors
Feedback with biogenic processes (above): Free oxygen re-

acts with greenhouse gases of climatic relevance, particularly
methane. This process reduces the concentration of green- Oxygen evolution
house gases in the atmosphere. At the same time, the higher The oxygen formed by oxygenic photosynthesis was initially used directly for the
concentrations of oxygen in the atmosphere lead to a decrease oxidation of reduced inorganic compounds (iron, manganese, and sulphur com-
in anaerobic methanogenic Archaea, thus reducing further pounds, among others). The oceans and atmosphere were only later enriched with
the release of atmospheric methane. This general reduction free oxygen, though initially only in minimum concentrations
in greenhouse gases leads to global cooling, which in turn re-
stricts biological growth processes, including photosynthesis
Feedback with geochemical processes (below): The concen-

tration of climatic relevant carbon dioxide, in particular, is
dependent on a geochemical feedback process. Higher con-
centrations of carbon dioxide led to increased carbonic acid
weathering and thus to increased releases of cations, such as
calcium. This results in increased carbonate precipitation in Autotrophy: oxygenic photosynthesis
the oceans and thus to further withdrawal of carbon dioxide In cyanobacteria, oxygenic photosynthesis emerged from the involvement of two
from the atmosphere. In the long-term, this mechanism is photosystems. The production of biogenic oxygen began with the evolution of ox-
embedded within geochemical cycles via subduction of car- ygenic photosynthesis
bonates and the volcanic release of carbon dioxide into the
atmosphere
increase of calcium
release into
the oceans Autotrophy: chemosynthetic and anoxygenic photosynthesis
Autotrophic metabolic pathways developed shortly after the origin of life. Since the
increase of increase of availability of dissolved organic molecules was low at the time, there was a high
carbonic acid carbonate evolutionary pressure to use alternative energy sources. Initially, these different
weathering formation metabolic pathways were chemosynthesis and anoxygenic photosynthesis (the lat-
increase of decrease in ter has only one photosystem and no oxygen formation)
CO2- CO2-
concentration concentration
decrease in decrease in
carbonate carbonic acid Heterotrophy: glycolysis and fermentation
formation weathering The first living beings were heterotrophic and fed on dissolved organic molecules.
decrease in calcium Glycolysis and fermentation were particularly important metabolic pathways for
release into the assembly and disassembly of simple sugars. The energy gained, two ATP mol-
the oceans ecules per molecule, was relatively limited as wells as the availability of organic
molecules
48 Earth's history
2.2.2.2
Climatic effects of oxygen evolution:

the Huronian glaciation (from 2.4 to 2.1 billion years)
In the Upper Archaean, roughly 2.8 billion years ago, the billion years. Iron compounds became more easily oxidized
formation of continental crust increased. As a result, shal- within terrestrial environments and subsequently deposited
low marine continental shelf areas were formed at conti- as red sediments. These circumstances lessened further the
nental margins and ocean convection started. There was an formation of banded iron ores. Meanwhile, the freely availa-
increase of nutrients supply within near-surface water layers, ble oxygen also increasingly oxidized atmospheric methane.
eventually leading, together with larger habitat availability to Methane decreased in concentration and thus weakened
the spread of stromatolites. At the same time, photosynthetic the greenhouse effect, leading to widespread glaciation (the
production became more significant, as did the availability Huronian or Makganyene glaciation) extending at least into
of free oxygen. the subtropics. This widespread spread of ice reduced the
In the beginning, the atmosphere remained free of oxygen. dispersal of stromatolites. At the same time, oxygen and
Iron compounds released through weathering processes were methane concentrations in the atmosphere levelled off. The
washed into the oceans in their reduced forms and were sub- trigger point for the end of the Huronian glaciation remains
sequently precipitated by chemolitho-autotrophic bacteria. unclear, though reinforced volcanism is considered to be a
This process resulted in banded iron ores. Later, atmospheric possible cause.
oxygen concentrations rose to around 0.2 % by around 2.3
The global climate depends on a number of factors. For ex- but are summarized as Huronian glaciation based on the lo-
ample, 4.6 billion years ago solar radiation was only around cation of Ice Age relic. During this time period, free oxygen
70 % of its present-day power, and it has been increasing ever was either not at all available or only present in traces, and
since. During the Precambrian, levels of solar radiation were probably had no climatic effect on the concentration of at-
relatively low, yet the moderate temperatures at the time were mospheric greenhouse gases. Moreover, it is likely that the
due to high atmospheric concentrations of greenhouse gases, global cooling trend was driven by reduced volcanic activity
of which methane played a particularly important role. Vol- and, therefore, reductions in volcanic releases of carbon di-
canism also played an important role influencing the climate oxide and other greenhouse gases.
by emitting large amounts of carbon dioxide and ash into the Free atmospheric oxygen is at least verified since around
atmosphere. In addition to the cosmic and geological factors, 2.3 billion years. The Makganyene glaciation 2.3–2.22 bil-
the biogenic formation of methane, mainly by Archaea, as lion years ago, which followed the evolution of oxygen, was
well as the formation of oxygen by oxygenic photosynthesis additionally driven by the decrease in volcanic activity de-
also played a major role for the climate. scribed above. The Makganyene glaciation stretched as far
Several glaciation events occurred between 2.45 and 2.1 as the lower latitudes, covering nearly the whole planet in
billion years. Three separate events can be detected in the ice. This extensive glaciation is summarized under the term
Huronian formation in Canada dating back to 2.45–2.32 bil- 'Snowball Earth'. A complete glaciation of the entire Earth,
lion years. These glaciations were probably spatially limited as the expression suggests, remains a moot point.
red sediment: sediment which is coloured red due to the pres- Precambrian ice ages, but it remains a moot point whether the
ence of Fe(III) minerals equator was indeed covered in ice
Snowball Earth: term given to the hypothesis that the Earth’s stromatoliths: (Grk.: stroma = blanket, lithos = stone) biogen-
surface, including the equatorial region, was once completely ic sedimentary rock formed by the trapping and binding of sedi-
covered in ice; the term is used in discussions relating to several mentary particles or the accumulation of salts resulting from the
growth of microorganisms
See also: Ice ages: 2.3.5.6; Evolution of oxygen: 2.2.2.1; Volcanism: 2.1.2, 2.1.2.1
solar radiation
In the beginning of the Proterozoic, the sun only emitted
70 % of its present-day radiation. This difference is signif-
icant: under current atmospheric conditions, the Earth O2 concentration
would be permanently frozen over with such weak radia-
tion. Since then, solar radiation continues to increase
The spread of stromatolites and the increasing availability

CH4 + 2 O2 → CO2 + H2O
of nutrients as a result of the onset of ocean convection
promoted photosynthesis. As a result, atmospheric oxy-
gen concentrations increased to around 0.2 % by roughly
Increasing concentrations of atmospheric oxygen promot-
2.3 billion years ago
ed the oxidation of atmospheric methane and thus a de-
crease in the methane-driven greenhouse effect
CH4 concentration
As long as the atmosphere remained oxygen-free, With the availability of atmospheric oxygen, free iron
iron compounds released by weathering processes became oxidized on land and was deposited as hema-
reached the oceans. The widespread banded iron tite in reed sediments. The release of iron compounds
ores dating back to between 2.5 and 2.3 billion years into the oceans was thus reduced, leading to a decline
can be traced back to iron precipitations by chemo- in the availability of banded iron ores
litho-autotrophic bacteria
The reduction of the greenhouse effect led to a global cooling

and a glaciation of the Earth around 2.3 billion years ago, known
as the Huronian glaciation. This led to a decline in the presence
of stromatolites and microbial mats. The Earth’s climate initially
settled at low oxygen and significantly reduced methane concen-
trations (though still higher than they are today)
The formation of continental plates and thus shallow

marine shelf regions enabled the spread of stromato-
lites. Their prevalence, and the increasing availability
of nutrients as a result of ocean convection, promoted
photosynthesis which, in turn, made oxygen available S
Initial continental crust formation was slow but increased considerably
(initially in the sea)
around 2.8 billion years ago. Continental masses were a prerequisite for
the onset of oceanic convection. In the Archean, surface waters were nutri-
ent-poor as a result of the lacking ocean convection, containing under 25 %
of today’s orthophosphate concentrations. Deep waters, moreover, were
completely anoxic, nutrient-rich, and heavily influenced by hydrothermal
Portion of continental crust vents
4 Ba 3 Ba 2 Ba 1 Ba
50 Earth's history
2.2.2.3
Metabolic effects of oxygen evolution: cytotoxic effect

Atmospheric oxygen produced by the onset of photosyn- dases which decomposed free oxygen and oxygen radicals.
thesis directly impacted the global climate and therefore the The remaining, broadly dispersed, anoxic habitats allowed
further evolution of life on Earth. Moreover, oxygen had a for the survival of some organisms lacking such detoxifica-
direct impact on organisms: tion mechanisms.
Oxygen and oxygen radicals in particular are toxic to Photosynthetic processes were also influenced by rising
cells, for a wide variety of organic molecules reacting with oxygen concentrations in the atmosphere. The enzyme rib-
oxygen. Exposed cell structures, such as the outer cell mem- ulose-1.5-bisphosphate carboxylase/oxygenase (RubisCO)
brane, became exposed to increasing levels of atmospheric can use both, carbon dioxide and oxygen as a substrate. The
oxygen. Fatty acids, especially unsaturated fatty acids, react- incorporation of oxygen, thus, leads to the formation of
ed with free oxygen radicals forming aldehydes. The radi- phosphoglycolate, which cannot be used in the Calvin Cycle
cals formed within these reactions provoked the onset of a and must be converted by other metabolic pathways. This in-
chain reaction to further destruction of organic molecules. corporation of oxygen, known as photorespiration, became
The emergence of free atmospheric oxygen therefore likely relevant only later, when atmospheric oxygen concentrations
led to a mass extinction event, since only organisms with the rose significantly. With oxygen levels remaining relatively
appropriate detoxification mechanisms survived the newly low during the Paleoproterozoic, photorespiration played a
oxygenated conditions. Surviving organism possessed oxi- minor metabolic role for life on Earth.
The energy problems inherent in effective carbon fixation In streptophyte algae and land plants, glyoxylate is further
by way of RubisCO were solved in a number of ways by the metabolized by peroxisomes and mitochondria, in a process
different organismal groups: that is linked to, among others, the amino acid metabolism.
In cyanobacteria, carbon is actively accumulated within Ultimately, glycerate is formed and after phosphorylation,
carboxysomes. Due to the high resulting intracellular carbon fed back to the Calvin cycle. In other green algae, the Chlo-
dioxide concentrations, the oxygenase function of RubisCO rophyta, the metabolic pathways run in a similar manner, but
is largely negligible. Photorespiration is, however, proved in without the involvement of peroxisomes.
cyanobacteria. The resulting phosphoglycolate is turned into Some other groups of algae do not further convert gly-
glyoxylate, which is subsequently metabolised by way of a colate, but excrete it. Depending on algal group, however,
number of different metabolic pathways in eukaryotic algae mechanisms to increase concentration of intracellular car-
and land plants. bon dioxide are present. This reduces the effect of photores-
piration.
aldehyde: organic compound containing an aldehyde group unsaturated fatty acids: in contrast to saturated fatty acids,
(-COH- group) unsaturated fatty acids possess at least one carbon-carbon dou-
RubisCO: ribulose-1,5-bisphosphate carboxylase/oxygenase; act ble bond in their chain
as centres of carbon dioxide enrichment
See also: C4 photosynthesis: 2.3.5.3, 2.3.5.4

In a Fenton reaction, hydrogen peroxide reacts with iron, resulting in free

hydroxyl radicals. These can react with organic molecules. The resulting
radicals react with elemental oxygen to form various products. Shown
here is the reaction of a fatty acid with oxygen, forming an aldehyde
Fe2+ + H2O2 → Fe3+ + OH. + OH–
+ O2
O
– H2O
H2C O Effective detoxification systems are required to manage the damaging
effect of oxygen, especially by oxygen radicals and hydrogen peroxide.
linoleic acid Most organisms convert the highly reactive superoxide ions via super-
O oxide dismutase into hydrogen peroxide and molecular oxygen. Super-
HC O oxide dismutases contain metal ions in their reactive centre, usually iron
or manganese ions. In eukaryotes, these are represented by zinc-copper
oleic acid complexes. A few organisms, such as Lactobacillus plantarum, use man-
O ganese polyphosphate for this detoxification reaction. These organisms
H2C O do not possess superoxide dismutases. Catalases decompose hydrogen
peroxides into water and molecular oxygen. The availability of free ox-
palmitic acid ygen exerted strong selection pressures because organisms could not
survive without these detoxification mechanisms. Many extant anaero-
bic organisms have likely secondarily lost these detoxification enzymes.
They are therefore obligate anaerobic and die in the presence of oxygen
2 NADP+
2 NADPH/H+
In eukaryotes, the metabolic functions involving superoxides or hydrogen per- 2,6 ADP + 2,6 Pi
oxide, are located in the peroxisomes. In addition to oxygenases and oxidases, 12 H+
which catalyse the formation of organic4molecules
e
-
by consuming oxygen, peroxi-
somes also contain high concentrations of peroxidases and catalases 2,6 ATP
PS II Cyt b6f PS I
2 H20 O2 Rising oxygen concentrations are not without problems for photosynthetic pro-
cesses. The enzyme ribulose-1.5-bisphosphate carboxylase/oxygenase (RubisCO)
can use PSboth,Icarbon dioxide and oxygen as a substrate. The reaction with oxy-
gen ultimately leads to the formation of 3-phosphoglycerate. There are, however,
4 H+ only84.5
+
H molecules of 3-phosphoglycerate (C3-body) formed from three C5-sugars,
thereby producing carbon dioxide. This reaction is therefore also known as pho-
torespiration.
At high oxygen concentrations, photorespiration can result an inefficient photo-
synthesis. In eukaryotes, mitochondria are involved, along with chloroplasts, in
the photorespiratory reactions (and also the peroxisomes in Streptophyta)
6 ATP
1.5 3-phosphoglycerate
3 O2 3 CO2 6 ADP + 6 Pi
3 2-phosphoglycolate 6 3-phosphoglycerate
RubisCO
1.5 glycerate 6 NADPH/H+
3 2-phosphoglycolate 3 ribulose-1.5-bisphosphate
6 NADP+
photo-
respiration 3 ADP + 3 Pi
1.5 serine 3 ATP 6 glycerinaldehyde-3-phosphate
3 glycine 3 ribulose-5-phosphate
glycerinaldehyde-3-phosphate
1.5 CO2
Pi
H2O 5 glycerinaldehyde-3-phosphate
mitochondrion peroxisome
52 Earth's history
2.2.2.4
Metabolic consequences of oxygen evolution: aerobic respiration

Although the use of oxygen as a terminal electron accep- and later oxygenic photosynthesis and oxygen detoxification.
tor drastically improved energy yield, an increase of oxy- They were only later used for aerobic respiratory chains: the
gen-use genes occurred only towards the end of the archaic enzymatic degradation of oxygen was finally used energeti-
expansion. Redox genes that arose during the early archaic cally via membrane-bound enzymes – the terminal oxidases
expansion probably were related to photosynthesis or fer- of the aerobic respiratory chains. First, the anaerobic elec-
mentation. The aerobic electron transport using oxygen as tron transport, and later the aerobic electron transport with
an electron acceptor was only developed later. Oxygen reacts oxygen as an electron acceptor evolved.
with many organic biomolecules and therefore was highly In contrast to the anaerobic respiration, the fermentation
selective for organism adapted to anoxic conditions. Only processes, the energy efficiency of the aerobic respiration is
organisms with enzymes that decompose peroxides or other significantly higher. Depending on the organismal group and
oxygen metabolites – such as superoxide dismutases, peroxi- the redox conditions in the organism's environment, roughly
dases and catalases – could survive in the oxygen-containing 14 times more ATP compared to fermentation is produced.
environment. Due to this energy advantage, evolution in the Proterozoic
With the increasing availability of free oxygen the aerobic could develop much faster after formation of aerobic respi-
respiratory chain eventually emerged. The early redox genes ration.
were probably related to the fermentation, the anoxygenic
Different organisms have different forms of terminal ox- of the mitochondria oxidative decarboxylation with forma-
idases; sometimes an organism possesses several types of tion of acetyl-CoA and the citric acid cycle take place. The
them. This suggests a parallel evolution of these oxidases. formed reduction equivalents (NADH and FADH2) build up
Such a parallel evolution in different organismal groups a proton gradient via the inner mitochondrial membrane in
seems likely because the various phylogenetic lineages all the terminal oxidation. The electrons are finally transferred
needed such 'detoxification enzymes' with the increase of it over four protein complexes and oxygen. The proton gradi-
oxygen concentration. ent is used by ATPase to form ATP.
The membrane-bound oxidases build up a proton gradi- In prokaryotes, the reactions of the citric acid cycle and
ent. The membrane potential is finally again converted to oxidative decarboxylation take place in the cytoplasm, the
chemical energy in the form of ATP via another enzyme terminal oxidation in the plasma membrane. The electron
complex, the ATP synthase. The ATP synthase is also in- gradient is built up between the cytoplasm and the internal
volved in other metabolic pathways such as photosynthesis membrane space between two bacterial outer membranes.
and chemosynthesis and existed before the evolution of the With respect to aerobic respiration the cytoplasm of prokar-
respiratory chain. yotes corresponds to the lumen of the mitochondria and the
In the case of eukaryotes, the pyruvate, formed by the gly- plasmalemma (the inner bacterial membrane) to the inner
colysis, is transported into the mitochondria. In the lumen mitochondrial membrane.
ATP: adenosine triphosphate – transporter of energy within cells pyruvate: anion of pyruvic acid; provides energy for the citric
acid cycle and is the end-product of glycolysis
See also: Archaic expansion: 2.2.1.3

Glykolysis Energy advantages of respiration

Glycolysis does not require oxygen. The energy gain is low, however, with only two
Glucose ATP per molecule of glucose. If there is no present oxygen and thus the terminal
2 ATP oxidation of the resulting NADH/H+ is not possible, this needs to be re-oxidized to
2 ADP + 2 Pi NAD+ by fermentation processes.
The reaction of the reducing equivalents NADH/H+ with oxygen in the terminal
oxidation associated with the generation of reducing equivalents in the citric acid
fructose-1.6-bisphosphate cycle, however, provides roughly 30 ATP
Evolution and evolutionary importance of respiration

Aerobic respiration requires an oxygen concentration of at least 1 % of the present
2 glycerinaldehyde-3-phosphate
day concentration (i.e. 0.2 %). It developed roughly 2 to 1.5 billion years ago. After
2 NAD+ oxygen was more widely available by oxygenic photosynthesis, oxygen-oxidases
2 NADH/H+ initially developed as detoxification enzymes – that is simply to remove the cell
4 ADP + 4 Pi toxin oxygen. Only later these enzyme complexes have been integrated into ener-
4 ATP gy generation processes. By aerobic respiration provides about 14 times more ATP
2 H2O than fermentation. This energetic advantage may explain why evolution was much
faster after the start of aerobic respiration
2 pyruvate
Oxidative decarboxylation
2 CoA In the matrix of the mitochondria a
2 NAD+
2 NADH/H+ carboxy group is split off and the re-
2 CO2 sulting hydroxyl group is oxidized. In
addition to the conversion of pyruvate
to acetyl-CoA and succinate in the citric
2 Acetyl-CoA acid cycle is metabolised by oxidative
decarboxylation
Citric acid cycle 2 H2O 2 CoA Endoxidation
26 ATP
2 oxalacetate 2 citrate 26 ADP + 26 Pi
2 NADH/H+
12 H2O complex 4:
2 NAD+ 2 NAD+
H+ cytochrome-c-oxidase
2 NADH/H+ 6 O2
2 CO2
2 malate
complex 3:
H+ cytochrome-c-reductase
2 H2O 2 ketoglutarate
2 NAD+
2 FAD complex 2:
2 fumarate 2 NADH/H+ Ubiquinone-
2 FADH2 oxidoreductase
2 CO2
2 GDP + 2 Pi 2 NAD+
2 FADH2 H+ complex 1:
2 GTP 2 NADH/H+ NADH-dehydrogenase
2 FAD 2 succinate
In eukaryotes, the citric acid cycle takes place in the mitochondria, in prokaryotes usu- In eukaryotes, enzymes of the respiratory chain are locat-
ally in the cytoplasm. The citric acid cycle is the acetyl residue of the acetyl-CoA is ed in the inner mitochondrial membrane, in prokaryotes
gradually reduced to carbon dioxide and water. Thereby, reduction equivalents (NADH, in the cell membrane. In the terminal oxidation the elec-
FADH2) are formed and energy in the form of GTP recovered. tron NADH/H+ (and FADH2) is gradually transferred via four
Besides its importance for the aerobic respiration, the citric acid cycle also provides enzyme complexes to oxygen. In this case, protons are re-
various precursor molecules for anabolism, for example for the synthesis of various leased into the internal membrane space. The resulting
amino acids proton gradient is used by ATPase to generate ATP
54 Earth's history
2.2.2.5
Evolution of the eukaryotic cell in the Mesoproterozoic

Eukaryotic cells originated around 1.8 billion years ago. drogenosomes – in all eukaryotic cells, they must have been
They are fundamentally different in their organizational added to the eukaryotic cell architecture either at the origin
structure compared with prokaryotic cells. Firstly, eukar- of the eukaryotic cell or shortly thereafter. In some extant
yotes possess an endomembrane system. Their nucleus, anaerobes, mitochondria have been secondarily reduced.
surrounded by a double membrane, is connected to the en- Older eukaryotic fossils are usually difficult or impossi-
doplasmic reticulum. Some of their organelles are also sur- ble to classify. These are collectively known as acritarchs, or
rounded by double membranes, including mitochondria and organic fossils with an uncertain systematic classification.
– in the case of the photosynthetic lineages – also plastids. Some of these ancient fossils possess cell structures typical
In contrast with prokaryotes, eukaryotic cells are capable of of eukaryotes. Geochemical evidence suggests, therefore,
ingesting by way of phagocytosis. that eukaryotes may have emerged earlier than previously
Since mitochondria are monophyletic and are generally thought.
present – with some variations, such as mitosomes or hy-
The origin of eukaryotes is unclear. Their genome con- the corresponding phagocytosis mechanisms. The develop-
tains both genes originating in gram-negative bacteria as well ment and finer details of eukaryotic cell emergence processes
as those stemming from archaea. remain, therefore, disputed.
Furthermore, it remains unclear whether the formation of The intracellular membrane system allows the cells to
the eukaryotic cell and the cell’s mitochondria assimilation compartmentalize metabolic pathways. In this manner, the
were separate or part of the same process. nucleus and nuclear envelope provide separate physical lo-
The classical view relates to eukaryotic precursor cells, cations for transcription – the formation of mRNA – and
which, by the uptake of a gram-negative bacterium via en- translation – the formation of proteins at the ribosome. This
docytobiosis, developed into a mitochondrion. This theory spatial segregation is necessary in eukaryotes because genes
remains problematic for a number of reasons: Firstly, there contain many non-coding introns; these likely spread across
is no evidence of eukaryotes that had been primary free of the genome when eukaryotic cells took up mitochondria.
mitochondria – these groups, if they ever existed, must all Introns must be cut out, or spliced, before the start of the
be extinct. Secondly, this symbiosis-based theory is unlikely RNA translation process. In eukaryotes, this takes place in
because, as in aerobic mitochondrial respiration free oxygen specific RNA-protein complexes, known as spliceosomes.
radicals are formed – that is just the reactive oxygen species. Since this process takes place relatively slowly, the nuclear
Consequently, the problem of oxygen detoxification would envelope provides the spatial segregation necessary to pre-
have been aggravated by taking on a mitochondrion. vent non-spliced raw RNA to be processed at the ribosomes.
An alternative theory proposes that the eukaryotic cell However, it remains unclear to what extent the need to sep-
emerged by way of a symbiosis between a facultative anaero- arate these processes has contributed to the evolution of the
bic bacterium with an archaeon. The cell organization char- nuclear envelope. Since bacteria generally carry little or no
acteristic of eukaryotes would, therefore, have developed introns, the separation of transcription and translation pro-
secondarily. This scenario is energetically more plausible, cesses is not necessary.
though at the moment there are no known prokaryotes with
phagocytosis: (Grk. : phagein = to devour, cytos = cell) process spliceosome: structure in eukaryotic cells which acts as a cata-
in which eukaryotic cells actively consume particles lyst during splicing (the removal on introns from the pre-mRNA)
reactive oxygen species (ROS): on the one hand free radicals, transcription: part of gene expression when a DNA segment is
such as the hyperoxide anion, the hydroxyl radical, and the per- copied into RNA
oxyl radical, on the other hand stable molecular oxidising agents translation: synthesis of proteins in the cells of living organisms
such as peroxide, ozone and the hypochlorite anion, as well as using mRNA molecules
unstable oxygen molecules, also known inaccurately as oxygen
radicals
See also: Archaea: 4.1.2.2; Bacteria: 4.1.2.1; Diversity of eukaryotes: 4.1.2.3, 4.1.2.4
The organismal structure of eukaryotic flagella is basically different

from those in prokaryotes. They have nine peripheral double-tu-
buli and two central micro-tubuli. Each flagellum is surrounded by
a membrane. The flagellar origin is unclear: a possible appearance
through endosymbiosis is controversial
All eukaryotes have a nucleus. The nuclear genome contained

therein consists of multiple linear chromosomes. In addition, eu-
karyotes also have a mitochondrial genome, or chondroma, and
eukaryotes with plastids also have a plastid genome, known as a
plastome
exon intron exon intron exon
Genes may contain non-coding sequence segments, known as in-

trons. Before translation into proteins, these must be removed,
or spliced, from the sequence. Bacterial genes, which are usually
self-splicing, rarely contain introns; they catalyse their own re-
moval from the RNA. In contrast, eukaryotic genes often contain
introns which often do not have the ability to self-splice them-
selves out of the sequence. Instead, these are removed by way of
a spliceosome, comprising proteins and small RNA fragments (sn-
RNA, or small nuclear RNA). The relatively slow process of splicing
and the need to remove introns prior to translation necessitate
the spatial separation of non-processed RNA and the ribosome,
where translation happens. This necessity may have favoured
Unlike prokaryotes, eukaryotes are capable of evolution of a nuclear envelope. At the same time, the nuclear
phagocytosis, in other words the ability to absorb membrane also reduces the insertion of mobile elements into
in particulate substances. The endomembrane sys- the nuclear genome. Since eukaryotes contain multiple genomes,
tem and cytoskeleton (made of actin, myosin, and the probability of insertion by such elements would increase in
tubulin) facilitate the formation of food vacuoles principle
Mitochondria are a result of endocytobiosis, though it remains unclear whether Traditional scenario
the host cell already had a eukaryotic cell structure. The traditional viewpoint
(right) is based on the phagocytosis of an obligate aerobic bacterium by a fully
developed eukaryotic cell, which possessed a nucleus. This conventional the-
ory is questioned: the oxygen radicals formed by the endocytobiont would be
problematic for the host to deal with. Secondly, all primeval mitochondria-free
eukaryotes ought to have gone extinct. eukaryotic
Since all known eukaryotic cells possess mitochondria or derivations thereof, amitochondrial cell
it is increasingly seen as likely that the origin of mitochondria was associated aerobic
with the emergence of eukaryotic cells. According to this viewpoint, eukaryotic bacterium
cells emerged from a symbiosis between a facultative anaerobic bacteria and
an archaeon (below). This symbiosis may have occurred by the use of excretion
products of a bacterium, such as hydrogen, as a substrate for the ATP-genera-
tion of an archaeon
endocytobiosis
Alternative scenario
formation of eukaryotic cell

endocytobiosis organization
archaeon host cell with prokaryotic modern eukaryotic cell

cell organization and endosymbiont
anaerobic bacterium
56 Earth's history
2.2.2.6
Evolution of the eukaryotic algae in the Mesoproterozoic

Fossil evidence from eukaryotic algae can be traced back ed between the two plastid membranes. Even their pigment
around 1.2 billion years to the Mesoproterozoic. The endo- is similar to that of cyanobacteria, composed of chlorophyll
cytobiosis of a cyanobacterium, creating eukaryotic algae a and phycobilisomes.
is likely to have evolved shortly after the emergence of the Since cyanobacteria possess two cell membranes, endo-
eukaryotic cell. Likewise, plastids evolved as a result of en- cytobiosis by phagocytosis should results in a structure sur-
docytobiosis of a cyanobacterium within an eukaryotic cell. rounded by three membranes. The outer membrane should
The plastids of eukaryotic algae, correspondingly, are mor- correspond to the feeding vacuole of the eukaryotic host,
phologically similar to cyanobacteria. Among other things, whereas the inner membranes are both bacterial. Primary
they possess circular DNA and 70S-type ribosomes, indicat- plastids are, however, only surrounded by two membranes.
ing a bacterial origin. Additionally, molecular phylogenies of It is assumed that the cyanobacterial outer membrane was
plastids demonstrate their relationship to cyanobacteria. reduced.
Glaucocystophyta possess a primordially plastid type. It
features a murein layer, a relic of the bacterial cell wall, locat-
All plastids are monophyletic and can be traced back to endocytobioses are known. In two algal groups, the Chlo-
a single endocytobiosis event. Plastids then spread across rarachniophyta (Rhizaria) and the Euglenida (Excavata),
different eukaryotic lineages through secondary endocytobi- the endocytobiont was a green algae. In the Alveolata, Stra-
osis, a process that includes the ingestion of an eukaryotic menopiles, Haptophyta, and Cryptophyta, the plastid can be
alga by an eukaryotic host cell and the subsequent reduc- traced back to an endocytobiosis of a red alga. In these cases,
tion of this ingested algae into a secondary plastid. Plastids however, it is not yet clear whether the plastids come from a
which emerged via a secondary endocytobiosis possess more single endocytobiosis event or multiple independent events.
than two plastid membranes. They also sometimes possess Members of the Dinophyta (dinoflagellates) also possess
structures that relate them back to their eukaryotic origins, several different plastid types, which can be traced back to
such as a nucleomorph, the greatly reduced nucleus of the even more complex origins. Some taxa possess plastids that
ingested alga. emerged through an endocytobiosis event with an alga with
Secondary plastids can be observed in many different al- secondary plastids; these are known as tertiary plastids. Why
gal groups. These can be traced back to a number of different such complex endocytobioses occur, and why exclusively in
ingested algal species. At least three independent secondary dinoflagellates, remains unknown.
70S-ribosome: prokaryotic ribosome with a sedimentation co- murein: cell wall in bacteria made from peptidoglycan (N-acetyl-
efficient (S) of 70S; mitochondrial and plastid ribosomes also be- glucosamin and N-acetylmuraminic acid)
long to the 70S type due to their origin phagocytosis: (Grk. : phagein = to devour, cytos = cell) process
to ingest: consume, take in in which eukaryotic cells actively consume particles
See also: Secondary plastids: 4.1.2.3; Tertiary plastids: 4.6.1.2

The plastids of Glaucocystophyta display many features of cyanobacterial origins. For

Glaucocystophyta
example, they are the only algal group to possess a layer of peptidoglycan between
their two plastid membranes, the same substance found in the cell walls of bacteria.
Glaucocystophyta plastids also have phycobilisomes and chlorophyll a, similar pigments
to those carried by cyanobacteria. Finally, the plastids of Glaucocystophyta possess 70S
ribosomes and circular DNA, both characteristics of bacteria
outer plastid membrane

peptidoglycan
inner plastid membrane
thylakoide
circular DNA
phycobilisomes
70S ribosomes
Phycobilisomes
Phycoerythrin is found exclusively in the phycobilisomes of cyanobac-
teria and the Rhodophyta. The phycobilisomes of Glaucocystophyta
contain phycocyanin. They do not contain phycoerythrin
phycoerythrin
phycocyanin
Cyanobacteria
thylakoide membrane
allophycocyanine
outer membrane
peptidoglycan
plasmalemma
thylakoide
70S ribosoms circular DNA

50Ss subunit
5S-rRNA
23S-rRNA
30S subunit
16S-rRNA
58 Earth's history
2.2.2.7
The 'boring billion' years (1.85–0.85 billion years)

After the extensive glaciation events of the Paleoprotero- cies-rich fossil record exists only in the period after the Neo-
zoic, the Earth’s climatic and geochemical conditions stabi- proterozoic glaciations.
lized. The evolution of life hardly progressed over the follow- In this phase, the super continent Rodinia was formed
ing billion years. This time period of environmental stability from all known land masses: Laurentia, Siberia, northern
is therefore known as the 'boring billion'. China formed a continental mass, as well as Australia and
Eukaryotic cells appeared at the beginning of this period, east Antarctica around 1.1 billion years ago. A number of
around 1.8 billion years ago, and the radiation of eukaryotes other cratons, and Baltica, were still separated from these
probably begun shortly after that. In contrast, fossil evidence continental masses by oceans.
of eukaryotes is significantly younger than this: among the Around 900 million years ago, all these known continen-
oldest known fossil eukaryotes is a 1.2 billion years old red tal masses were merged into a super continent (Rodinia).
alga Bangiomorpha pubescens. Roughly 850 million years ago, Around 825 million years ago, magmatic activity increased
the number of eukaryotic fossils increased, but the more spe- and around 750 million years ago, Rodinia started to break
apart into individual cratons.
During the 'boring billion' years, everything below the up- Eukaryotic algae require several of these metals for their
permost layer of the ocean remained anoxic. Today, similar survival. For example, enzymes responsible for the uptake of
conditions can still be found in the Black Sea. Large amounts nitrate require both molybdenum and iron, both which were
of sulphates were released into the sea as a result of terres- lacking in the anoxic ocean. Nitrate uptake was therefore
trial weathering processes. In anoxic water, these sulphates limited. The few nutrients that did rise from marine deep-wa-
were reduced to sulphide by sulphate-reducing bacteria (sul- ters were for the most part used by anoxygenic photosyn-
phate respiration). Also iron(II)ions, released into the oceans thetic bacteria in the anoxic deeper water layers as well as by
by weathering processes were precipitated by the sulphides; cyanobacteria inhabiting the boundary layer between aerobic
the sulphidic ocean was therefore iron-poor compared to the and sulphidic water layers.
primordial ocean. In addition to iron, other metals, such as Eukaryotic algae were strongly nutrient-limited. In addi-
copper, zinc, and molybdenum, were removed by sulphides tion, the sulphidic conditions were generally toxic to eukar-
from the cycle and deposited. yotes. As a result, eukaryotic algae were only able to survive
in the uppermost, aerobic layers of the water column.
Baltica: continental plate covering northern and eastern Europe Huntington/Chuckanut Formation: 1.2 billion-year-old fluvi-
craton: continental shield; central region of a continent which al sedimentary formation in Canada (Summerset Island, Nunavut,
was formed in the early Precambrian and which has suffered no Canada)
tectonic deformation since the Precambrian Era Laurentia: North American continental shield
See also: Anoxygenic photosynthesis: 2.2.1.4, 2.2.1.5

In the ocean waters, only the uppermost layer of the photic zone was well oxygenated and free
of sulphide. Nutrients were hardly available: on the one hand, many metal ions were precipitated
by sulphide and, on the other, ascending nutrients were for the most part consumed in deeper
layers by anoxgenic photosynthesis before they could reach the upper aerobic layers of the water
column. These conditions lasted around one billion years, drastically slowing down evolutionary
processes
Sulphide is toxic for eukaryotes. Eukaryotic algae are therefore found only in the upper
aerobic layers of the water column. Eukaryotic algae were often poisoned by ascending
sulphides. Theses waters are also poor in nutrients, as most ascending nutrients are con-
sumed by organisms inhabiting deeper layers
Under aerobic conditions, Cyanobacteria conduct oxygenic photosynthesis

photic zone
at the boundary layer between oxic and sulphidic water layers. In the pres-
ence of sulphides, the photosystem II is down-regulated to sulphide-driven The first verified eukaryotic fossils can be
anoxygenic photosynthesis traced back to the Middle Precambrian. These
fossils are for the most part difficult to clas-
In the sulphidic layers of the photic zone, green sulphur
sify systematically. They are summarized as
bacteria and purple bacteria use sulphide as an electron
acritarchs, small, acid-insoluble organic struc-
donor for anoxygenic photosynthesis, forming elemental
tures. In addition to the eukaryotic acritarchs
sulphur or sulphate
In addition, sulphate shown here, this term is also used to describe
is entering from ter- some prokaryotes
restrial environments
anoxygenic
S2– SO42–
photosynthesis
aphotic zone
S2– sulphate SO42– The species Bangiomorpha pubescens found

respiration in carbonates of shallow waters (Huntington
formation; 1.2 billion years) in Arctic Canada is
considered the oldest species of red algae
Sulfate-reducing bacteria convert the erosion-released
sulphate to sulphide
S22–
Fe2+
Sulphide forms hardly soluble bonds with many metal ions. A number of fossils from the Proterozoic can be
Particularly important in this regard is the formation of py- interpreted as belonging to Metazoan or traces
rite (above) from disulphide ions and iron(II)ions. However, of metazoan organisms. Such fossils are gener-
other metal ions, such as molybdenum, are barely soluble in ally rare and their assignment to the Metazoa
sulphidic water is, in most cases, questionable. Similar fossils
dating back to the Upper Proterozoic are more
frequent, including the trace fossils pictured
here from the Ediacaran
60 Earth's history
2.2.2.8
Evolution of complex multi-cellularity in the Neoproterozoic

Simple multi-cellularity arose independently on multiple rect contact with the external medium, a three-dimensional
occasions. The term 'simple multi-cellularity' refers to the structure and organization for supplying nutrients to cells
formation of filaments, clusters of cells or cell layers, each inside the body is of central importance. The evolution of
stemming from a single progenitor cell. Differentiation into mechanisms that bypass the limitations of diffusion process-
somatic and reproductive cells is also common in simple es, can therefore be regarded as a key development.
multi-cellularity. Further differentiation cannot be found, Oxygen concentration was a major limiting factor in the
and all cells are generally in direct contact with the external development of eukaryotic cells in the Upper Proterozoic.
medium. Though oxygen was present in the atmosphere and the sea,
On the other hand, complex multi-cellularity only its concentrations (around 1 % of the present-day concen-
emerged on six occasions: in the embryophytes, the Meta- tration) was low at first. Internal cells were further limited
zoa, the Basidiomycota, the Ascomycota, the Rhodophyta, by low oxygen concentrations caused by the long diffusion
and the Phaeophyceae. Moreover, complex multi-cellularity pathways into cell clusters and only an indirect supply of ox-
is more than just a mere aggregation of cells, with cells op- ygen to internal cells. Evolution of multi-cellularity was thus
erating in intensive contact with each other. Cell communi- made possible only by strong increases of oxygen concentra-
cation and (generally) tissue differentiation are characteristic tions around 600–700 million years ago.
of complex multi-cellularity. Since only a few cells are in di-
A vital prerequisite for the evolution of complex mul- larity possess these channels, though their structure differs
ti-cellularity was the organization of the eukaryotic cell, in across groups. For example, in metazoans such pores are
particular featuring the cytoskeleton and the possibility of achieved via a protein complex, known as gap junctions.
active transport of signalling molecules within membrane Embryophytes have plasmodesmata, larger channels that are
vesicles (endosomes). The evolution of complex multi-cellu- traversed by extensions of the endoplasmic reticulum; brown
larity started in all cases with the inclusion of genes respon- algae have similar designed plasmodesmata. Red algae pos-
sible for cell adhesion. sess 'pit connections' locked by proteins, whereas multi-cellu-
Critical steps within evolution of complex multi-cellulari- lar fungi (Basidiomycota and Ascomycota) possess a variety
ty had been molecular channels for cell communication and of complex pores.
the transfer of nutrients and signalling molecules. Exchang- With the further development specialized transportation
es of signalling molecules, electrical signals, and nutrients tissue eligible for long-distance transport of nutrients, gases,
require direct cell-to-cell communication via specialized water and metabolites are added.
channels. All organismal groups with complex multi-cellu-
cell adhesion: state of binding between cells mation, and aids cell migration; it aids intracellular transport and
cytoskeleton: network of microtubules and microfilaments movement
which serves to provide shape, mechanical resistance to defor-
See also: Brown algae: 4.6.2.2; Land plants: from 4.4.3.1 to 4.4.3.9; Holozoa: from 4.2.1 to 4.2.19; Fungi: from 4.2.2 to 4.2.2.5
Plasmodesmata are cell-to-cell connections in land plants. Measuring between 50 and 60 nm in diameter, they are traversed by a thin plasma strand
that is surrounded by a plasma membrane. They contain a central strand (desmotubule), a local modification of the endoplasmic reticulum (ER) in both
neighbouring cells that is connected to the cisterns of the ER. Similar plasmodesmata can be found in brown algae
In the Metazoan, cell-to-cell channels are composed of channel-forming protein complexes, known as gap junctions. A gap junction is formed of two
hemi-channels. The pore's diameter is around 2 nm. As a result of the gap channels, adjacent cells are fixed to a distance of around 4 nm
Cell-to-cell junctions in Basidiomycota (pillar fungi) are known as dolipores. These are surrounded on both sides by characteristic mug-shaped protru-
sions. Dolipores are 100–200 nm in size. Membranous caps, known as parenthosomes, which are protrusions emerging from the endoplasmic reticu-
lum, can lie on both sides of the dolipore. Rust fungi (Pucciniales) and smut fungi (Ustilaginomycotina) do not have parenthosomes. Ascomycetes do
have a simple circular interconnecting pore between adjacent cells
62 Earth's history
2.2.2.9
Neoproterozoic glaciations (0.85–0.72 billion years)

The break apart of the super continent Rodinia and the algae increased photosynthesis and thus accelerated the in-
distinct hotspot volcanism contributed to a change in ocean crease of oxygen in the oceans.
chemistry. Due to the hotspot volcanism large amounts of Also, due to the break apart of Rodinia into smaller con-
material of the Earth's mantle were transported to the sur- tinents, the climate became more humid. While Rodinia's
face. The resulting mafic rocks had been much richer in iron large intra-continental masses had been rather dry, there was
than the rocks of the continental plates. Weathering and a more oceanic climate on the smaller continents now. In-
erosion therefore released increasing amounts of iron into creased precipitation led to an increased silicate weathering
the oceans. At the same time large amounts of sulphidic and thus to an increased release of calcium and magnesium
sediments that had been deposited during the Middle Pro- ions into the oceans. There was an increased deposition of
terozoic were subducted, increasingly taking away sulphur carbonates, leading to a decrease in atmospheric carbon di-
from the oceans. The remaining sulphides were precipitated oxide.
enhanced by increased amounts of iron ions. As a result, the Roughly 716 million years ago, decreasing carbon dioxide
deeper water layers of the oceans had been oxygenated. The concentrations led to a sharply decrease in the greenhouse
decline in sulphidic conditions led, besides the oxygenation effect resulting in extensive glaciations. Unlike to earlier the-
of the deeper water layers, to an improved availability of ories (known as 'Snowball Earth') the planet was not com-
various metal ions. In particular, the increase of molybde- pletely covered by ice. At least the oceans of tropical regions
num concentrations, for molybdenum is an important metal probably remained ice-free even during the most extensive
for enzymes within the nitrogen metabolism, stopped the glaciation (Stuart glaciation). The continental masses had
widespread nitrogen limitation for algae. Oxygenation and been covered by ice up to low latitudes, around the planet’s
increased nutrient availability provided the necessary condi- equatorial areas, however, ice-free areas are also likely.
tions for the spread of eukaryotes. The spread of eukaryotic
The diversification of green algae and metazoan was syn- continent was largely covered by ice, erosion was reduced
chronous with the oxygenation of the oceans and the exten- during glaciation and only a few nutrients were released into
sive glaciations. Regardless of the precise extent of glacia- the ocean. These nutrient-limited conditions (additionally
tion climatic conditions have had a strong selective influence light-limited conditions blow the ice cover) are expected to
on the development and diversification of eukaryotes. have been significant for the evolution of Chlorophyta, es-
In the green algae, different metabolic pathways are found pecially for the energy preserving modification of photores-
with regard to photorespiration. The Chlorophyta have a mi- piration.
tochondrial glycolate dehydrogenase, and use the resulting Streptophytic algae (including the precursor of land
NADH in the respiratory chain. In contrast, the Strepto- plants) lived in fresh water – in ice-free waters in equatorial
phyta transform via a catalase glycolate in the peroxisomes areas and in the periodically thawing freshwater ponds on
releasing hydrogen peroxide at the same time. In this case or at the edge of the glacier ice. The limnic habitats near the
there is no formation of NADH. This difference matches the equator had been neither light nor nutrient-limited. Metabol-
different habitats of Streptophyta and Chlorophyta. ic fluxes within photorespiration of these organisms could
In the green algae Chlorophyta were adapted to marine therefore be optimized.
conditions and lived in the open areas of the oceans. As the
hotspot: limited, stationary geographical location with anoma- mafic: dark, rock-forming minerals which are rich in magnesium
lously hot areas in the asthenosphere due to mantle plumes and iron (Lat.: ferrum)
hotspot volcanism: particularly active volcanism at hotspots,
also at great distances from the edges of tectonic plates
See also: Subduction: 2.1.1.2

The decrease of the ice was a self-reinforcing process, as the ice-free

land and ocean surface reflected less sunlight. In addition, methane
was released from thawing permafrost, which increased the green-
house effect. Again, the climate became warm and humid leading to
another re-cooling. The last major glaciation event of the Neoprotero-
South China
Australia Siberia
zoic was the Marinoan glaciation roughly 635 million years ago.
India
Since the deep waters became rich in oxygen, organic carbon was in-
Laurentia North China
Antarctica creasingly aerobically re-mineralized. This changed the kinetics of the
Congo carbonation and the climatic effect was weaker now. Therefore, roughly
Amazonia
Arabia Sahara 580 million years ago, the Gaskiers glaciation was only local in nature
West Africa
Baltica
630 Ma
Increased weathering processes led directly – and indirectly via the pro-
motion of eukaryotic algae – to an increased formation of carbonates
and thus to a decrease in atmospheric carbon dioxide concentrations.
The reduction of the greenhouse gas carbon dioxide led to a global
cooling. Since most of the continental masses were close to the equa-
South China Siberia
Australia tor, weathering processes – and therefore the decrease in carbon diox-
India
North China ide concentrations – further continued, despite the onset of glaciation.
Antarctica
Laurentia The most pronounced Neoproterozoic glaciation was the Stuart glacia-
Arabia
Sahara tion roughly 716 million years ago. The ice cover reached the equator,
Amazonia at least on the continental plates. Probably near the equator the oceans
Congo Baltica
remained ice-free.
West Africa During increasing glaciation processes of the tropical zones precipita-
tion and erosion processes decreased. Hardly any carbon dioxide was
removed from the atmosphere. On the contrary, the carbon dioxide
concentration again increased due to volcanic activity
720 Ma
By weathering and erosion of mafic basalts erupted by hotspot vol-

canism iron release into the oceans increased. The near-surface water
plate boundaries with
layers increasingly became aerobic as sulphide precipitation as iron
hotspot volcanisms sulphides was intensified. This contributed to an increase in oxygenic
photosynthesis and in particular the growing importance of eukaryotic
algae. The comparatively larger eukaryotes sank faster, leading to an
Siberia
South China accelerated export of organic carbon from the photic zone. Among the
Australia
India North China more anoxic conditions in the deep waters anaerobic re-mineralization
of carbon led to increasing pH values and ultimately fixation of carbon
Antarctica
Laurentia as carbonate.
Arabia
Sahara Amazonia
Congo Baltica
The break apart of the super continent Rodinia into many smaller equa-
torial plates (India, Arabia, South China, etc.) led to a less continental,
West Africa
but more humid climate. These climatic conditions resulted in a sharply
increase of weathering and thus to the release of calcium and magnesi-
um ions. Hydrogen carbonate was increasingly precipitated (as calcium
carbonate), reducing the concentration of carbon dioxide and thus the
greenhouse effect
750 Ma
During the Middle Proterozoic the super continent Rodinia was formed.
Beneath Rodinia, hot mantle material ascended towards the surface
and formed extensive anomalously hot areas within the Earth's crust
Australia (diapir or 'plume'). There was a pronounced hotspot volcanism. As the
Antarctica Siberia magma contained molten mantle material, they were very rich in iron
India
South China North China (mafic). This volcanism contributed to the break apart of the super con-
tinent Rodinia
Laurentia
Arabia
Sahara Amazonia
Congo Baltica
900 Ma West Africa

2.3
The Phanerozoic eon

The Phanerozoic eon is usually divided into the Palaeo- ary (PTB). Although the first reptiles appeared as early as
zoic, Mesozoic, and Cenozoic eras. The largest Phanerozoic in the Palaeozoic, these were ecologically relatively insig-
mass extinction event tags the Permian–Triassic boundary, nificant compared to fish and amphibians until the Upper
which also serves as the boundary between the Palaeozoic Permian. Reptiles, and dinosaurs in particular, subsequently
and Mesozoic eras (252 million years ago). Another nota- dominated terrestrial habitats following the Permian-Triassic
ble mass extinction event tags the Cretaceous–Palaeogene mass extinction event. At the same time, mussels replaced
boundary, also the boundary between the Mesozoic and Ce- brachiopods as the dominant filter-feeders in marine benthic
nozoic eras (66 million years ago). These eras roughly align habitats. Trilobites disappeared completely, along with 96 %
with evolution steps of vertebrates: the Palaeozoic was dom- of marine animal species.
inated by fish and amphibians, the Mesozoic by reptiles, and Many dominant groups also disappeared, and over 75 %
the Cenozoic by birds and mammals. The evolution of land of species are thought to have been affected, by the mass ex-
plants, on the other hand, is temporal shifted, especially in tinction event at the Cretaceous-Palaeogene boundary. Am-
view of the colonisation of terrestrial habitats and the sub- monites in the oceans and most vertebrates in terrestrial hab-
sequent domination of ferns (Palaeophytic), gymnosperms itats went extinct, only some smaller species survived. Birds
(Mesophytic), and the angiosperms (Cenophytic). were the only surviving dinosaurs. Overall, species depend-
Many dominant floral and faunal groups disappeared ei- ent on primary producers, those feeding on terrestrial plants
ther completely or were replaced by other groups during the or algae, were more strongly affected, whereas detritivorous
mass extinction event at the at the Permian-Triassic bound- organisms were more resilient.
Both the Permian-Triassic and Cretaceous-Palaeogene greenhouse gases which, in turn, heated the deep waters in
mass extinction events were driven by severe climatic fluc- the oceans that increasingly became anoxic.
tuations. The warming at the poles completely cut ocean currents,
The Permian-Triassic event is thought to have been the further increasing levels of anoxia in the marine environ-
direct consequence of the strongest period of Phanerozoic ments and promoting the growth of anaerobic microorgan-
volcanism, the Siberian Traps volcanism. Additionally, a re- isms, which released metabolic hydrogen sulfide. As a con-
gression of the sea led to far-reaching loss of shallow water sequence, hydrogen sulfide toxic for anaerobic organisms,
habitats. spread throughout surface waters and in the atmosphere near
From the Middle to Upper Permian, atmospheric oxygen coasts. The event is thought to have lasted between 40,000–
concentrations lowered from 30 % to 16 %, and then further 80,000 years, likely too long to justify a meteorite impact as
to around 12 % during the Lower Triassic. In the oceans, a the root cause.
fast turnover of anoxic carbon dioxide-rich waters and deep The Cretaceous-Palaeogene mass extinction event was
hydrogen sulfide-rich waters took place. Increasing tempera- probably triggered by multiple factors, though a meteorite
tures lead to a release of methane hydrates, further reinforc- impact is thought to have been the main starting point.
ing the global greenhouse effect. Overall, the temperature Connected to this and as a direct consequence of the me-
rose by around 10 °C at the Permian-Triassic boundary. teorite impact, released carbon dioxide, sulphuric acid, and
Climatic changes as well as declining oxygen levels and nitrogen oxides (from ‘burnt’ rock) led to a acidification of
increases in carbon dioxide and toxic hydrogen sulfide to- the water bodies. Moreover, large amounts of dust were
gether contributed to global, are expected to have interacted ejected into the atmosphere and the friction energy of falling
as a cause for the mass extinction. Although the initial start- meteorite fragments contributed further to atmospheric heat-
ing point for these geochemical changes remains unknown, ing and extensive fire damages. Photosynthesis was massive-
research suggests that increased volcanism and meteorite im- ly impaired and food webs that based on primary producers,
pacts may have triggered the events at the PTB. Most likely, collapsed. In the meteorite’s aftermath, atmospheric dust led
however, is that increased volcanism may have set off a chain to a short-term global cooling by several degrees, followed by
reaction across the planet: the erupting volcanoes released an increase in temperatures by around 10 °C triggered by the
release of greenhouse gases.
methane clathrate: (Lat.: clatratus = latticed) also methane nitrogen oxides: gaseous compounds of oxygen and nitrogen
hydrate; clathrates are chemical substances in gases (in this case regression: marine regression takes place when the sea retreats
methane) which trap host molecules (in this case water) in a lat- from continental regions and is caused by a rise in the sea floor
tice. Methane clathrates exist in permafrost and on the sea-bed or a decline in sea level
See also: Mass extinction: 2.3.1; Stratigraphic overview: 2.3.3, 2.3.4, 2.3.5
65 The Phanerozoic eon: an overview 65
Neogene
Cenozoic
Cenophytic
Palaeogene
Mammuthus sp. Cretaceous Carpinus grandis

The dinosaurs went extinct at the Cretaceous-Pal- The angiosperms spread widely during the Upper
aeogene boundary. The Cenozoic still continued Cretaceous and were the dominant land plants in
and is known as the age of mammals and birds the Cenophytic
Mesozoic
Mesophytic
Jurassic
Triassic
Tyrannosaurus rex Permian Zamites feneonis

Following the Permian-Triassic mass extinction After their development, the seed plants, better
event, reptiles dominated the terrestrial verte- adapted to water-poor conditions, spread rapidly
brate fauna of the Mesozoic. These animals were to dominate the terrestrial flora of the Mesophytic
enormous in size, exemplified by the dinosaurs
Carboniferous
Palaeophytic
Palaeozoic
Devonian
Silurian
Cleithrolepis extoni Asterophyllites sp.
Fish and amphibians were the dominant verte- Spore plants colonised terrestrial habitats, includ-
brate fauna during the Palaeozoic, whereas rep- ing mosses, ferns, club mosses, and their relatives.
tiles, although present, remained ecologically in- Ordovician These were the dominant flora of the Palaeophytic
significant
Eophytic
The Phanerozoic aeon is also referred to as the

Eophytic, a time when there were no land plants
Cambrian
2.3.1
The Phanerozoic eon: an overview

Species have become extinct at any time since the ori- ‘Big Five’. Present-day species extinction is often referred to
gin of life. Individual species usually survive between a few as the sixth mass extinction event. On the other hand, Pre-
thousand and several million years. However, this requires cambrian mass extinction events are usually not taken into
a ‘natural’ extinction rate of a few percent of total species account, as they are difficult to prove based on fossil records
per million years. A mass extinction event occurs when the and are often indirectly detected based on changes of geo-
number of species decreases disproportionately within a chemical conditions.
short geological period of time. Such occurrences can often The ‘Big Five’ mass extinction events occurred during the
be attributed to a mass extinction of species. In contrast, the Upper Ordovician, the Upper Devonian, at the Permian-Tri-
Devonian and Triassic mass extinction events were mainly assic boundary, the Upper Triassic, and the Cretaceous-Pal-
driven by decreased rates of speciation. aeogene boundary. Of these, the largest mass extinction in
In most cases, mass extinctions can be attributed to a spe- Earth’s history occurred at the Permian-Triassic boundary:
cific cause or combination of causes. Mass extinction events over 50 % of families and 80–96 % of species became extinct.
are global and affect a wide range of ecosystems, usually en- It is possible that other extinction events, at the boundary
compassing aquatic and terrestrial habitats. between the Proterozoic and Phanerozoic, i.e. in the Upper
Although Earth’s history has been characterised by many Ediacaran and Lower Cambrian, were of comparable impor-
extinction events, the five most widespread are known as the tance.
The precise time-frame of mass extinction events is diffi- quence, sharply dropping ocean temperatures. This cooling
cult to ascertain since the last survivors of a species are of- is also associated with increases in chemical weathering in
ten not the ones that are fossilised. Therefore, even sudden terrestrial habitats, exacerbated by the colonisation and ex-
extinction events are represented as gradual within the fossil pansion of land plants.
record. However, most major extinction events stretched out The Upper Devonian mass extinction event is actual-
across at least some tens of thousands of years. ly composed of a sequence of extinctions over a period of
There are many and varied causes for mass extinction around 20 million years. This event included the disappear-
events, though often they are associated with strong declines ance of many marine animal groups and likely led to reduced
in temperature. oceanic oxygen concentrations. As a result, starting during
Presently, a fundamental periodicity in speciation pro- the Upper Devonian, this event set the selection pressure for
cesses, both in the creation and extinction of species, are the development of air breathing mechanisms.
discussed, potentially driven by astronomical factors, such The Permian-Triassic mass extinction event is probably
as changes in solar activity levels. On the other hand, there related to heavy mafic volcanism – high amounts of volcanic
are some clear indications that some mass extinction events gases lead to an abrupt climate warming and a decline of
have been caused by a singular catastrophic event. Such as the oxygen concentration. In the long run, the weathering
the largest Phanerozoic mass extinction event at the Permi- of volcanic flood basalts released large amounts of iron,
an-Triassic boundary that was driven by the heaviest volcan- magnesium, and calcium into the environment, resulting in
ic activities of the Phanerozoic and the mass extinction at the increased carbonate precipitation and subsequently, due to
Cretaceous-Palaeogene boundary, probably associated with decreasing atmospheric carbon dioxide concentrations, to
a meteorite impact. global cooling. A similar scenario is also discussed for the
The Upper Ordovician mass extinction event affected Upper Triassic mass extinction.
reef-building organisms as well as many brachiopods, tri- The mass extinction at the Cretaceous-Palaeogene bound-
lobites, and other marine animals. Especially tropical fau- ary is associated with a meteorite impact, which resulted in
na was affected by global climate cooling and, as a conse- massive forest fires and the formation of massive ash clouds.
chemical weathering: processes leading to the chemical alter- flood basalts: usually the result of inviscid lava flows, coating
ation or dissolution of minerals large expanses of land with basalt lava
See also: Cenozoic mass extinction: 3.2.1.8; Volcanism: 2.1.2.1

marine metazoans tetrapods land plants

Neogene
birds mammals angiosperms
23 Ma
Palaeogene
66 Ma
At the Cretaceous-Palaeogene boundary (≈66
mya): 75 % of all animal species went extinct,
including all the dinosaurs with the exception
Cretaceous of birds. Likely caused by a meteorite impact
(Yucatan) or increased volcanism
reptiles
145 Ma
Upper Triassic (≈200 mya): 80 % of all species
gymnosperms
went extinct. Likely caused by a strong mag-
Jurassic matism and volcanism related to the break
apart of Pangaea
201 Ma
Triassic
252 Ma
Permian Permian-Triassic boundary (≈252 mya): 96 %

of all marine and two third of terrestrial
species went extinct during this, the largest
Phanerozoic mass extinction event. Likely
298 Ma
caused by a dramatic increase in temperature
(by around 5–10 °C)
amphibians
Carboniferous
spore plants
359 Ma
Devonian Upper-Devonian (≈360 mya): 75 % of all spe-

cies died out (Kellwasser event). This mass ex-
tinction events was composed of a sequence
of extinctions. Reef-building organisms were
419 Ma particularly affected, limiting the global
Silurian spread of reefs
443 Ma
Upper Ordovician (≈444 mya): 85 % of all

Ordovician species, including many brachiopods and tri-
lobites went extinct, resulting in a sharp de-
crease of trilobites variety. Likely caused by a
485 Ma
strong global cooling by around 5 °C
Cambrian
541 Ma
2.3.1.1
Plate tectonics and climate evolution during the Phanerozoic

During the Silurian, the continents Baltica and Laurentia Upper Cretaceous, the Adriatic micro-plate, which segregat-
drifted towards each other and collided, forming the super ed from the African plate, collided with the Eurasian plate,
continent Laurussia (= Old-Red-Kontinent). The Caledoni- setting off the Alpine orogeny which continued into the Pal-
an mountains were formed as a result of the collision. Con- aeogene. Also during the Palaeogene, the Indian and Eura-
tinental collisions, and thus orogeny, ended during the De- sian plates collided, forming the Himalayas. A land bridge
vonian. The Caledonian mountains forms the hull mountain between the North American and South American plates
ridges of Scandinavia, the British Isles, and parts of the Ap- was formed during the Neogene, facilitating the exchange of
palachian Mountains of North America. The Rheic Ocean, flora and fauna between the two American continents.
which lay in between Laurussia and Gondwana, reached its The Cambrian and Lower Ordovician climate was very
greatest extent during the Silurian. warm before the planet cooled sharply, by around 5 °C, dur-
In the Upper Devonian, the collision of the north conti- ing the Upper Ordovician. This sudden temperature shift
nent Laurussia with the south continent Gondwana started, led to a glaciation of parts of Gondwana. Traces of this gla-
causing the Variscan Orogeny which formed the Central Eu- ciation event can still be detected in the Sahara (hence, the
ropean, eastern North American, and Central Asian moun- Saharan glaciation). The climate warmed again during the
tain ranges. Silurian and Devonian, before cooling yet again – by around
During the Permian, the continent Siberia collided with 8 °C – during the Carboniferous, leading to the Permo-Car-
the two other major continents, uniting all major continen- boniferous glaciation which lasted until the Lower Permian.
tal masses within the super continent Pangaea. The Tethys The Permian was also characterised, as a result of the large
Ocean opened up as a large bay to the continent’s east. Sev- continental land masses, by a relatively dry and increasingly
eral rift systems began to form in the Upper Triassic, which warming climate. The Triassic, was characterised by a large-
eventually led to the present-day continental configuration ly hot and dry climate and, consequently, by large desert are-
through the break apart of Pangea during the Jurassic. This as. The Jurassic and Cretaceous climates were also generally
development occurred firstly with the separation of North warm, with the increasing continental fragmentation leading
America from Eurasia, leaving behind the southern conti- to a more stable and humid climate. The climate began to
nents unified as the Gondwana super continent. The south- cool again in the Upper Cretaceous, a trend which continued
ern continents finally drifted apart during the Cretaceous: into the Palaeogene, leading to further extensive glaciation
the South American plate separated from the African, and events in the Neogene.
the Indian plate began to drift towards the north. During the
The colonisation of terrestrial environments by land ly, high oxygen concentrations required only relatively less
plants probably supported the global cooling of the Upper effective respiratory organs, many animals were adapted to
Ordovician. On the one hand, land plants fixed carbon di- high oxygen concentrations. Those less efficient respiratory
oxide, but their presence increased chemical weathering and organs caused problems and contributed to the Upper Per-
thus the release of calcium and magnesium into the oceans. mian mass extinction event, when atmospheric oxygen levels
The resulting precipitation of carbonates drastically reduced began to decrease yet again.
atmospheric carbon dioxide concentrations. The development of land plants was also responsible for
At the same time, the emergence and development of the third major Neogene and Quaternary glaciation event. As
plant life was vital in driving climatic changes during the the Indian and Eurasian plates collided, the Himalayas were
Carboniferous. Tree-like ferns and club mosses spread wide- created, at the same time increasing the release of calcium
ly during the Devonian and Carboniferous along humid cos- and magnesium from weathering products into the oceans.
tal lines and flood plains, forming extensive swamp forests. This process increased the ocean precipitation of carbonates,
Since the decomposing food chains were initially poorly withdrawing carbon dioxide from the atmosphere: carbon
developed, plant biomass was for the most part not con- dioxide reacts with water to form carbonic acid and, subse-
sumed and, instead, was deposited, eventually turning into quently, by way of equilibrium reactions turns into hydrogen
coal. Therefore, large amounts of carbon dioxide were with- carbonate and carbonate. At the same time, C4 and CAM
drawn from the atmosphere, but on the other hand, oxygen photosynthesis became increasingly important. Carbonate
was strongly enriched. During the Carboniferous, oxygen precipitation and more efficient photosynthetic pathways led
concentrations reached over 30 %. The high oxygen concen- to a sharp decline in atmospheric carbon dioxide concentra-
tration was a prerequisite for gigantism in insects. Basical- tions during the Palaeogene.
hydrogen carbonates: simple salts in carbonic acids contain- weathering: the breaking down of rocks in mechanical or
ing the HCO3– anion chemical processes
See also: C4 photosynthesis, CAM photosynthesis: 2.3.5.3, 2.3.5.4; Mass extinction: 2.3.1
Neogene
23 Ma N
Palaeogene
mass extinction event

66 Ma
Cretaceous
145 Ma
Jurassic
201 Ma S
Triassic
N
252 Ma
Permian
298 Ma
S
Carboniferous
359 Ma
Devonian
S
419 Ma
Silurian
443 Ma mass extinction event
Ordovician
485 Ma
Cambrian
S
541 Ma
low high 5 °C 25 °C 0.3 ‰ 4.5 ‰
sea level average global temperature CO2-concentration
2.3.1.2
Lagerstätten
Fossils are found in many rock layers. Unusually fossil-rich either Konzentrat-Lagerstätten (concentration Lagerstätten) or
areas are known as Lagerstätten. A selection of the most im- Konservat-Lagerstätten (conservation Lagerstätten).
portant such deposits on Earth is shown here. The term La- Konzentrat-Lagerstätten are characterised by a high con-
gerstätte is ambiguous and is used differently in the German centration of fossils, often consisting of unrelated individual
and Anglo-American literature: in German, Lagerstätten refer pieces each conserved to a greater or lesser degree. Examples
to general areas of the Earth’s crust that contain mineable of such deposits are bone beds, in which fossil remains have
concentrations of raw materials (what in english is referred been washed together.
to as deposits). In English, on the other hand, this term is Konservat-Lagerstätten on the other hand, are characterised
used to refer to fossil sites with exceptionally well-preserved by exceptionally well preservation of fossils and often also
or many fossils (what in German is referred to as Fossillag- some of their soft tissues. Such deposits do not necessarily
erstätten). Lagerstätten can be further characterised as being contain many fossils, though they are some of the most sci-
entifically important sites.
Due to the exceptionally well preservation of fossils in The exceptional preservation of such deposits can be
Konservat-Lagerstätten, fossils offer deeper insights into the or- attributed to a number of different factors. In stagnation
ganisation and behaviour of organisms, as pure hard-shelled Lagerstätten, fossils are exposed to hostile environments, in-
fossils would provide. Such deposits are therefore vital for cluding anoxic and sulfidic conditions (such as oil or black
palaeoecological reconstructions and for the better under- shales). An example of this type of deposit is the Messel pit,
standing of the anatomy of extinct organismal groups. Germany. High salt concentrations, such as those present
A particularly important discovery from a Konservat-La- during the formation of the Solnhofen Plattenkalk (or Sol-
gerstätten is the discovery of a conodont animal in Carbonif- nhofen limestone), have a preservative effect. Another type
erous oil shales near Edinburgh. By this discovery conodonts of Konservat-Lagerstätten are the Obrution Lagerstätten, where
were recognised as tooth-like elements of basal chordates. ground-level fauna is suddenly buried by fine-grained sedi-
Another example relates to the discovery of Ediacaran ment before decay or decomposition can take place.
fauna, which demonstrates that metazoans radiated well The Burgess Shale or Bundenbacher Schiefer are exam-
before previous, hard-shelled fossil evidence from the lower ples of such deposits. A third type of Konservat-Lagerstätten
Cambrian. are conservation-traps, where organisms are rapidly embed-
ded, as in moors or asphalt and bitumen lakes.
Lagerstätte: (German: Lager = storage; Stätte = place) is a sed- Fossillagerstätte whereas Lagerstätte in German refers to differ-
imentary deposit that exhibits extraordinary fossils with excep- ent kinds of deposits including ore deposits
tional preservation. In German the corresponding term would be oil shale: sedimentary rock rich in liquid or gaseous hydrocar-
bons
See also: Fossil formation: 2.3.1.3; Hard tissue: 2.3.3.2

The Messel Pit

Neogene Ashfall Fossil Beds (USA) The Messel Pit in Hesse, Germany, is a shutdown
open cast mine. The oil shales of Messel were de-
23 Ma Dominicanian amber posited around 47 mya by the sedimentation within
(Dominican Republic) a volcanic lake (maar). The Messel pit contains a va-
Palaeogene riety of fossils, including mammals, birds, reptiles,
Messel Pit, oil shale (Germany) fish, arthropods, and plants. Soft tissues are par-
ticularly well preserved from this location
66 Ma Zhucheng (China)
Santana Formation (Brasil) Solnhofen Plattenkalk or Solnhofen Limestone

Cretaceous The Solnhofen Plattenkalk is found in Middle Fran-
conia and Upper Bavaria, Germany, where lime-
Las Hoyas (Spain) stone was deposited in shallow lagoons during the
Upper Jurassic. The relatively high salinity of the
lagoon water reduced decomposition of organisms
145 Ma Solnhofen Limestone (Germany) at this site, which contains many marine fossils, in-
cluding fish, crustaceans, molluscs, as well as many
land animals. This site is most famous for the dis-
Jurassic covery of the ‘primaeval bird’, the Archaeopteryx
Posidonia Shale at Holzmaden
(Germany)
Brickworks at Hagen-Vorhalle
201 Ma The former quarry of the Vorhallener Brickworks,
is located in North Rhine-Westphalia, Germany. Ar-
Karatau (Kazakhstan)
gillaceous shales were deposited in a river delta in
Triassic Madigen Formation (Kyrgyzstan) the lower Upper Carboniferous. This site contains
various plant fossils, including horsetails, ferns,
and cordaites, as well as many insects and spiders.
252 Ma Mussels, brachiopods, crabs, and goniatites (Am-
Korbacher Spalte (Germany)
monoidea) were also deposited here by periodic
marine transgressions
Permian
The Rhynie Chert

298 Ma The Rhynie chert, located in Aberdeenshire, Scot-
Mazon Creek (USA)
land, was formed in a floodplain system in the Low-
er Devonian. The site contains first vascular plant
Brickworks Hagen-Vorhalle (Germany) fossils, including Rhynia and Horneophyton, but
Carboniferous also many fossilised fungal species, including my-
corrhizal fungi, as well as one of the oldest lichen
fossils (Winfrenatia reticulata)
359 Ma
Bundenbacher Shale (Germany)
Gogo Formation (Australia)
Miguasha National Park (Canada) The Burgess Shale
Devonian
The Burgess Shale, located in Yoho National Park,
Canada, was deposited during the Middle Cambri-
Rhynie Chert (Scotland) an at an oceans depth of 200 m. Fossils from this
419 Ma site are known for the extraordinary conservation
of their soft tissues. In addition to arthropods and
Silurian sponges, the site contains many animals lacking a
Ludlow Bone Bed (England) hard skeleton. Many of the fossils found at Burgess
443 Ma
Soom Shale (South Africa) bear no relation to extant animal lineages, for ex-
ample Opabinia, Anomalocaris, and Hallucigenia
Ordovician
The Ediacara Hills

485 Ma Fezouata Formation (Morocco) The Ediacara Hills are one of the oldest known
fossil deposits containing a diverse range of shell-
Burgess Shale (Canada) less metazoans. The sandstones found here were
Chengjiang Fauna Community (China) deposited around 600 mya and were diagenetically
Cambrian
transformed to quartzite. The Ediacaran quartzite
contain, among others, sponges, cnidarians, and
various other unidentified fossils. Most fossils of
541 Ma genus Dickinsonia are interpreted as Placozoa
Ediacara Hills (South Australia)

2.3.1.3
Fossilisation – the formation of fossils

Fossils represent the geological evidence for past life on Some environments may be more conducive to the preser-
Earth. These can be in the form of fossilised bodies, tracks, vation of soft tissues than are others. These habitats include
burrows, or excrements. Most often, though not always, fos- bitumen, bogs, or salt. However, these same environments
sils are mineralised (petrified). are not always the best for permanent fossilisation: salt, for
Fossilisation, or the formation of fossils, takes place on example, will eventually dissolve embedded organisms and,
a geological period of time, beginning with the death of an similarly, bodies buried in bogs will only be preserved if the
organism in an environment in which the carcass is not de- bog dries out or the fossil is reburied.
stroyed by microbial degradation and scavengers. A rapid embedding, which cuts off the carcass from at-
Soft tissues decay relatively quickly. As a result, these are mospheric oxygen and the access of scavengers, is an essen-
less abundant within the fossil record compared with hard tial prerequisite for fossilisation. Surrounding rocks solidify
tissues as bones or shells. The quite abrupt start of a good throughout the process of diagenesis and, subsequently, due
fossil record in the Ediacaran to Lower Cambrian is attrib- to increased pressure, drain and compact the carcass to form
uted to the emergence of shells and skeletal elements on a fossils. Exchange processes in the soil solution lead to leach-
number of different animal groups, and represented a piv- ing; finally, the fossil gets the same crystalline structure as
otal time point in the creation of the fossil record of Earth’s the environment.
history. This almost simultaneous appearance of hard parts If the fossil-containing rock is exposed to too high pres-
across so many taxa was most likely ecologically caused by sures or temperatures, the fossils will finally be destroyed.
increased predation by multicellular eukaryotes. Metamorphic rocks, therefore, contain no fossils.
Special forms of fossilisation include carbonisation or such circumstances, carbon is enriched relative to other ele-
embedding in tree resin. Insects, above all, as well as spi- ments, whilst other elements, such as oxygen, hydrogen, and
ders, woodlice, earthworms, and snails, can often be found nitrogen, are withdrawn. The sample first turns into peat,
embedded in tree resin (amber). Since amber is easily de- then lignite, and with progressive carbonisation, into hard
stroyed by diagenesis and metamorphism, such fossils are coal, and then, finally, it becomes anthracite. The first steps
only significant from the Cenozoic. Few amber deposits are in the carbonisation process are mainly characterised by the
older. Examples of old amber deposits are the coal mines of microbial degradation of carbohydrates and proteins. As the
Middleton (310 million years) or occurrence in the Swiss and carbonisation process progresses, the conversion of lignite to
Austrian Alps, in particular the occurrence in Golling (about hard coal and anthracite is mainly determined by increasing
225 million years). pressure and temperature conditions.
Carbonisation of plants occurs when they are embedded
in an air-free environment immediately after death. Under
bitumen: (Lat.: bitumen = earth pitch) organic mixture formed compaction: the process in which increased stress levels cause
from petroleum sediment to densify and consolidate
carbonisation: formation of organic fossil materials releasing diagenesis: compression of sediments by lithification; chemical,
water, CO2 and hydrocarbons and leaving almost only pure car- physical or biological change at relatively low temperatures
bon leaching: the loss of fine nutrients from the soil due to water
seeping into the ground from the upper soil horizon
See also: Index fossils: 2.3.2; Fossil deposits: 2.3.1.2

Erosion processes take away the deposited rock layers on Oil is derived from dead planktonic organisms. The required
top of the fossil and the fossil is finally exposed again high planktonic biomass can mainly only be achieved from for-
mer continental shelves in tropical and subtropical climates.
Petroleum is formed at temperatures between 60–200 °C at
around 2,000–4,000 m depth within the Earth‘s crust
Over time, salt levels in the environment and the fossilised Bitumen can from viscous, sticky tar pits (bitumen lakes). An-
carcass are evened out. The most silicate-rich solutions are imals can drown in these lakes and can be embedded. Fur-
recrystallised, where the structure of the fossil is preserved thermore, their rotting carcasses attract carnivores, leading
but chemical composition has changed. The fossil is ‘pet- to the coincidal fossilisation of several individuals of different
rified‘ species, known as thanatocoenosis, or a death assemblage
At increasing sediment depositions and thus increased tem- By way of the carbonisation process, plant material cut off
perature and pressure, the carcass is progressively drained from oxygen is gradually turned into peat, lignite, and even-
and compacted. As a result of rock pressure from above, tually hard coal. Today’s coal reserves used to be coastal
the fossil is mainly flattened in a vertical direction swamps and floodplains during the Carboniferous. Pictured
here is a fern fossilised by carbonisation
A dead animal may become fossilised if it is protected from Fossils of insects and spiders in particular, but also of worms
scavengers and general decay processes almost immediate- and plant parts (pollen and seeds), are sometimes found in
ly after its death. Such circumstances take place after rapid hardened tree resin, known as amber. Amber fossils mainly
embedding in ideally muddy (anoxic) sediment date back to the Palaeogene and Cretaceous
2.3.1.4
Geochronology and stratigraphy

Determining the age of rocks and fossils is the aim of two variety of stratigraphic methods has led to a fairly detailed
separate disciplines: stratigraphy and geochronology. Stratig- knowledge of the relative sequence of geological events.
raphy provides a relative dating system of rock formations, in Geochronological methods are necessary for absolute dat-
other words examining the relationship of rock formations ing. In general, these methods utilise the radioactive decay of
on the geological time scale. Chronostratigraphy, thus, using isotopes in minerals to date the timing of mineral formation.
timestamps in rocks; biostratigraphy uses fossils, in particular In igneous rocks, the time point of formation refers to their
their known first appearance and disappearance. In contrast, solidification; on the other hand, in metamorphic rocks, this
geochronology, an entirely separate discipline from stratigra- point is the moment of metamorphic overprinting. The most
phy, is concerned with the absolute dating of rock formations. reliable geochronological dating techniques make use of a
The combination of these two disciplines enables researchers combination of different radiometric methods, though small
to temporarily reconstruct Earth’s history. errors, often within the range of a few percent of the meas-
The aim of stratigraphy is to create a chronostratigraphic ured value, are anticipated. Errors caused by the geology of
sequence, in other words a temporal sequence of geological the rock formation itself – by diffusion of radioisotopes in or
events. Underlying strata (underneath) are generally older out of the rock targeted for testing, or changes in the concen-
than the top (hanging side; above). Based on this stratigraph- tration or misallocation of rocks to older or younger rock lay-
ic principle, rock layers and the fossils they contain can be ers – are often significantly larger than a metrological error.
dated relative to each other. Tectonic processes, especially The older the rocks, the longer the period of time to which
folding and overthrust can reverse this rule of stratification. uncertainty refers to.
Stratigraphy makes use of a number of different rock fea- Since the (relative) determination of stratigraphic age of
tures, for example, the appearance and disappearance of rock layers relies timestamps of a short geological period of
fossils (biostratigraphy), the occurrence of certain rock units time, stratigraphic age determination is often far more accu-
(lithostratigraphy), or polarity reversals within the terrestrial rate than are (absolute) geochronological age determination
magnetic field (magnetostratigraphy). All these features can when analysing older rock formations.
be ordered chronostratigraphically. The combination of this
The basic unit in chronostratigraphy is the stage; for ex- Transfer and parallelisation with other rock layers is
ample, the lowest Quaternary stage is the Gelasian. Higher carried out using other stratigraphic methods, including
units are series (e.g.: Pleistocene), system (e.g.: Quaternary), absolute dating by geochronology methods. Since the
erathem (e.g.: Cenozoic), eonothem (e.g.: Phanerozoic). The temporal occurrence of fossils or other stratigraphic features
corresponding geochronology units are age, epoch, period, do not always correlate with the chronostratigraphic units,
era, and eon, respectively. these are described by the independent unit of chronozone.
Chronostratigraphy relates to a specific rock body For example, a chronozone marker for fossils is known as
Moreover, chronostratigraphic boundaries, which define the a biozone. To that end, the lowest age of the Triassic, the
units, are set according to a reference profile and are thus Induan, correlates to the appearance of the conodont species
defined clearly and objectively. The upper boundary of a Hindeodus parvus. The Induan itself is defined, however,
stage is not explicitly defined; rather, it is set according to the according to its type locality which in the province of
lower boundary of the next stage. Zhejiang, China.
burial metamorphism: metamorphism caused when rocks are metamorphic rock: rock formed by being subjected to high
buried at great depth in the ground pressure or temperatures without losing its solid form
contact metamorphism: metamorphism caused by tempera- type locality: the place where a particular rock type is first iden-
ture increases due to hot magma tified
See also: Conodonts: 2.3.2.7

Neogene Radiocarbon dating uses the decay of 14C
C: half-life 5,730 years

(carbon) to 14N (nitrogen), with a half-life
23 Ma
of 5,730 years. It can only be applied to rel-
K: half-life 1.28 billion years

atively young rocks, dating back to around
Palaeogene 70,000 years
U: half-life 703 million years and 238U: half-life 4.468 billion years
66 Ma The basic unit of biostratigraphy is the biozone.
As a chronologic unit it characterizes a period of
14
time based on the lifetime of a biologic species. As
a stratigraphic unit it characterizes newly formed
rocks within this period of time. A precise tempo-
40
Cretaceous ral classification, for example, of conodonts at the
Permian-Triassic boundary, is achieved by its com-
bination with geochronology
145 Ma Potassium-argon dating is suitable for rocks that

are some 100,000 years old at least. It uses the
decay of 40K (potassium) to 40Ar (argon) and 40Ca
Isarcicella (calcium) with a half-life of 1.28 billion years.
Jurassic
isarcica Only the rarely occurring 40Ar is suitable for age
determination, since 40Ca is too abundant
201 Ma
Rb: half-life 47 billion years

Isarcicella
staeschei
Triassic
235
Hindeodus
parvus
252 Ma Uranium-lead dating, suitable for uranium-bear-
Neogondolella ing minerals, relies on two separate decay series
taylorae with intermediate products: the uranium series
Permian from 235U (uranium) to 207Pb (lead), with a half-
87
Hindeodus life of 703.8 million years, and the series from
changxingensis
238
U to 206Pb, with a half-life of 4.468 billion
298 Ma years. This method is suitable for the dating of
Neogondolella
rocks that are several million years old
maishanensis
Carboniferous
Neogondolella
yini
359 Ma
Rubidium-strontium dating method uses the

decay of 87Rb (rubidium) to 87Sr (strontium) with
Devonian a half-life of 47 billion years. It is especially suit-
able for dating feldspars, mica, or hornblende in
very old minerals
419 Ma
Silurian
Stratigraphy Geochronology
443 Ma
Stratigraphy investigates the temporal sequence of rock Geochronology examines the absolute age of rocks. The decay of
formation and, therefore, their relative age classification. radioactive elements, incorporated into the crystal lattice of min-
Ordovician The stratigraphic principle states that older sediment lay- erals during their formation, is used for age dating. Conclusions
ers generally are underlying strata (bottom) than hanging about the time of emergence of particular rocks can be drawn
side strata (top). Stratigraphy makes use of a range of from the ratio of radio isotopes and their decay products. 14C (car-
485 Ma markers to improve accuracy of assessments, including bon) is used to date samples from the past 70,000 years, whereas
geochemical markers, deposits from catastrophic events older samples require the targeting of other radioisotopes. The
(e.g.: volcanism or tsunamis), or detectable changes in the period around 100,000 years ago is difficult to date using radi-
geomagnetic field within the rock. Biostratigraphy, or the oisotopes; for the youngest past, since the last glaciation event,
Cambrian
relative time determination based on fossils, is of central dendrochronology (growth rings in wood) and varve chronology
importance in analyses relating to the Phanerozoic (deposits in water sediments) can be used for absolute age de-
termination
541 Ma
2.3.1.5
Termination and biostratigraphic definition of the

Phanerozoic systems
The onset of the Phanerozoic systems is defined in terms however, linked to the defining of systems. Newer (accurate)
of type localities. These type localities are known as GSSP dating of these rock layers can therefore lead to slight shifts
(Global Stratotype Section and Point ). The beginning of in the age dating. The systems derive their names from the
each system correlates with the occurrence or disappearance geographical regions in which they are present at the surface;
of certain index fossils, used to define the system bounda- for example, the Cambrian is named after Cambria (Wales),
ries. The age of type-localities is geochronologically quite ac- or the Devonian from Devonshire, UK.
curately dated, though these geochronological data are not,
We distinguish between geological periods (eon, era, pe- disappearance of index fossils is used for the chronostrati-
riod), which are geochronologically defined, and rock strata graphic calibration of rock layers. Index fossils, used for the
(eonothem, erathem, system), which are associated to these delimitation of systems (and erathems), are usually pelagic
time periods. The Phanerozoic is a geochronological eon di- rather than benthic, since pelagic species often have a wider
vided into three eras (Palaeozoic, Mesozoic, Cenozoic) and geographical distribution. In some cases, macrofossils are
these are, in turn, further divided into periods. Rock layers used. For example, the ammonite Psiloceras spelae is used to
deposited during respective time periods are chronostrati- define the start of the Jurassic whereas the ammonite Beri-
graphically subdivided. Thus, the chronostratigraphic eo- asella jacobi marks the start of the Cretaceous. For the most
nothem here corresponds to the geochronological eon, the part, however, index fossils are planktonic microfossils, since
erathem to the era, and the system to the period, respectively. these are both abundant and broadly distributed, allowing
Rock layers (strata) are chronostratigraphically defined for effective relative dating of rock layers from different con-
based on their type locality. In addition, the appearance and tinents and geographical regions.
stratotype: layer of rock in a particular location on the basis of type locality: the place where a particular rock type is first
which a stratigraphic unit is defined identified
See also: Stratigraphic and geochronologic periods of time: 2.3.1.4

Neogene
The start of the Neogene is defined by the first appearance of
23 Ma
the foraminifera species Paragloborotalia kugleri
Palaeogene
The beginning of the Palaeogene is characterised by an in-

66 Ma creased concentration of the element iridium, as well as the
mass extinction of many vertebrates and invertebrates
Cretaceous The name ‘Cretaceous’ is derived from the abun-

dant carbonate-rich deposits
Hindeodus parvus: index fossil from the start of the Triassic

The start of the Cretaceous is defined by the first appearance
145 Ma
of the ammonite species Beriasella jacobi
Jurassic The name ‘Jurassic’ was introduced to define the rock

layers from the Jura Mountains (France/Switzerland)
The beginning of the Jurassic is defined by the first appear-

201 Ma
ance of the ammonite species Psiloceras spelae
The ‘Triassic’ refers to the striking trisection (Bunt-

Triassic sandstein, Muschelkalk, Keuper) in Central Europe
The beginning of the Triassic is defined by the end of a carbon Streptognathodus isolatus: index fossil from the start of
252 Ma isotope anomaly and the first appearance of the conodont the Permian
species Hindeodus parvus
Permian The name ‘Permian’ is derived from the Russian Perm

region, located at the foot of the Ural mountains
The beginning of the Permian is defined by the first appear-

298 Ma
ance of the conodont species Streptognathodus isolatus
The name ‘Carboniferous’ refers to the globally dis-

Carboniferous
tributed coal seams from the Upper Carboniferous
The beginning of the Carboniferous is defined by the first ap-

359 Ma
pearance of the conodont species Siphonodella sulcata
The ‘Devonian’ is named after the southern Eng-

Devonian lish county of Devonshire
Siphonodella sulcata: index fossil from the start of the
The beginning of the Devonian is defined by the first appear- Carboniferous
419 Ma ance of the graptolite species Monograptus uniformis
The ‘Silurian’ is named after the Silures, a Celtic
Silurian
tribe from South Wales
443 Ma The beginning of the Silurian is defined by the first appear-
ance of the graptolite species Akidograptus ascensus
Ordovician The ‘Ordovician’ is named after the Ordovices, a
Celtic tribe from Wales
485 Ma The beginning of the Ordovician is defined by the first ap-

pearance of the conodont species Iapetognathus fluctivagus
The name ‘Cambrian’ is derived from the Latin

Cambrian name for Wales (Cambria)
The beginning of the Cambrian is defined by an anomaly of

541 Ma the carbon isotopes ratio 12C to 13C, as well as the first appear-
ance of fossil tracks from Trichophycus pedum (feeding tracks) Trichophycus pedum: index fossil from the start of the
Cambrian
2.3.2
Fossil biodiversity
Different palaeontological analyses focus on different ecologically differing habitats. A worldwide distribution of
properties in target organisms. This will be illustrated taking target organisms would thus enable researchers to synchro-
stratigraphy and palaeoecology as examples: stratigraphy nise rock formations in various regions of the world. Any
aims to understand relative temporal classification whereas spread of organisms into various habitats facilitates synchro-
the goal of palaeoecology is to reconstruct habitats and eco- nisation of different biospheres. As a result, planktic species,
logical conditions. which are usually widespread (or even drift after having died)
Organisms with narrow ecological niches and a low ten- and can be detected in a variety of habitats and geographi-
dency for dispersal are most suitable for palaeoecological cal regions, are particularly suitable for chronostratigraphic
analyses, since these organisms provide the basis for conclu- analyses.
sions of specific habitat characteristics. To that end, species Index fossils are fossils that allow for a stratigraphic clas-
that are stationary (sessile), or even buried in sediment, such sification of rock formations. Therefore, they should have
as mussels, are particularly appropriate study subjects. The lived in a geologically short period of time only to allow the
morphology of these organisms allows researchers to better closest possible chronostratigraphic classification. At the
understand their way of life. Furthermore, due to their en- same time, these species need to have existed in high frequen-
dobenthic lifestyle, such organisms are usually found only in cies in order to ensure their identification within respective
their former habitats. strata. Index fossils are therefore often small organisms, no-
On the other hand, chronostratigraphic analyses are bet- tably conodonts, graptolites, and foraminifers.
ter based on fossils that are geographically widespread across
Various organismal groups can serve as index fossils. Most Cephalopods are particularly important index fossils,
of these are significant in only certain specific geological sys- especially the Nautiloidea, Ammonoidea, and the Belem-
tems, even though they may have existed over far longer time noidea, because their housing (shell) and skeletal elements
periods. Most major metazoan clades already existed since are particularly well preserved. Due to their pelagic lifestyle,
the Cambrian, though certain groups are only important as many of these taxa are widely distributed.
index fossils for the recent past. For example, mussels and Trilobites and graptolites are important index fossils from
gastropods, which have existed since the Cambrian, serve as the early Palaeozoic; as are corals, brachiopods, and ammo-
important index fossils only for the Cenozoic. Other groups, noids from the Upper Palaeozoic, Foraminifera from the
such as the nautiloids, serve as index fossils for the entire Upper Mesozoic, and other molluscs – especially snails and
duration of their existence. mussels – from the Cenozoic.
drifting: passive distribution of organisms in their different niche: (Lat.: nidus = nest) totality of abiotic and biotic factors
morphological phases which are necessary for a species to survive and reproduce
endobenthic: living in the sediment suture: (Lat.: sutura = sew together) seam; the lobe line in ceph-
alopods
See also: Fossil formation: 2.3.1.3; Stratigraphy: 2.3.1.4

79 The Phanerozoic eon: fossil biodiversity 79
Unlike mussels, the bivalve bra-

Neogene chiopods have an upper and
lower valve. They were the
Gastropods
23 Ma
dominant group of benthic filter
Bivalves
feeders during the Palaeozoic
Palaeogene
Echinoids
Crinoids
66 Ma
Foraminifers
Cretaceous
Extinct rugose corals are of par-

145 Ma ticular biostratigraphic impor-
Belemnoids
tance
Jurassic
Snails (gastropods) and mussels
(Bivalvia) dominated the ben-
thos during the Cenozoic
201 Ma
Ammonoids
Triassic
The Nautiloidea (Cephalopoda)
have an external housing and
252 Ma simple-suture chambers
Permian Sea urchins (Echinoidea) and

Foraminifers
sea lilies (Crinoidea) belong to

Brachiopods
the Echinodermata
298 Ma
Carboniferous
Trilobites are extinct arthro-
pods. They lived in the benthos
of coastal seas
359 Ma
The Belemnitida (Cephalopoda)
have an inner skeleton struc-
Corals
Devonian tures
419 Ma
Silurian
Graptolites
443 Ma
Nautiloids
Ordovician The Ammonoidea (Cephalop- Usually, casings of Foraminifera

oda) have an external housing were made of chalk. They lived
and simple-suture chambers plantically or benthically
485 Ma
The graptolites (Hemichorda-

Trilobites
ta) were particularly morpho-

Cambrian logically diverse during the Or-
dovician and Silurian. Planktic
species developed from the
541 Ma originally benthic lineages dur-
ing the Ordovician
2.3.2.1
Foraminifers
Foraminiferan fossils are known since the Cambrian, of cellular plasma emerge. Most of the tests are usually made
though the group likely evolved far earlier than that. At of calcium carbonate, usually calcite, but sometimes arago-
present, around 10,000 recent and 40,000 fossil species are nite. In agglutinating foraminifers, the casing is composed of
known. The calcareous skeletons of foraminifers are often small pieces of sediment that are glued together by proteins.
well preserved and serve as important index fossils, especial- In the Allogromiida, the casings are purely made of proteins
ly of the Cretaceous period and Cenozoic era. or they are missing; as a result, this group plays no role in the
Foraminifers are single-celled organisms, usually some fossil record.
100 μm in size, but larger specimens may be several centime- Foraminifers are predominantly marine, only a few spe-
tres in size. Foraminifers are characterised by a multi-cham- cies occur in freshwater. Most species are benthic, with the
bered skeleton, featuring perforations from which fine strands exception of the planktic Globigerinida.
The relationship between foraminifer lineages remains of particular importance as fossils. Nummulitidae are large
largely unknown. Foraminifers‘ systematic classification, foraminifers that can reach several centimetres in diameter,
especially of fossil taxa, therefore relies heavily on morpho- with the largest species growing to around 15 cm in size.
logical features. They live in shallow marine benthic habitats and in symbio-
The extant Allogromiida, which emerged in the Cambri- sis with photosynthetic endosymbionts (often diatoms with-
an, possesses organic casings although these may sometimes out casings). Orbitoideae that went extinct in the Miocene
be completely lacking. They are therefore rarely featured in had been of similar importance in the Upper Cretaceous and
the fossil record. the Palaeogene. The Langenida that also are reöated tp the
The Textulariida (Cambrian until present), which includes Rotaliida reached their highest levels of diversity in the Ju-
the Lituolaceae and Orbitolinaceae – both significant during rassic and Cretaceous with the Nodosariaceae.
the Jurassic and Cretaceous – possess agglutinated casings, The Fusulinida (Lower Silurian to Upper Permian) had
in which sediment particles are glued together by carbonates microgranular calcite, coiled, discus- or spindle-shaped cas-
or organic matter. Casings are multi-chambered and for the ing. Families Endothyraceae and Fusulinaceae are particu-
most part coiled and continuously serial. larly important index fossils of the Upper Palaeozoic.
The Globigerinida (Jurassic until present) possess hyaline The Miliolida (Carboniferous until present) have two or
calcite casings with almost spherical (globular), finely per- multi-chambered non-porous casing (imperforate). The cas-
forated chambers. The group is planktic and can make up ings are agglutinated or composed of calcite. The randomly
a large proportion of marine calcareous sediments from the oriented calcite crystals refract light in all directions – the
Cretaceous, Palaeogene, and Neogene. casings thus have a porcelain-like appearance.
The Rotaliida (Jurassic until present) possess multi-cham-
bered hyaline calcite casings. The coiled Nummulitidae are
agglutinated: consisting of clumps of particles coiled: flat, spiral shape

aggregation: (Lat.: aggregatio = accumulation) accumulation, hyaline: with a glassy or translucent appearance
clustering Tethys: ocean that existed between Laurasia and Gondwana be-
tween the Permian and the Tertiary
See also: Foraminifera: 4.5.2.1

Neogene
Discorbidae
Nummulitidae
Rotaliidae
23 Ma
Miliolacea
Palaeogene
Orbitoididae
Alveolinidae
66 Ma
Globigerinida
Orbitolinacea
Nodosariidae (Lagenida)
Rotaliida
Cretaceous
145 Ma
Lituolacea
Lagenida: Lagena sp. (Upper Cretaceous,

Jurassic left) and Rotalida: Rosalina sp. (Eocene,
right)
The Lagenida and Rotaliida have hyaline
201 Ma casings; which were disc-shaped flattened
in many taxa. Especially in the Nummulites
reached diameters of several centimetres
Triassic
252 Ma
Permian
Miliona sp. (Eocene) Globotrunaca sp. (Cretaceous, left) and

Globigerinoides sp. (Pliocene, right)
Fuslinacea
298 Ma
Miliolida casings are made of mi- The planktic Globigerinidae have hya-
cro-crystalline calcite, with ran- line (translucent) casings with inflated,
Endothyracea
domly oriented individual crystals spherical chambers. They are wide-

Carboniferous giving each casing a porcelain-like spread as a result of their planktic life-
appearance style
359 Ma
Devonian
Textularia spp. (Textulariida, 2 species, Pliocene)

419 Ma
Textulariida casings are agglutinated, made of
Silurian sediment particles glued together with organic
substances or calcite
443 Ma
Ordovician
485 Ma
Triticites sp. (Permian, Cross-section along the casing)

Cambrian
The casings of the Fusulinida are mostly composed of
fine-crystalline calcite. They are multi-chambered and
mostly discus- or spindle-shaped. Fusulinida are impor-
541 Ma tant index fossils of the Tethys Ocean of the Upper Car-
boniferous and Permian
2.3.2.2
Reef-builders
Reefs are complex three-dimensional structures arising after the extinction of the Archaeocyathids. During the Or-
from the growth and aggregation of calcifying organisms. dovician, the diversity of reef-building organisms increased
There are a number of main types of reef, including, shallow yet again until the Upper Ordovician mass extinction. In the
marine reefs made of hyper-calcified organisms (i.e. animals Silurian and Devonian tabulate corals and stromatoporids
with a high skeleton-biomass ratio), deep and cold water played a significant role. After the Upper Devonian mass
reefs, as well as microbial reefs, where animals occur only extinction the reef community changed radically. Microor-
sporadically. ganisms, rugose corals, bryozoans, and chaetetide sponges
Speciation rates in reefs tend to be higher than in other dominated the reefs until the Upper Palaeozoic.
benthic communities. Similarly, reef species richness is also During the Upper Permian, calcified sponges became in-
relatively high compared to other marine habitats. creasingly important reef-builders, followed by scleractinian
The first reefs were microbial, made primarily of cyano- corals in the Upper Triassic. During the Cretaceous the im-
bacteria and other bacteria. During the Proterozoic, these portance of scleractinian corals was replaced by bivalvian
reefs became increasingly complex, due to the absence of Hippuritoida (rudists). After the extinction of the rudists,
predators. Metazoan species became important reef-builders scleractinian corals became again important during the Ce-
during the Phanerozoic: Archaeocyathids were important nozoic. Additionally, the proportion of calcified red algae
within the Cambrian reef communities, but microorganisms found in reefs increased.
once again came to dominate reefs in the Upper Cambrian
The Archaeocyatha were reef-building organisms with tubes without septa, and featured siliceous spicules. Calcar-
calcium carbonate skeletons. Though their precise systemat- eous sponges (Calcarea) were mainly important within the
ic position remains uncertain, they are likely closely related Mesozoic reefs.
to the sponges. They had funnel-shaped bodies divided by Corals (Zoantharia) have been significant members of
radial septa (pseudosepta) and lived often as solitary individ- reefs-building communities since the Ordovician. The Tab-
uals in water shallower than 100 m, suggesting they might ulata are exclusively colony-forming corals with underdevel-
have lived, as do modern corals, in symbiosis with photosyn- oped, thorn-like septa. Their corallites are thin and tubular.
thetic algae. The wide geographic distribution of Archaeocy- Rugosa and Scleractinia are groups with both colony-build-
atha taxa indicates they may have had a planktic larval stage. ing and solitary forms. Both groups have well-developed but
The Stromatoporoidea are an extinct group of colo- different septa, starting initially with the development of a
ny-forming sponges likely related to the Demospongiae. They foundation of six protosepta, on which the Scleractinia con-
form dense calcareous masses through their finely-meshed tinues to grow septa at each interstitial space, keeping the six
calcite skeleton and possess spicules. Based on the fossil ev- a as determinative feature (septa are present in all six sec-
idence, they are known to have existed from the Ordovician tors). In contrast, the Rugosa only grows septa from four of
to the Upper Devonian and from the Triassic until the Upper the six interstitial spaces.
Cretaceous. From the Carboniferous to the Permian fossil In addition to the sponges and corals, Rudista, a type of
records are missing. Stromatoporoidea lived as filter-feeders mussel, were also important reef-building organisms, espe-
in benthic, shallow, marine habitats. Another group of Dem- cially during the Cretaceous.
ospongiae are the extinct Chaetida, which formed calcareous
aggregation: (Lat.: aggregatio = accumulation) accumulation, Scleractinia: stony corals; they dominate modern coral reefs;
clustering septa are present in all six sectors, therefore displaying radial
Rugosa: ‘wrinkled’ coral; Palaeozoic coral taxon with additional symmetry
septa in only four of the six sectors, therefore displaying bilateral solitary: living alone
symmetry Tabulata: Paleozoic group of corals; they always possess six
septa (therefore displaying radial symmetry) but they are often
incomplete
See also: Diatoms: 4.6.2.4; Corals: 4.2.1.3; Radiolaria: 4.5.2; Sponges: 4.2.1.2; Spiculae: 4.2.1.2
Neogene
23 Ma
microorganisms and algae

Palaeogene
sponges
66 Ma Scleractinia: schematic plan, fossil overview,
corals and general view
Scleractinia
mussels
Cretaceous others
145 Ma Rugosa: schematic plan, fossil overview, and

general view
Jurassic
201 Ma
Pharetronida
Triassic Tabulata: schematic plan, fossil overview, and
general view
252 Ma
Sphinctozoa
Permian
298 Ma
Pharetronida: calcareous spong-
Chaetetes
es with triactins; polyphyletic
Carboniferous
359 Ma
Rugosa
Devonian Sphinctozoa: segmented calcar-

eous sponges; polyphyletic
Stromatoporoidea
Tabulata
419 Ma
Silurian
443 Ma
Archaeocyatha
Ordovician
Chaetetida: polyphyletic; pre-
sumably Demospongia
485 Ma
Cambrian
Stromatoporoida (Vermutlich
Demospongia kalkig-Strukturen )
##
541 Ma relative importance of
different reef-building The assignment of Archaeocyatha (left, centre) is unclear. Stro-
organismal groups matoporoidea (right) likely belong to the Demospongia
2.3.2.3
Cephalopods
Cephalopoda (cephalopods) are thought to have existed Argonauta spp. (Nautiloidea, paper nautiluses). The casing of
since the Upper Cambrian. 1,000 extant and over 30,000 nautiloids is either elongated (orthocon), bent (cyrtocon), or
extinct fossil species are known. Cephalopods can be fur- coiled.
ther broken down into the Nautiloidea, Ammonoidea, and The ammonoids still had an outer casing, which was
Coleoidea, though precise phylogenetic relationships between generally coiled. In the Coleoidea, the casing was displaced
the lineages remains unclear. Cephalopods are the most im- within the body or completely reduced. The seams between
portant group of macroscopic index fossils, particularly for the casing and the chamber septa are known as sutures or su-
the timespan between the Devonian and Cretaceous periods. ture lines. In the nautiloids, these are either straight or slight-
The Nautiloidea were most diverse from the Ordovician to ly curved, whereas in the ammonoids they are increasingly
the Devonian, the Ammonoidea from the Carboniferous to complex folded.
the Cretaceous, and the Coleoidea during the Neogene. Cephalopods are an exclusively marine and widely dis-
The primaeval cephalopods had an external casing. Ex- tributed group.
ternal casings are also found in members of the extant genus
Nautiloidea shells are either elongated or coiled and have meniida (Upper Devonian; simple or goniatitic sutures),
a simple or slightly undulated suture. The Nautiloidea can Goniatitida (Middle Devonian to Upper Permian; goniatit-
be divided into six orders: the most diverse groups were the ic), Prolecantida (Lower Carboniferous to Upper Permian;
Endoceratida (Upper Cambrian until Lower Devonian; elon- goniatitic to ceratitic), Certitida (Upper Permian to Upper
gated to coiled shells) and the Orthoceratida (Ordovician to Triassic; ceratitic), Phylloceratida (Triassic to Cretaceous;
Triassic; elongated to lightly coiled shells). The only extant complex, leaf-shaped [phylloid] sutures), Lytoceratida (Ju-
group is the Nautilida (from the Devonian until present; rassic to Cretaceous; complex, non-leaf-shaped sutures),
coiled shells). The Tarphyceratida (Ordovician until Devo- Ammonitida (Lower Triassic to Upper Cretaceous; ammo-
nian, Discosorida (Middle Ordovician until Lower Carbon- noid sutures), and the Ancyloceratina (Cretaceous; shell
iferous) and the Oncoceratida (Middle Ordovician to Upper only partially coiled in many species, ammonoid sutures).
Carboniferous) achieved a far lower diversity. The Coleoidea comprise an important extant group of
Over geologic periods of time, ammonoid sutures became eight-armed octopus (Vampyropoda), including the Octop-
increasingly complex folded. The Goniatitida were charac- oda (octopus), as well as ten-armed groups (Decabrachia)
terised by a smooth, undulated or bended suture (‘goniatit- with Teuthida (squid) and Sepiida (cuttlefish), all prevalent
ic’), whereas the Ceratitida possessed sutures that were pos- today but poorly represented in the fossil record. The inter-
teriorly zig-zagging but anteriorly smooth (‘ceratitic’). The nal skeletons of Decabrachia are partially preserved in the
Ammonitida, on the other hand, had highly ramified sutures fossil record. The most important fossil group are the Belem-
in both directions. The Ammonoidea are divided into nine noidea (belemnite, thunderbolts).
orders: The Anarcestida (Devonian; simple sutures), Cly-
lobe: clearly identifiable anatomical extension or projection suture: (Lat.: sutura = sew together) seam; the lobe line in ceph-
lobe lines: suture lines between the shell and the chambers in alopods
the phragmocone (septa) in fossil Ammonoidea and nautiloids
See also: Spiralia: 4.2.1.6

Belemnitida (Coeloidea)
Neogene proostracum
The internal skeleton consists of the
23 Ma proostracum (a stick-like reduced liv-
ing chamber), the phragmocone (a phragmocone
chambered buoyancy element) and
Sepiida
Palaeogene the rostrum (a chalky tip used for
counterbalancing). The body cham-
ber of the primaeval Belemnoids like rostrum
66 Ma
Aulacoceratida (Carboniferous to Ju-
rassic) was nearly closed
Cretaceous
Nautiloidea
The Nautiloidea include most of the
primitive cephalopods with an out-
Octopoda
er casing and simple suture. They
Ammonitida
serve as important index fossils for
145 Ma
Belemnitida
the Palaeozoic, in particular the En-
Teuthida
doceratida and Orthoceratida. These
groups have straight or only slightly
Jurassic bent casings
201 Ma
Ceratitida
Triassic
252 Ma
Permian
Prolecantida
298 Ma
Goniatitida
Nautilida
Carboniferous
Clymeniida
359 Ma
Oncoceratida
Anarcestida
Discosorida
Devonian
Orthoceratida
Ammonoidea Coleoidea
419 Ma Ammonoidea
Ammonoidea had an outer casing, which is usually
Tarphyceratida
Silurian coiled. The suture patterns are more strongly fold-

ed than in the Nautiloidea. Primaeval ammonoids
Endoceratida
443 Ma possessed simple and goniatitic sutures, whereas

subsequent lineages were characterised by cera-
titic and ammonitic sutures. The ammonoids are
Ordovician significant macro index fossils from the Upper Pal-
aeozoic and Mesozoic
485 Ma
Cambrian
Nautiloidea
541 Ma
goniatitic ceratitic ammonitic

2.3.2.4
Benthic filter-feeders: brachiopods and bivalves

The Brachiopoda (brachiopods; Lophotrochozoa) pos- were distinctively prevalent during the Devonian. Around
sess an upper and lower valve, with a symmetry axis running 300 species are thought to be alive today.
perpendicular to the valves and thus dividing these into left- The brachiopod body is surrounded by a double-lobed
and right-hand, symmetrical valves. In contrast, the bivalves mantle that secretes the valve. The eponymous arm appara-
(mussels; Mollusca) possess left- and right-hand valves, with tus (lophophore) is located inside the animal. Brachiopods
a symmetrical axis running along the edge of the valve. As are marine sessile filter-feeders.
a result of their similar benthic, filter-feeding lifestyle and Mussels (Bivalvia) have been around since the Cambri-
their being made up of two outer valves, these two groups an. Their diversity sharply increased during the Ordovician.
are presented together here, although they are systematically They became a significant component of ecosystems only
different. after the Permian-Triassic mass extinction event. Around
Brachiopods have been around since the early Cambri- 20,000 fossil and 8,000 extant species of mussels are known.
an, from 530 million years ago until today. Around 30,000 In the Palaeozoic, mussels were predominantly found in
brachiopod species are thought to have existed, all of which coastal habitats but subsequently, especially in the Mesozoic,
are divided into three subphyla (eight classes with 26 orders). they began to dominate offshore shelves, previously occu-
The brachiopods were most diverse in the Palaeozoic but pied by brachiopods.
The brachiopods are divided into three subphyla: the and tropical provinces can be distinguished. In the Ordovi-
Linguliformea with organophosphatic valves and including cian, several fauna provinces could be further classified, in-
five orders. The Craniformea with organocarbonatic valves cluding the cold-water fauna of the northern hemisphere, the
comprise three orders. Both subphyla comprise only brachi- subtropical and tropical fauna of the low latitudes, as well
opods, in which the two valves are not connected by a hinge as the Baltic-Russian fauna. Fauna appearing directly after
(inarticulate). The third subphylum, the Rhynchonelliformea the Upper Ordovician glaciation was initially cosmopolitan,
also have valves made of organocarbonate and include 19 but its biogeographic provincialism increased again in the
orders. Within this subphylum, there are inarticulated (with- Upper Silurian (Clarkeia- and Tuvaella-/Atrypella-fauna).
out lock) groups (Chileata, Kutorginata and Obolellata) and This ecological differentiation further increased during the
articulated groups (Strophomenata and Rhynchonellata). Devonian and Carboniferous. The Mesozoic was primarily
Both articulated classes are monophyletic within the Rhyn- characterised by a boreal cold-water and a warm-water fauna
chonelliformea. of the Tethys. Present-day brachiopods can be assigned to
Biogeographically, various distribution areas (biogeo- either North Pacific, North Atlantic, and Southern province.
graphic fauna provinces) can be distinguished. Basically, the Bivalves are divided into six sub-classes based mainly on
Linguliformea were widely distributed due to their planktiv- soft tissue characteristics: Palaeotaxodonta, Cryptodonta,
orous, long-lived and free-swimming larvae. The larvae of Pteriomorpha, Palaeoheterodonta, Heterodonta, Anom-
Craniata and Rhynchonelliformea, on the other hand, gained alodesmata. Since the most obvious physical feature of bi-
their nutrients through a yolk sac and were therefore short- valves, the shape of its valve strongly depends on its lifestyle,
lived and less widely dispersed. The species of these subphy- this trait is not phylogenetically stable and further character-
la were therefore less prevalent. During the Cambrian, polar isation s of sub-classes are waived.
articulated: possessing a joint permitting angular movement yolk sac: organ providing nourishment attached to the embryo
planktivorous: plankton-eating in various animals
See also: Boreal: 3.2.2.4

All major groups of mussels (bivalves) radiated

Neogene during the late Cambrian and Ordovician. They
23 Ma only became significant after the mass extinction
event at the end of the Permian. Mussels are par-
ticularly meaningful for palaeoecological analyses
Palaeogene as a result of the relationship between their valve
structure and lifestyle. The coral-like Hippuritoida
(rudists, right) are strongly modified with unequal
66 Ma valves and one shell cemented to the substrate,
relatively atypical for mussels. The rudists were
important reef-building organisms during the Cre-
taceous
Cretaceous
left right left right
145 Ma
Jurassic
201 Ma
Triassic
252 Ma
bivalves brachiopods
Permian
Mussels have a left and right shell. The plane of symmetry runs between the shells, so
that the left and right shells equal mirror images of each other. Brachiopods, on the
298 Ma other hand, have upper (brachial) and lower (pedicle) valve, with a plane of symmetry
that runs perpendicular to the valves. Upper and lower valves are often differentially
assigned. However, the left and right halves of each valve are equal mirror images of
Brachiopoda
each other. Both mussels and brachiopods are benthic filter-feeders. Both groups have
Bivalvia
Carboniferous existed since the Cambrian. Brachiopods were prevalent during the Palaeozoic, where-
as mussel populations grew strongly in the Mesozoic and Cenozoic
359 Ma
Brachiopods are important index fossils, especial-
ly for the Palaeozoic. Extant brachiopods are usu-
Devonian ally around 5 cm large, fossil species could reach
up to 30 cm in size. The most striking feature of
Brachiopods is their bivalve casing, consisting of a
pedicle valve and a brachial valve, protecting the
419 Ma lophophores (‘arms’). An important feature for
identification purposes is the brachidium, found in
Silurian the pedicle valve, which attaches the animals with
443 Ma a muscular pedicle (peduncle) to the substrate. Brachidium (Foramen) of the
The decline in brachiopod dominance and the cor- pedicle valve
responding rise in dominance of the mussels corre-
Ordovician lates with the Upper Permian mass extinction event
and the subsequent emergence of starfish. With
few exceptions, brachiopods live, with few excep-
485 Ma tions, on the substrate (epifaunal) whereas most
mussel species are burrowed within the substrate
(infaunal); as a result, brachiopods were more ex-
Cambrian posed to starfish predators when these became
more prevalent
541 Ma
Cyrtospirifer verneuili (Devonian)

2.3.2.5
Trilobites
Arthropods are the most species-rich metazoan group. To for classification purposes as well as for understanding tri-
that end, trilobites, in particular, are important index fossils lobite functional morphology. Their exoskeleton is divided
for the Palaeozoic era. into three lobes along the longitudinal axis of the body: the
Trilobites are an extinct group of marine arthropods, axial lobe flanked on each side by right and left pleural lobes.
which existed from the Lower Cambrian (≈521 million years The axial lobe protects the inner organs, whereas the left and
ago) until the Upper Permian mass extinction event (≈251 right pleural lobes protect the body’s appendages. Trilobites
million years ago). Their prominence in the fossil record is derive their name from their three-lobed body (Grk: trilo-
largely due to their calcium carbonate exoskeleton, which bite = three lobed). They are the oldest known animals with
is generally well preserved. Over 15,000 trilobite species are eyes.
known, divided into nine orders. The first appearance of tri- Most trilobites lived in benthic environments, with dis-
lobites defines the boundary for the start of the second epoch tinct species or taxonomic groups in different habitats.
within the Cambrian. From Series 2, the Cambrian ages are Most known fossils are from shallow marine habitats. More
correlated with the first appearances of various trilobite spe- streamlined trilobite body forms are known from the Ordo-
cies. Trilobites reached their peak diversity during the Cam- vician and these were presumably active swimmers. Most
brian and Ordovician. trilobites are thought to have been predatory or scavengers,
Trilobites display a morphology typical of arthropods, though some derived forms were also filter- or sediment-feed-
featuring a cephalon (head), thorax (chest), and pygidium ers. Many lineages displayed pronounced spines, which like-
(tail piece). The sutures on the cephalon are important both ly offered protection from predators.
The trilobites comprise nine orders: Redlichiida (thorax unclear, though recent studies suggest that it may be a crus-
segments with many pleural spines; Lower to Middle Cam- tacean rather than a trilobite.
brian); Corynexochida (elongated glabella and well-devel- The biogeography (fauna provinces) of trilobites can be
oped eyes; Lower Cambrian to Middle Devonian); Asaphida broken down into a variety of smaller distribution areas. Tri-
(morphologically diverse group; Upper Cambrian to Low- lobite fossils from the Cambrian differ between the high lat-
er Silurian); Ptychopariida (also a morphologically diverse itudes of the northern hemisphere (including Redlichoidea
group; Upper Cambrian to Lower Devonian); Harpetida [Redlichiida]) and from the low latitudes of the Pacific (in-
(large and well-developed cephalon fringe; Lower Ordovi- cluding Olenoidea [Corynexochida]).
cian to Middle Devonian); Phacopida (morphologically very From the Ordovician, four fauna provinces can be identi-
diverse group; Lower Ordovician to Upper Devonian); Li- fied: the cold water fauna of the northern hemisphere (North
chida (pronounced cephalon and pygidium, with the latter and Central Europe); the continental shelf fauna of the lower
often larger than the cephalon; Middle Cambrian to Middle latitudes (southern China and Australia); the tropics (North
Devonian); Odontopleurida (with distinctive spines; Lower America, Siberia, Northern China); and the Baltic-Russian
Ordovician to Middle Devonian); Proetida (small body size; fauna.
Lower Ordovician to Upper Permian). After the Upper Ordovician glaciation, the tropical fauna
The systematic position of the Agnostida (only a few mil- province dispersed and this trend continued until the Devo-
limetres in size; Lower Cambrian to Upper Ordovician) is nian, when the biogeographic provincialism was once again
more strongly pronounced.
lobe: clearly identifiable anatomical extension or projection pygidium: posterior body part in trilobites and other anthro-
pleura: lateral part of body segments in trilobites pods; also the unsegmented section of annelids
provincialism: term given to the division of animal communi- series: stratigraphic time scale
ties into distinct fauna provinces (roughly equivalent to faunal suture: (Lat.: sutura = sew together) seam; the lobe line in ceph-
kingdoms) alopod
See also: Ecdysozoa: 4.2.1.5

Neogene pleural axial pleural

lobe lobe lobe
23 Ma
}
}
}
Palaeogene
} cephalon
66 Ma
} thorax
Cretaceous } pygidium
Dolichoharpes sp. (Harpetida): Phillipsia sp. (Proetida): The

The Harpetida are characterised Proetida are generally small and
by a wide seam on their ceph- were the only trilobites to sur-
Trilobites derive their name from their distinct alon vive until the Permian
145 Ma
morphology comprising three lobes (an axial
and two pleural lobes). Apart from these, tri-
lobites display the body segments typical of
Jurassic arthropods, with a body plan divided into a
cephalon, thorax, and pygidium. Illustrated
here is genus Taihungshania (Asaphida). The
201 Ma pygidium is of similar size as the cephalon, as
it is generally within the Asaphida. The Asa-
phida is one of the largest trilobite orders,
making up around 20 % of known species
Triassic
252 Ma
Permian Paradoxides sp. (Redlichiida): Kettneraspis sp. (Odontopleu-

These primitive trilobites, char- roidea): The Odontopleuroidea
acterised by a small pygidium. are very spinose and densely
298 Ma Their cephalon and thorax seg- sculptured
ments are elongated into spines
Carboniferous
359 Ma
Devonian
419 Ma
Silurian Dalmanites limulurus (Phacopida) from

the Silurian (left) and Reedops cephalotes
Odontopleurida
443 Ma (Phacopida) from the Devonian (right)

Phacopida
Harpetida
Ordovician
Proetida
Lichida
Asaphida
Corynexochida
Trilobita
Ptychopariida
485 Ma
Redlichiida
Agnostida
Cambrian
Diversity and stratigraphic Boedaspis ensifer Stratigraphic distribution of different trilobites

541 Ma distribution of Phanerozoic (Odontopleurida) orders
trilobites from the Ordovician
2.3.2.6
Echinoderms
The Echinodermata (echinoderms) likely emerged in the up of 620 extant and around 4,000 extinct species, whereas
Upper Precambrian, initially radiating during the Cambrian. Eleutherozoa comprise 5,700 extant and 9,000 extinct spe-
However, many of the major Cambrian echinoderm groups cies.
went extinct relatively soon thereafter. Modern echinoderm The Echinodermata belong to the bilateral metazoans.
groups evolved from the Eocrinoidea and Edrioasteroidea, Their bilateral larvae develop the pentameral symmetry
which emerged in the Cambrian and began their radiation in (five-fold organisation of skeleton) during the ontogeny.
the Ordovician. Echinoderms comprise Pelmatozoa, which The echinoderms are a predominantly marine and ben-
include with the Crinoidea (sea lilies and feather stars) as the thic organismal group. While sea lilies are mainly feeding on
only extant representatives, and the Eleutherozoa, which in- plankton, sea urchins are grazers, mainly eating algae and
cludes the Asterozoa (Asteroidea – starfish and Ophiuroidea aufwuchs; the starfish are predators of mussels and other
– brittle stars) and the Echinozoa (Echinoidea – sea urchin benthic animals. Finally, sea cucumbers include both, plank-
and Holothuroidea – sea cucumbers). Pelmatozoa are made tivorous and sediment-grazing taxa.
The Pelmatozoa include the extant Crinoidea as well as a The Crinoidea (Ordovician to present) possess a calyx of
number of extinct groups. Most taxa were sessile and used a either five basal plates (monocyclic) or two rings of five basal
specialised stem to secure themselves at the sea floor. Eocri- plates each (dicyclic), followed by numerous radial and bra-
noidea (Lower Cambrian to Silurian) were characterised by chial plates (arm plates), featuring either branched or non-
cup-like or flattened calyx (theca) fixed to a stem from where branched brachioles.
with two to five food gathering appendages (brachioles). Eo- The Eleutherozoa includes both extant groups and the
crinoidea were sessile; a stem securing the organism at the extinct Edrioasteroidea (Ediacaran to Carboniferous), which
sea floor. The Paracrinoidea (Middle Ordovician) were sim- had a spherical to sac-like calyx and a mouth located cen-
ilar to the Eocrinoidea, featuring an irregularly structured trally on its upper side, as well as an anus located laterally
calyx with irregularly shaped plates. between the ambulacral grooves.
The Blastoidea (Ordovician to Permian) possessed a calyx The Asteroidea (starfish; Ordovician to present) are
made of at most 13 interconnected plates: three basal plates free-living and have a mostly flat central disk with a min-
(basalia), five plates located around the mouth (deltoid), and imum of five, but up to 25, arms emerging outwards. The
five radial plates (radialia). In the upper part of the calyx, mouth is located centrally on the body’s underside whereas
a set of folded thecal entrances (hydrospires) was located, the anus sits on the body’s upper surface.
probably acting as respiratory organs. The Blastoidea also The Ophiuroidea (brittle stars; Ordovician to present)
featured many brachioles, attached to two alternating rows have five sharply defined arms, up to 60 cm in length, ema-
of plates. nating from the central plate.
The Diploporita (Middle Cambrian to Devonian) had a The Holothuroidea (sea cucumbers; Ordovician to pres-
calyx made of numerous irregularly arranged plates with ent) have an elongated, cucumber-shaped body and a mouth
pairs of irregularly ordered double pores (diplopores) and at the body’s anterior end, usually surrounded by branched
two rows of non-branched brachioles. tentacles.
The Rhombifera (Upper Cambrian to Devonian) had a The Echinoidea (sea urchins; Ordovician to present) are
calyx structure similar to the Diploporita but, rather than di- almost spherical or disc-shaped and have a casing made of
plopores, featured a rhombic-shaped array of simple pores. interconnected calcite plates.
ambulacral grooves: grooves running along the radial arm of ambulacral system: system for channeling coelom fluid in
an ambulacral system echinoderms
ontogeny: the individual development of an organism
See also: Brachiopods and mussels: 2.3.2.4, 4.2.1.6; Deuterostomia: 4.2.1.7

Neogene
23 Ma
Palaeogene
Echinoidea
Asteroidea
66 Ma
The Asteroidea (starfish, left), Ophiuroidea (brittle stars, centre), and the Holothuroidea
(sea cucumbers, right) emerged already in the Palaeozoic but became ecologically signifi-
cant later on during the Mesozoic and Cenozoic
Cretaceous
Echinoidea
The Echinoidea can be divided into two groups according to
the position of the mouth and anus. In Regularia, the anus
lies opposite to the mouth and is surrounded by a circlet of
145 Ma 10 plates, forming the apical system. However, in the Irreg-
ularia, the anus lies laterally outside the apical system or is
even shifted towards the oral side, and the body shape is
Jurassic flattened. This irregular organisation is an adaptation to a
digging lifestyle in stagnant marine habitats.
The names of Regularia and Irregularia are purely descrip-
201 Ma tive and carry no taxonomic meaning. To that end, the ir- Regular sea urchin Coe-
regular Echinoidea are likely monophyletic, whereas the lopleurus coronalis from
regular lineages are paraphyletic. Huseca, Spain (Eocene)
The diversity of Lower Palaeozoic Echinoidea sharply de-
Triassic
clined during the Upper Carboniferous and only a few taxa
survived the Permian-Triassic mass extinction event. Sub-
sequently, the regular Echinoidea diversified during the
252 Ma Upper Triassic and Lower Jurassic, whereas the Irregularia
emerged in the Lower Jurassic and diversified during the
Mesozoic. Echinoidean diversity again dropped sharply at
Permian the Cretaceous-Palaeogene boundary but diversity recov-
ered quickly thereafter in the Cenozoic. This group serves as
an important index fossils, in particular for the Cretaceous
298 Ma and Cenozoic
Irregular sea urchin Mellita
Crinoidea
quinquiesperforata is flat-
tened as an adaptation to a
Carboniferous digging lifestyle
Crinoidea
Extant Crinoidea (crinoids) live primarily in deep-sea habi-
359 Ma tats. Fossil species of the group, on the other hand, appear
to have lived in shallow marine areas. Most known Crinoidea
were sessile, secured themselves by a specialised stem at the
Devonian sea floor. Moreover, the extant crinoidean feather stars are
also known to freely swim in recent oceans.
A number of crinoid groups are important in the fossil record:
The Camerata (Ordovician until Permian) were the largest cri-
419 Ma noid fossil group. They had no radial plates, and their brachial
plates were firmly incorporated into the calyx .
Silurian Sea lily Agaricocrinus amer-
The Flexibilia (Middle Ordovician to Upper Permian) were
icanus
443 Ma characterised by their lower arms, which were flexibly con-
nected to the calyx. The polyphyletic Inadunata (Ordovician
to Triassic), the arms sit freely above the radial plates of the
Ordovician calyx. In the Articulata, to which almost all Mesozoic to extant
crinoids belong, the calyx is greatly reduced. In some line-
ages, such as the feather stars, the calyx is completely absent.
485 Ma
Cambrian
Feather star Comaturella

541 Ma formosa from Solnhofener
Plattenkalk (Upper Jurassic)
Fossil assemblage of sea lilies
2.3.2.7
Graptolites and Conodonts

Graptolites and conodonts are important index fossils Conodonts’ basal cavity was made of tooth-like structures
from the Palaeozoic. Nevertheless, their phylogenetic classi- of around 0.1–2 mm in length consisting of layers of skeletal
fication remains unresolved. phosphates and organic substances. These are often the only
Graptolites, rod-like fossils, can be found in the fossil remaining conodont animal body parts found in the fossil
record from the Middle Cambrian to the Upper Carbonif- records. From an evolutionary perspective, conodonts are
erous. They are particularly widespread in rocks from the likely convergent with the teeth of vertebrates, resembling
Lower Palaeozoic. Graptolites built tubular skeletons of half each other in shape because of their similar function. Since
tubes, brought together by a zig-zagging stitch. Initial, sexu- most species occurred for only a relatively short period of
ally formed zooid of colony (sicula) giving rise to additional time, and due to their abundance and mostly pelagic lifestyle,
chambers by budding (theca). they serve as important index fossils from the Palaeozoic and
Graptolites are sometimes considered the fossil body Lower Mesozoic.
housings of hemichordates. The primaeval graptolites were Fossilised conodonts are also used as palaeothermom-
benthic, a way of life retained in the Dendroidea whilst the eters, for they change their colour at higher temperatures,
Graptoloidea developed towards a planktic lifestyle. such as those rock experienced during diagenesis and met-
Conodonts are fossils from the Cambrian to the Upper amorphism. This property of the conodonts is particularly
Triassic. Around 3,000 conodont species have been identi- important for the oil and natural gas exploration industry:
fied, of which the greatest diversity was achieved in the Or- since hydrocarbons are unstable at higher temperatures, only
dovician. Conodont animals were likely pelagic predators, rock layers that have not been exposed to such temperatures
reaching a length of only a few centimetres, and are widely may be potential reservoir rocks.
thought to be basal chordates.
Although the Dendroidea (lower Lower Ordovician to droidea. Due to a reduction of the number of arms thecae
Carboniferous) were the primaeval graptolites, their mor- differentiated in the Graptoloidea. In addition, the arms of
phology was relatively complex. They rhabdosomes are mul- some taxa were positioned above the sicula and featured
ti-branched. Three different kinds of thecae make up their outgrowths; resulting in species displaying double rows of
simple stipes: autothecae, bithecae, and stolonothecae. The thecae (Diplograptidae) in the Upper Ordovician. A thecal
rhabdosoma were connected either directly or via an adhe- reduction led to the emergence of uniserial morphologies,
sive disc and short stem to the sicula. Some species, such as known as Monograptidae.
the genus Dictyonema, lived hemi-planktic. This genus was Conodonts can morphologically be identified within three
the ancestral lineage which eventually developed a reduction different types: single cone type, platform type, and bar type.
in the number of arms and thecae. The conodonts generally display a concentric lamellar skele-
The Graptoloidea (lower Middle Ordovician to mid- ton. They lack the pulp cavity of real teeth.
dle Lower Devonian) can be traced back to simple Den-
contact metamorphism: metamorphism caused by tempera- rhabdosomes: rod-like colonies of graptolites

ture increases due to hot magma rock metamorphism: changes in rocks under high pressure
diagenesis: compression of sediments by lithification; chemical, and temperatures without them melting into liquid magma
physical or biological change at relatively low temperatures
See also: Index fossils: 2.3.2; Stratigraphy of the Palaeozoic: 2.3.3

Conodonts are 0.1–2 mm long tooth-like structures made of calcium phosphate. Their systematic
Neogene classification is unclear, but they are likely related to vertebrates. Conodonts can be divided into
23 Ma three main groups, though these are not necessarily based on systematic affiliations
• simple cones: formed by a single tooth (Cambrian to Silurian)
• platform type: comprising a flat plate featuring a series of tiny teeth (Ordovician to Triassic)
Palaeogene • bar types: a thin bars with or without a bent shaft which is commonly branched with tiny teeth
(Ordovician to Triassic)
66 Ma
Cretaceous
145 Ma
Isarcicella staeschei: top view Isarcicella staeschei: side view

Jurassic
stratigraphic
occurrence of
conodonts
201 Ma
Triassic The geological development of graptolites is characterised by their transition from the sessile life-
style of Dendroidea (Middle Cambrian to Upper Carboniferous) to the planktic lifestyle of Grap-
toloidea (Lower Ordovician to Middle Devonian), as well as – within the Graptoloidea – from a
two-line, biserial to a single-line, uniserial set of rhabdosomes
252 Ma
stratigraphic The Monograptidae emerged in the

Permian occurrence of Silurian and, already by the Lower Si-
graptolites lurian, began to dominate graptolite
298 Ma communities. Their rhabdosome was
Dendroidea Graptoloidea uniserial due to an one-sided reduc-
tion of the thecae
Carboniferous
Monograptus sp.
The rhabdosomes of Diplograptidae

were biserial due to erection and ad-
Monograptidae
359 Ma
hesion of their arms. They emerged
Conodonts
in the Lower Ordovician. They dom-

inated graptolite assemblages from
Devonian the Middle Ordovician until the Si-
Diplograptidae
lurian
Diplograptus sp.
419 Ma
Dichograptidae
The rhabdosomes of Dichograptidae

Silurian (Graptoloidea) consisted of two to
several branches with a divergence
443 Ma angle of less than 180°. They domi-
nated graptolite assemblages in par-
ticular during the Middle Ordovician
Ordovician
Didymograptus murchisoni
485 Ma
The Dendroidea are the oldest grap-
tolite order, existing from the Middle
Cambrian Cambrian to the Upper Carbonifer-
ous. Dendroidea were benthic with
branching, tree-like rhabdosomes. A
handful of species were planktic
541 Ma
Rhabdinopora sp.
2.3.2.8
Vertebrates
Vertebrates (Vertebrata; or craniates (Craniata)) possess environments by animals required more efficient anatomi-
an internal skeleton and a head, which contains the brain cal supporting structures – bones – as well as adaptations
and main sensory organs. This concentration of brain for osmo-regulation and sensory organ developments. Am-
and sensory organs within the head in this arrangement is phibians remained highly water dependent, at least for the
unique. In addition, the internal skeleton grows quickly and reproductive portion of their life cycles. As the egg of the
is better suited – compared to an exoskeleton – to support- amniotes (Amniota) was better protected against desicca-
ing the relatively heavy tissues of large animals. In addition, tion, they were largely water-independent. The Amniota
damage to the exoskeleton can be repaired only by external emerged in the Lower Carboniferous, with major groups –
tissue (such as in mussels and graptolites) or by moulting (ar- the Anapsida, Diapsida, and Synapsida – developing during
thropods). Taken together, these two developments, the in- the Carboniferous and Permian. The amniotes eventually be-
ternal skeleton and head, were key elements in the evolution came ecologically significant after the Permian-Triassic mass
of vertebrates. extinction event.
The first vertebrates are known from the Cambrian. Reptiles dominated the Mesozoic. At the same time, mam-
Conodonts were the dominating species during the Cambri- mals developed successively during the Mesozoic, emerging
an and Ordovician. In addition, jawless fish (‘agnatha’) were from the primaeval synapsids. The first mammal-like ani-
also prevalent vertebrates at the time. After the evolution of mals already emerged in the Triassic, almost simultaneously
the jaw, several jaw-bearing vertebrates (Gnathostomata) with the dinosaurs. The mammals radiated strongly during
emerged during the Devonian: the first armoured prehis- the Upper Jurassic and Lower Cretaceous but only became
toric fish (placoderms) during the Devonian, the Actinop- dominant after the extinction of dinosaurs. Birds emerged
terygii (ray-finned fish) and the Sarcopterygii, the ancestors over the course of the Cretaceous, radiating more strongly
of tetrapods. Subsequently, the colonisation of terrestrial during the Palaeogene.
Placoderms (Placodermi; armoured prehistoric fish, Up- The Anapsida (Upper Carboniferous to present) include a
per Silurian to Upper Devonian) are a group of extinct, fish- number of extinct groups. It remains unclear whether turtles
like, jaw-bearing vertebrates. They were characterised by belong to this group or not.
heavy bony armour on the head and along the torso, made The Diapsida (Upper Carboniferous to present) include
of cosmine. The largest species were approximately 10 m in the Archosauromorpha (Crurotarsi, including the croco-
length. diles, pterosaurs, and dinosaurs including birds), Lepido-
The Acanthodii (spiny sharks; Silurian to Permian) are sauromorpha (lizards, snakes, Sauropterygia), as well as the
the sister group of bony fish (Osteichthyes), which together Ichthyosauria (ichthyosaurs), and other extinct reptiles.
form the taxon of Teleostomi. The membranous fins of the The Synapsida (Upper Carboniferous to present) include
Acanthodii were supported by a sting at their front edge. the mammals and extinct vertebrate groups, in particular the
The Lepospondyli (Carboniferous to Permian) are an paraphyletic Pelycosauria (pelycosaurs) and the therapsids.
extinct group of amphibian-like, primitive, and morpholog- The pelycosaurs were cold-blooded, reptile-like vertebrates,
ically very diverse terrestrial vertebrates (Tetrapoda). The exhibiting the first substantial progress of crawling to run-
skeleton was only weakly ossified; the eponymous spin- ning, from which therapsids emerged. The therapsids were
dle-shaped vertebral bodies may have been an adaptation to the dominant amniotes in the Permian and Lower Triassic,
a small body size, and thus a reduction feature. Their exact before the emergence of dinosaurs. Therapsida represent an
systematic relationship to amphibians (Lissamphibia) and intermediate between the reptile-like pelycosaurs and mam-
Labyrinthodontia is unclear. mals. Developed therapsids had legs located underneath
The Labyrinthodontia (Upper Devonian to Lower Creta- their body and a developed secondary temporomandibular
ceous) are not a natural group but, rather, a taxonomic col- joint, where elements from the primary jaw became auditory
lective of species linking the bony fish and terrestrial verte- ossicles. Most pelycosaurs and therapsids went extinct at the
brates. As a result, these taxa feature different combinations Permian-Triassic boundary, yet extant mammals emerged
of amphibian- and reptilian-like features. It remains unclear, from one of the surviving therapsid groups, the Cynodontia.
however, whether either amphibians or reptiles were derived
from this group.
amniotes: vertebrates in which the embryo is surrounded by an conodonts: tooth-like structures made of apatite and layers of
additional covering called the amnion – including reptiles, birds organic material, probably from basal chordates
and mammals
See also: Amniotes, Vertebrates: from 4.2.1.7 to 4.2.1.9

Squalomorpha
Lissamphibia
Galeomorpha
Batoidea
Anapsida
Lepidosauromorpha
Crurotarsi
Aves
Theria
Neogene
23 Ma
Palaeogene
66 Ma
Petrimyzontiformes
Myxiniformes
Protheria
Cretaceous
Ornithodira
145 Ma
Jurassic
201 Ma
Therapsida
Triassic
Archosauro-
morpha
252 Ma
Pelycosauria
Permian
‘Labyrinthodontia’
Diapsida
Actinopterygii
Lepospondyli
Holocephali
298 Ma
Sarcopterygii
Synapsida
Elasmobranchii
Amniota
Carboniferous
359 Ma Cynodontia (Therapsida): Thrinaxodon sp. (model, left)

Acanthodii
Tetrapoda and Belesodon magnificus (skeleton, right)

Placodermi
Devonian
Monorhina
Diplorhina
419 Ma
Silurian Ornithodira: Archaeopteryx lithographica (model, left;

fossil skeleton with feathers, right)
443 Ma
Ordovician
Gnathostomata
Labyrinthodontia: Elginerpeton sp. (drawing, left) and
485 Ma Discosauriscus pulcherrimus (skeleton, right), which
emerged in between Labyrinthodontia and Amniota
Cambrian
jawless organisms
541 Ma
Placodermi: Eastmanosteus sp. (head armour, left) and
Gemuendia stürtzi (skeleton, right)
2.3.2.9
Land plants
For the first land plants a socialisation with fungal com- lineages of spore plants during the Devonian, including the
munities was probably essential. Fungal communities served Lycopodiopsida (club mosses), Equisetopsida (horsetails),
both, as decomposers of organic matter and as nutrient sup- and Polypodiopsida (ferns). Vast forests emerged during the
plier, and on the other hand as mycorrhizal symbionts. The Carboniferous. Seed plants emerged as early as the Palaeo-
prerequisites for the evolutionary success of plants within zoic, with the gymnosperms (Cordaitopsida, Cycadopsida)
terrestrial environments were therefore likely offered by a initially radiating during the Carboniferous and Permian
preliminary terrestrial colonisation by fungi. The oldest li- and then again later, during the Mesozoic (Coniferopsida,
chen fossils were recorded from the Doushantuo formation Gnetales, Bennetitales). After the mass extinction event at
in China (Ediacaran). However, the oldest land plant fossils the Permian-Triassic boundary, the gymnosperms domi-
from the Cambrian remain controversial: moss tetraspores nated terrestrial vegetation. The angiosperms subsequently
have been found dating back to the Middle Ordovician, radiated during the Cretaceous, dominating the global flora
whereas the first verified vascular plant fossils date back to after the mass extinction event at the Cretaceous-Palaeogene
the Silurian. boundary.
Plants colonised terrestrial environments during the Or-
dovician and Silurian, subsequently developing into various
Origin of vascular plants/primaeval vascular plants: The and a pronounced xylem. Sporangia appeared terminally on
oldest verified vascular plant fossils date back to the Silurian. axes, usually concentrated on the lateral branches.
The Rhyniophytina (Upper Silurian to Upper Devonian) Origin of seed plants/primaeval seed plants: The Pro-
are a small group of dichotomously branched vascular plants gymnosperms (Upper Devonian to Lower Carboniferous)
with terminal sporangia and primitive vascular bundles. It display a mixture of characteristics between ferns and seed
is likely that Rhyniophytina are not the direct ancestors of plants. As with the ferns, they developed from the Trimero-
extant vascular plants but, rather, evolved in parallel. phytopsida and are considered potential ancestors of seed
The Zosterophyllopsida are also dichotomously branched, plants. The Progymnosperms were shrubs or trees with pseu-
though their sporangia sit laterally along their main axis. It is domonopodial branches; their leaves showed a dichotomous
possible that they represent an evolutionary link between the venation. Their sporangia were laterally located at the lateral
primaeval vascular plants and the club mosses. branches or at modified leaves. The Progymnosperm group
The Trimerophytopsida (Lower Devonian to Middle De- included the Archaeopteridales, the Aneurophytales, and the
vonian) are a group of extinct vascular plants whose charac- Protopitiyales.
teristics resemble a mixture between the rhyniophytes and It remains unknown from which of these groups the seed
extant ferns and seed plants. They are not a natural group, plants evolved. Presumably, all seed plants can be traced
but appear in a number of transitional forms between the back to the Aneurophytales. Alternative theories propose
rhyniophytes and the real vascular plants. The Trimerophy- that only the Cycadopsida evolved from Aneurophytales,
topsida were generally morphologically more complex than with the remaining lineages tracing back to the Archaeop-
the Rhyniophytina or Zosterophyllopsida. They are char- teridales.
acterised by dichotomous or trichotomous lateral branches
dichotomous: (Grk.: dichotomos = in two parts) splitting of a radiation: rapid diversification of a taxon giving rise to an array
shoot axis into two parts of new forms
monopodial: plant growth type in plants with a single trunk tetraspores: grouping of the four spores generated by meiosis
or stem
See also: Gymnosperms: 4.4.3.5; Mass extinction: 2.3.1; Monilophyta: 4.4.3.4; Bryophytes: 4.4.3.2; Mycorrhiza: 4.2.2.2; Rhyniophytina: 4.4.3.3
Neogene
23 Ma
Magnoliopsida (Angiosperms)
Palaeogene
66 Ma
Cretaceous
Gnetales
145 Ma
Bennettitopsida
Jurassic
Coniferopsida
Cycadopsida
Ginkgopsida
201 Ma
Triassic
Glossopteridopsida
252 Ma
Permian
Lycopodiopsida
Polypodiopsida
Marattiopsida
Equisetopsida
Cordaitopsida
Selaginellales
Psilotopsida
Isoetales
298 Ma
Lepidodendrales
Progymnospermen
Carboniferous
359 Ma
Zosterophyllopsida
Rhyniophytina
Trimerophytopsida
Devonian
Otozamites obtusus (Bennettitopsida) leaf

419 Ma
Silurian
443 Ma
Ordovician
485 Ma
Cambrian
541 Ma
Longitudinal (left) and cross-section section of the primaeval plant Rhynia (Rhynio- Bark of the tree-shaped club moss
phytina) Lepidodendron sp. (Lepidondrendrales)
2.3.3
The Palaeozoic era

The Palaeozoic is the oldest era within the Phanerozoic The Upper Devonian (Frasnian) witnessed another mass
eon, covering the time from 541 to 252.2 million years. It is extinction event, which led to an increased carbon deposi-
divided into six periods: the Cambrian, Ordovician, Silurian, tion in sediments. The event, known as the Kellwasser event,
Devonian, Carboniferous, and Permian. is named after the location in Harz, Germany, where such
The Cambrian period is divided into four epochs and ten characteristic rock layers were first described.
ages, some of which remain unnamed. The end of the Cam- The Carboniferous period is divided into two subsystems,
brian was characterised by a mass extinction event, likely trig- the Mississippian and the Pennsylvanian, which are in turn
gered by climatic change and associated fluctuations in sea divided into three epochs each. In Central Europe, fossil rich
level. In Central Europe, Cambrian rocks are rarely exposed. limestones (Kohlenkalkfazies) and, eroded material of the
The Ordovician period is divided into three epochs and Variscan Orogeny (Kulmfazies) to the South, date back to
seven ages. Limestones from the Ordovician are exposed in the Carboniferous. Typical are coal-bearing strata. In the
Scandinavia, whereas argillaceous shale from that period Upper Carboniferous the most extensive coal deposits were
can be found in some regions of Germany. The Upper Or- formed worldwide.
dovician was also characterised by a mass extinction event, The Permian period is divided into three epochs and nine
likely due to the climatic changes driven by the spread of ages. In Central Europe, peculiar red-coloured rocks from
land plants. the Lower and Middle Permian and the Kupferschiefer from
The Silurian period is divided into four epochs and eight the Upper Permian are remnants from the Permian period.
ages. Dark bituminous argillaceous shales known as grapto- In the Upper Permian, global climatic conditions led to four
lite shales are characteristic for the Silurian in Central Eu- major evaporation cycles leaving behind the largest known
rope. Phanerozoic salt deposits. The end of the Permian is char-
The Devonian period is divided into three epochs and acterised by the largest Phanerozoic mass extinction event,
seven ages. Compact reef limestone, mudstone, and sand- driven by the heaviest volcanic activities of the Phanerozoic;
stone are characteristic of the Devonian in Central Europe. the notorious Siberian magma fields emerged in this context.
The early Cambrian, and thus the beginning of the Palae- though the lower limit of the Dinantian and Mississippian
ozoic, was initially defined by the first appearance of fossils. match, the upper limit of the Dinantian is placed within
Subsequently, the Cambrian was thought to have begun 600 the Mississippian. The ages within the Carboniferous cor-
million years ago. However, since then fossils were discov- respond to each other, except for the Upper Pennsylvanian,
ered in far older rock layers. Later on, the beginning of the which is divided into two stages.
Cambrian became associated with the appearance of certain The European regional subdivision of the Permian also
distinct fossils and was thus shifted somewhat towards the deviates from the international classification. Two strikingly
present. Today, the beginning of the Cambrian is associated different rock strata in Central Europe led to the older Per-
with the first appearance of the trace fossil Trichophycus pe- mian (approximately the Cisuralian and Guadalupian) being
dum, dating back to 541 million years. This matches approx- called the Rotliegendes and the more younger Permian being
imately a global drop in carbon isotope 13C. called the Zechstein (around the Lopingian). The Rotliegen-
The Ordovician was only accepted as period in 1960. Be- des and the Zechstein, are still used in regional studies as
fore that point, Ordovician strata were generally attributed to lithostratigraphic terms. However, since these deposits do
either the Silurian or, less frequently, to the Cambrian. not correlate precisely with the recognised boundaries of
The original European division within the Carboniferous the respective epochs, they were abandoned as internation-
period (Dinantian and Silesian epoch) is different compared al stratigraphic terms and replaced by the terms Cisuralian,
to the international, originally American, classification. Al- Guadalupian, and Lopingian.
bituminous slate: oil slate, a soft form of clay slate impregnat- Variscan Orogeny: a mountain-building event in the Paleozoic
ed with bitumen caused by the collision of Gondwana and Laurussia
lithostratigraphy: spatial and temporal classification of rock
strata based on the characteristics of the rock; subdiscipline of
stratigraphy
See also: Fossils: 2.3.2, 2.3.1.2, 2.3.1.3

The Phanerozoic eon: the Paleozoic era 99
Lopingian Changsingian
254.1 Ma
Guadalupian Wuchiapingian
272.3 Ma 259.8 Ma
Permian Kungurian
283.5 Ma Capitanian
Artinskian
Cisuralian 265.1 Ma
290.1 Ma Wordian
Sakmarian
295.5 Ma 268.8 Ma
Asselian
298.9 Ma Roadian
Pennsylvanium
Gzhelian
Upper P. Kasimovian 303.7 Ma
307.0 Ma
Middle P. Moskovian
315.2 Ma
Lower P. Bashkirian
323.2 Ma
Carboniferous Upper M. Serpukhovian
330.9 Ma
Mississippium
Middle M. Visean
346.7 Ma
Lower M. Tournaisian
358.9 Ma
Famennian
Upper Devonian 372.2 Ma
Frasnian
382.7 Ma
Givetian Pridolian
Devonian Middle Devonian Eifelian
387.7 Ma 423.0 Ma
Ludfordian
393.3 Ma 425.6 Ma
Gorstian 427.4 Ma
Emsian Homerian
430.5 Ma
Lower Devonian 407.6 Ma Sheinwoodian
433.4 Ma
Pragian 410.8 Ma
Lochkovian Telychian
419.2 Ma 438.5 Ma
Pridoli Aeronian
440.8 Ma
Ludlow Rhuddanian
443.4 Ma
Wenlock Hirnantian
445.2 Ma
Silurian
Llandovery Katian
453.0 Ma
Upper Ordovician Sandbian
458.4 Ma
Ordovician Middle Ordovician Darriwillian
467.3 Ma
Dapingian
Lower Ordovician 470.0 Ma
485.4 Ma Floian
Age 10
489.5 Ma
Furongian Jingshanian 477.7 Ma
Paibian 494.0 Ma
497.0 Ma
Guzhangian
500.5 Ma Tremadocian
Epoch 3 Drumian
504.5 Ma
Age 5
509.0 Ma
Age 4
Cambrian Epoch 2 514.0 Ma
Age 3
521.0 Ma
Age 2
529.0 Ma
Terreneuvian
Fortunian
541.0 Ma Stratigraphic time scale of the Palaeozoic
2.3.3.1
The Ediacaran and Phanerozoic-Precambrian boundary

The Ediacaran period ranged from 635 to 541 million ‘broke up’ rock formations and exposed new rock layers, the
years, roughly the timeframe since the glaciations of the chemical weathering subsequently released huge quantities
Cryogenian and the beginning of the Cambrian (and thus of phosphates into the ocean over a long period of time. This
the Phanerozoic). increased availability of phosphates likely contributed to the
Originally, the onset of the Cambrian was defined by the formation of massive algal blooms, preserved within the
first mass occurrence of fossils but subsequently fossils were Doushantuo formation (acritarchs). Emitted phosphates and
found in far older strata. The ‘Cambrian explosion’, i.e. the ascending iron (II) ions resulted in steep increases of atmos-
sudden appearance of fossils of many different metazoa pheric oxygen. As a result of increasing oxygen availability,
groups, is now recognised to date back to younger Precam- metazoans diversified. Although the fossil record provides
brian strata from the Ediacaran period. a poor reflection of this phenomenon (i.e. Ediacaran) since
The Ediacaran featured a variable climate, which led to these organisms still lacked hard skeletons.
local glaciation events (Gaskiers glaciation). These local gla- Ediacaran animals possessed a hydro skeleton. The most
ciations contrasted with glaciation events of the Cryogenian lineages were either osmotrophic, grazing on microbial
period, which were global in nature. mats or living in symbiosis with photosynthetic symbionts.
Apart from local glaciation events, the Ediacaran climate These symbionts lived either within the animal’s body or on
was generally warm. The sudden onset of global warming their outer surface membrane, as in the case of Dickinsonia,
triggered the sudden release of methane from methane clath- which was covered with a layer of cyanobacteria. Overall,
rates, which likely further accelerated the warming trend. the ‘Cambrian explosion’ lasted longer than the name sug-
Higher temperatures increased rock weathering and raised gests and took place largely before the Cambrian period itself
salinity levels in the oceans. After the glaciers physically started.
Ediacaran habitats and ecosystems are typically named Demospongiae) for multicellular organisms dates back to
after important fossil deposits such as the Avalon-type bio- 600–550 million years. Aerobic protozoa and simply-con-
ta (calm, undisturbed deposits within the continental shelf structed metazoans were able to survive in roughly one-hun-
region), White Sea-type biota (near shore facies marked by dredth of the present-day oxygen concentration. However,
the influence of waves and currents), and Nama-type biota rising oxygen concentrations served as a prerequisite for
(fluviomarine facies). The evolution of multicellular eukary- the evolution of more complex multicellular organisms. To
otes already began in the Middle Precambrian. The extremes that end, an atmospheric oxygen level equivalent to around
climatic fluctuations brought on by the glaciations of the one-tenth of present-day values is required for the synthesis
late Precambrian (possibly) accelerated their diversification. of collagen, which provides the basis for connective tissues
They became ecologically important organisms in particular in higher metazoans. The oxygenation of the atmosphere,
during the oxygenation of the deep oceans. roughly 635 million years ago, predates the oxygenation of
Molecular analyses suggest that multicellular metazoans the deep oceans by around 55 million years. In other words,
must have emerged before the Ediacaran. Even the biochem- the deep oceans were oxygenated around 580 million years
ical evidence for sponges reaches back to the Cryogenian. ago, an essential prerequisite for the settlement of the sea-
Fossil evidence (silicate needles from Hexactinellida and floor by larger eukaryotes.
Doushantuo-Formation: a fossil deposit of the Ediacarium ge- methane clathrate: (Lat.: clatratus = latticed) also methane
ological period in Guizhou Province, China hydrate; clathrates are chemical substances in gases (in this case
erniettomorphs: sessile, flat but non-fractal forms of Ediacaran methane) which trap host molecules (in this case water) in a lat-
fossils tice. Methane clathrates exist in permafrost and on the sea-bed
facies: characteristics of rocks related to the history of rock for- rangeomorphs: flat, sessile, fractal Ediacaran fossils
mation
See also: Metazoa: 4.2.1; Symbiosis: 4.2.2.5; Glaciation: 2.2.2.5

The term ‘Small-Shelly-Fauna’ summarizes

many mineralised fossils only a few millime-
tres in size dating back from the Upper Edi-
acaran to the Lower Cambrian. The simulta-
neous occurrence of exoskeletons in many
Cambrian organismal groups and the occurrence of
bore holes in shells suggests that increasing
predation was of central importance for the
evolution of external skeletons
Small-Shelly-Fauna (left) and
Kaiyangites sp. (right)
541 Ma
Phase 3 of the oxygenation of the deep The Nama-fauna (550–541 million years,
oceans: the isotropic distribution of sul- fluviomarine deposits) comprised rangeo-
phur suggests that bacterial sulfate dis- morphs and erniettomorphs. The Nama fauna
proportionation increasingly played a role. holds the oldest fossil evidence for biominer-
The bacterial sulfate disproportionation of alisation (for example, Cloudina and Namaca-
sulphur compounds requires intermediate lathus)
redox steps, an indication of rising oxygen Cloudinia sp.
availability The White Sea-fauna (560–550 million years)
is known for its high level of diversity, includ-
ing trace fossils and representatives of the
core group of Bilateria. These are coastal sed-
iments, influenced by wave and currents
Phase 2 of the oxygenation of the deep
oceans: the increased entry of oxygen Kimberella sp. Dickinsonia sp.
caused the oxidation of dissolved organic The Avalon-fauna (575–560 million years) is
carbon in the oceans. Reduction of sulfate dominated by rangeomorphs and cosmopol-
by bacteria remains the most important itan organisms such as Charniodiscus. These
pathway in the sulphur cycle are calm, undisturbed continental shelf de-
posits. There are no known trace fossils with-
in this fauna
Charniodiscus sp.
Around 582–580 million years ago, the Gaskiers glaciation led to the extinction of many acritarchs. Unlike the Cryogenian glaciations,
the Gaskiers was local in nature
The diversity of phytoplankton expanded
greatly after the Marinoan glaciation. This
trend is reflected by the diversity of acritarchs
Ediacarian in sediments from that time
Phase 1 of the oxygenation of the deep

oceans: the atmospheric oxygen content Cambrian acritarchs
increases. Rising sulfate and decreasing
sulfide concentrations in the sediments
allow to conclude on increasing oxygen
concentrations. In these early stages,
oxygen-rich conditions were short-term
around the edge of continental shelves,
whereas the deeper ocean remained an-
oxic
Precambrian Acritarchs (bottom-

right: selected detail)
635 Ma
During the Marinoan glaciation around 650–635 million years ago, the Earth was largely covered in ice. It is likely that only the
Cryogenian equatorial regions were ice-free at that point. However, in terrestrial habitats, the ice was likely pushed all the way to the equator
2.3.3.2
Evolution of skeletal elements

Animals encased by a protective housing had emerged by gae Coelastrum the cohesion of cells is only possible at higher
the end of the Precambrian. This casing was made of vari- calcium concentrations.
ous materials, including organic materials, chitin, phosphate, Increasing predation then promoted the formation of
carbonate, and silicate. After the emergence of the first pred- hard skeletons in many organismal groups during the Low-
ators, the fauna was dominated by animals able to dig them- er Cambrian. Endo- and exo-skeletons (calcified skeletons
selves down into the sediment or those possessing skeletons. emerged around 549 million years ago) occurred almost si-
The most important mineral within Precambrian animal multaneously in various animal phyla at the Cambrian bor-
skeletons was apatite (calcium phosphate), whereas calcium der. Hard skeletal elements also served as a starting point for
carbonate prevailed from the Ordovician. muscles, vital in locomotion and feeding activities, and also
The development of hard tissue served a number of func- served to increase UV protection during the colonisation of
tions. Originally, the biomineralisation served the calcium the shallow seas.
detoxification and developed as a result from changing oce- The sponge or cnidarian Namapoikia rietoogensis (up to 1 m
anic chemistry: since calcium can be toxic in higher concen- in diameter and 25 cm in height) was one of the first organ-
trations, the calcium stress of the organisms increased with isms to display skeletal elements. The Small-Shelly-Fauna
increasing calcium concentration in sea water. Therefore, the then developed in the Lower Cambrian (Terreneuvian). Its
organisms increasingly developed protection mechanisms. fossils are preserved largely as a result of secondary phospha-
Biomineralisation probably originated as a detoxification tisation (recrystallisation of skeletal elements into apatite).
process. The emergence of multicellularity seems to have This fossilisation process became less frequent throughout
been related to increasing calcium concentrations; for exam- the course of the Lower Cambrian.
ple, in both a number of sponge species and in the green al-
Changes in marine chemistry were the geochemical pre- of the evolution of the respective organisms: calcite was fa-
requisite for the formation of carbon skeletons. Sodium voured under conditions of low magnesium concentrations
carbonate was increasingly replaced by calcium carbonate. whereas, at higher magnesium concentrations, the formation
First, the biochemically simpler but energetically more ex- of calcite was inhibited. Aragonite crystal lattices do not in-
pensive calcium phosphate precipitation was established. corporate magnesium, but the compound can still be formed
The energetically favourable carbon carbonate was formed under high magnesium conditions. Additionally, aragonite
later on, and has prevailed ever since. Vertebrates possess forms more readily under higher temperatures whereas cal-
calcium phosphate skeletons, but these remain due to the cite is more likely to form in colder conditions.
requirement of phosphates in high levels of muscle activity In the Upper Ediacaran, predominantly aragonitic skeletal
and the formation of neural tissue. elements evolved, whereas calcitic skeletal elements emerged
In addition to calcium phosphate skeletons (apatite: during the Terreneuvian. Calcitic skeletal elements can be
Ca5[(F,Cl,OH)(PO4)3]), silicate and carbonate skeletons are found in echinoderms, calcareous sponges, brachiopods, and
common. Calcium carbonate skeletons of some organisms arthropods. At the same time, molluscs, coelenterates, and
are constructed of either aragonite or calcite. This difference bryozoans have skeletons made of different minerals, includ-
is likely linked to the particular marine chemistry at the time ing aragonite.
aragonite: an orthorhombic crystal made of calcium carbonate endoskeleton: (Grk.: endon = inside, skeletos = frame) inner
(CaCO3) support structure (e.g. bones in vertebrates)
calcite: trigonal crystal made of calcium carbonate (CaCO3); con- exoskeleton: (Grk.: exo = outside, skeletos = frame) external
stituent of numerous biogenic sediment support structure (e.g. shells in molluscs and brachiopods
detoxification: process of detoxifying
See also: Mineralisation: 4.5.2, 4.5.2.1; Protection: 4.4.3.1

Outer armor, either as external skeletons (left) or bark (centre), plays a central protective role for a number of organisms. Exoskeletons appeared simul-
taneously in a broad range of organisms within a short timeframe. It is therefore likely that increased predation may have played a role in the evolution
and especially in the radiation of exoskeleton-bearing organisms. At the same time, many elements of the skeletal system also serve as starting points
for a more developed musculoskeletal system; in other words, predator protection and mobility also likely evolved in parallel. The occurrence of Small-
Shelly-Fauna organisms (right) in the uppermost Precambrian is interpreted as a reaction to increased predation by larger, multicellular organisms
The evolution of protective elements and skeletons must

be interpreted in the context of the evolution of preda-
tors and their mouthparts – their assault weapons. Similar
relationships can also be understood within the develop-
ment of military technology. By this analogy, increasing
external armour is highly effective as long as it reduces
the risk of damage caused by predator‘s mouthparts. In
the early evolution of fish, when jawless fish (top-left, a
modern-day lamprey) dominated, no strong armour was
necessary. This dynamic changed as simple mandibular
joints evolved and outer armour was developed to offer
protection from the stronger predatorial bite force. This
trend can be observed in the Dunkleosteus, the armored
fish (middle-left). The parallel development of strong-
er-hitting weapons is comparable to the increasing out-
er armour carried by a knight. However, armour is often
associated with a restriction of mobility. Therefore, a fur-
ther increase of armour is, also at increasing efficiency of
mouthparts or weapons, not useful. On the contrary, he
armour now causing more of a hindrance to the increas-
ingly important need for flexibility and mobility. Modern
fish (bottom-left, here an recent shark) are therefore not
or only lightly armored, but are agile and flexible swim-
mers. Again, similar to the development of military tech-
nology, the development of stronger-hitting weapons,
especially firearms, is associated with an increase in flexi-
bility and manoeuvrability at the expense of armor
2.3.3.3
The Cambrian period

The Cambrian period stretches between 541 and 485 mil- level and an increase in atmospheric carbon dioxide concen-
lion years. It is divided into four epochs, the Terreneuvian trations to around 4.5 ‰, roughly 15 times the present value.
(541–521 million years ago), Epoch 2 (521–509 million years This was the highest atmospheric carbon dioxide concentra-
ago), Epoch 3 (509–497 million years ago), and the Furongi- tion in the Phanerozoic. At the same time, the concentration
an (497–485 million years ago). of oxygen increased slightly during the Cambrian, remaining
During the Cambrian, the planet’s large land masses were lower than it is today, at around 14 %.
largely located south of the equator. These continents were Almost all modern animal phyla developed during the
the Laurentia (parts of North America and Greenland), Bal- Cambrian period. During the same time period, many spe-
tica (North-East Europe) and Siberia, as well as the large cies developed hard skeletal parts or housing. It is thought
southern continent Gondwana. Gondwana comprised the that the almost simultaneous development of skeletal ele-
land masses of Africa, South America, India, Madagascar, ments in many organismal groups was an adaptation to in-
Australia, Antarctica, Saudi Arabia, as well as smaller sub- creases in predation. For these hard parts of the skeleton are
continents. The Iapetus Ocean separated Gondwana from better fossil records, the number of fossils sharply increased.
the northern continents and the Panthalassic Ocean took up No land plants are known from the Cambrian period,
most of the northern hemisphere. The global climate warmed though terrestrial fungi are thought to have existed; their fos-
strongly during the Cambrian, accompanied by a rising sea sils are, however, controversial.
The ‘Cambrian explosion’, hence the sudden improve- organisms pushed biogenic calcium carbonates and calcium
ment of the fossil record is largely due to the increasing prev- phosphates out of their cells, was fundamental in the devel-
alence of animal groups with hard shells and housings. The opment of exoskeletons.
first animals with small skeletal elements emerged around Calcareous exoskeletons, in turn, provided protection
the Proterozoic/Cambrian boundary. Changes in marine from predators. Furthermore, a variety of different forms of
chemistry coupled with increased pressure from the rising body armour appeared in the lowermost Cambrian, rang-
prevalence of predators then contributed to the further devel- ing from continuous shells to individual sclerites, a series of
opment of the Cambrian explosion. plates which together connects into a chainmail-type armor.
At the transition between the Precambrian and Cambrian, Shells were the dominant form of body armour from the
sea level rose and flooded many areas along the edges of Middle Cambrian, offering better protection from predators.
continental plates, forming extensive shelf zones. The trans- This development suggests that the evolution of outer ar-
gression of the oceans increased rates of silicate weathering mour was associated with the rise of jaw- and tooth-bearing
and thus the input of ions in the oceans. The ion input initial- predators, such as Anomalocaris.
ly led to increased precipitation of carbonate, thus reducing The increase of shell use also suggests increases in oce-
the alkalinity of the oceans. Further ionic increases led to anic oxygen concentrations: the planar Ediacaran animals
heightened ion concentrations in the sea, especially of cal- only required oxygen concentrations of around 8 % of mod-
cium. ern-day values but, due to limitations in diffusion across the
Organisms had to develop mechanisms of transporting body surface, animals with exoskeletons required oxygen
otherwise toxic levels of excess calcium from their cells, concentration with at least above 10 % of modern-day values
against a diffusion gradient. The excretion process, whereby (i.e. 2 %).
sclerite: hard parts in the body of invertebrates transgression: marine transgression takes place when the sea
advances rapidly into continental regions and is caused by a drop
in the sea floor or a rise in sea level
See also: Hard skeleton: 2.3.3.2; Metazoa: 4.2.1; Fungi: 4.2.2.3

The first forerunner of the vertebrates arose in the Cambrian. The species There were no land plants in the Cambrian. Fossil Acritarchs (here:
Pikaia gracilens, which belonged to the Cephalochordata, is regarded as Timofeevia lancarae) help document a broad diversity of eukaryotic algae,
the oldest known representative of the Chordata even if their systematic assignment remains unclear
Panthalassic Ocean
Siberia
Laurentia
Gondwana
Baltica
Iapetus Ocean
Sahara India
Cape Siberia
Cambrian fossil reef (right): One of the most important reef-building organisms Persian Gulf Ruhr area
from the Cambrian were primitive corals (top-left: Protolyellia sp.) and the
Great Lakes South China
sponge-related Arcaheocyathids (bottom-left)
Mexico Australia
Amazon Basin Antarctica
Castericystis vali was a 7 cm long metazoan from Trilobites occurred from the second epoch of Graptolites are an extinct group of animals, likely
the Middle Cambrian. Its phylogenetic classifica- the Cambrian and served as a major component belonging to the hemichordates. The genus
tion is controversial, perhaps it might group with in the Cambrian fossil record from that point on. Dictyonema, a representative of the Dendroidea,
the echinoderms Shown here is the species Ellipsocephalus hoffi, lived during the Cambrian and Silurian
which belongs to the Ptychopariida
2.3.3.4
The Ordovician period

The Ordovician period ranges between 485 and 443 mil- first graptolites and bryozoa can be found in great numbers
lion years ago and is divided into the Lower (485–470 million within the Ordovician fossil record. Within the vertebrates,
years ago), Middle (470–458 million years ago), and Upper different lineages of jawless fish and the conodonts appeared.
(458–443 million years ago) epochs. Plants colonised the land in the Upper Ordovician, ini-
During the Ordovician, Laurentia and Siberia drifted tially moss-like organisms whereas vascular plants evolved
northward towards the equator. At the same time, Baltica later. The colonisation of terrestrial habitats by land plants
also drifted northward and slightly away from Gondwana. increased chemical weathering, which in turn increased
Laurentia and Baltica drifted towards each other and the the release of calcium, magnesium, and iron. In effect, car-
Iapetus Ocean, which separated to the two continents, be- bonate depositions in the oceans increased. This phenom-
gan to close. During the Lower Ordovician, the climate was enon eventually reduced the concentration of atmospheric
still very warm and the poles were not frozen yet. However, carbon dioxide through balanced reactions. Therefore, the
the Upper Ordovician included one of the largest glaciation colonisation of terrestrial habitats by plants is presumably
events of the Phanerozoic, covering a vast majority of the causally related to the cooling and subsequent glaciation of
southern hemisphere in ice. the planet in the Upper Ordovician. Furthermore, the ocean-
Biodiversity increased markedly during the Ordovician, in ic currents likely shifted at the beginning of the Ordovician
particular featuring an explosion of (food) specialist species, Ice Age, moving oxygen-poor deep waters to shallow shelf
following on from the Cambrian domination of generalists. areas.
Corals also formed in the oceans, especially Rugosa and The late-Ordovician glaciation led to a mass extinction
Tabulata, as well as bryozoans and stromatoporoids making event, causing many families of organisms to completely go
up major reef components. The brachiopods underwent a extinct. In the ocean, around 57 % of genera and 80 % of
strong radiation during the Ordovician and became a domi- species disappeared, especially those living in deeper marine
nant group of marine benthic filter feeders. In addition, the habitats.
Jawless fish can be found in fossils dating back to the The myelin sheath, which surrounds nerve fibers, is also a
Upper Cambrian, though the group underwent a radiation differentiation of the neural crest cells and its presence ena-
not before the Ordovician period. In addition to the cono- bles a faster stimulus conduction compared to invertebrates:
donts, the polyphyletic ‘Agnatha’ (jawless organisms) and vertebrates can reach action potential speeds of 50–100 m/s
chondrichthyes (cartilaginous fish) were present during the with an axon diameter of only 1–40 µm, compared with in-
Ordovician. vertebrates reaching speeds of only 1 m/s (with the exception
A key evolutionary step within the development of verte- of cephalopods, which increase their action potential speed
brates was the emergence of a new embryonic cell type from through a broadening of the nerve by several millimetres).
which the neural tube and subsequently the central nervous The myelin sheath is therefore of central importance for the
system with brain and spinal cord, gill apparatus, and senso- evolution of animals with larger bodies.
ry organs (eyes, nose) emerged. This new cell type therefore The development of the myelin sheath appears to have
enabled the development of a novel body plan, in particular accompanied the emergence of jaws. Recent jawless species
related to the development of a head with complex sensory have no myelin sheath, and presumably this was missing in
organs. This new body shape gave organisms the ability to the extinct ostracoderms and conodonts. The Chondrichthy-
orient themselves directionally, a change that likely played es already had a myelin sheath. It is therefore likely that the
an important role in the subsequent shift in dietary habit sheath arose before the Chondrichthyes lineage split from the
from filter feeding to active predation. A funnel-like sucking other Gnathostomata during the Ordovician.
mouth, such as the one in recent lampreys, can be seen for
the first time in jawless fish fossils from the Cambrian.
bryozoa: moss animals, classified among the protostomes Rugosa: ‘wrinkled’ coral; Palaeozoic coral taxon with additional
continental shelf: underwater landmass extending out from septa in only four of the six sectors, therefore displaying bilateral
the edge of a continent (up to a depth of 200 m) symmetry
generalists: organisms able to survive under a variety of con- stromatoporoida: extinct, colony-forming organisms classified
ditions as sponges which were important reef-formers in the Silurian and
graptolites: extinct fossil colonial animals with a chitin-like ex- Devonian
oskeleton (thecae) Tabulata: Palaeozoic group of corals; they always possess six
septa (therefore displaying radial symmetry) but they are often
incomplete
See also: Reef forming organisms: 2.3.2.2; ‘Agnatha’: 4.2.1.7, 4.2.1.8

Jawless fish dominated during the Ordovician, including Sacabambaspis The first trilete spores also occurred during the Ordovician. Trilete spores
sp., with its characteristic frontally positioned eyes. The first jaw-bearing show a three-Y-shaped arrangement of colpi, such as present in club
fish (Gnathostomata) developed in the Upper Ordovician mosses and ferns: Ambitisporites avitus (above-left), Ambitisporites sp.
(bottom-left), Synorisporites sp. (middle), and two other unidentified
trilete spores (right)
Panthalassic Ocean
Siberia
Laurentia
an
ce
sO
Gondwana
tu
Baltica
pe
Ia
Rheic Ocean
Sahara India
Cape Siberia
Conodonts, first detected in the Upper Cambrian fossil record, radiated mark- Persian Gulf Ruhr Area
edly during the Ordovician, and remain important index fossils. Mostly, these
are represented by tooth-like structures (top: Lenodus variabilis), with the fossil
record rarely displaying entire animals (bottom: sketch of a conodont animal) Mexico Australia
Seelilien
(Ordovizium)
Graptolites are among the most important The Crinoidea (sea lilies) radiated rapidly The trilobites order Asaphida (here: Subasaphus
Ordovician index fossils. Dichograptidae is only during the Ordovician and were an important platyurus) is recorded from the Upper Cambrium
known from the Ordovician (here: Didymograptus component of marine benthic fauna (here: until the Silurian.
murchisoni) and are characterised by having Anthracocrinus primitivus)
several branches with a characteristic divergence
angle of under 180°
2.3.3.5
The Silurian period

The Silurian period ranges from 443 to 419 million years the continental shelves. As a result of the rapidly spreading
and is divided into the Llandovery (443–433 million years), terrestrial vegetation, levels of atmospheric carbon dioxide
Wenlock (433–4276 mya), Ludlow (427–423 million years), decreased whereas oxygen concentrations rose.
and the Pridoli (423–419 million years) epochs. At low latitudes, extensive reefs formed in the shallow seas.
Laurentia and Baltica collided in the lower Silurian, clos- Corals (Tabulata and Rugosa) were important reef-builders.
ing the Iapetus Ocean and subducting the oceanic plate un- The first jawed vertebrates, gnathostomata, also emerged in
derneath the two continents. The merge of Laurentia and the Silurian. The first Placodermi emerged in the Lower Si-
Baltica created the super continent Laurussia (= old red lurian and the first bony fish are thought to have appeared in
continent, named after its characteristic reddish sandstone) the Upper Silurian.
and formed the Caledonian orogenic belt. In the Silurian, the The first vascular plants arose in the Middle Silurian: pri-
Rheic Ocean reached its maximum extension. In the Upper mordial plants, such as Rhyniophytina, as well as the Zos-
Silurian, the Hun-Superterrane broke off from the northern terophyllopsida, presumably an evolutionary link between
edge of Gondwana and drifted northward towards Lauras- the Rhyniophytina and the club mosses. For example, mem-
sia. The Rheic Ocean, located between the Hun-Superter- bers of the genus Cooksonia (Rhyniophytina) spread across
rane and Laurussia, was subducted underneath the Hun-Su- Laurussia and members of Baragwanathia (Zosterophyllop-
perterrane and the Palaeo-Tethys Ocean began to open. The sida) spread across Gondwana. The earliest vascular plants
Silurian climate was again generally temperate to warm, and branched dichotomously and had no leaves. The oldest con-
the occurrence of glaciation events is backed up only by rare firmed lichen fossils date back to the Silurian whereas lichen
and anecdotal evidence. During the Silurian, the sea level fossils from the Ediacaran remain unconfirmed.
was very high, thus forming extensive shallow seas along
Liverwort-like plants first emerged in the Ordovician, for example, this was evident in the genus Cooksonia. Plant
though perhaps even in the Upper Cambrian. Moreover, in specimens were markedly larger in samples from the Upper
the Upper Ordovician, communities of liverworts and cen- Silurian. The first rhyniophytes displayed pseudomonopodi-
tipedes broke the hitherto dominant microbial mat arrange- al branches with lateral sporangia. Rhizomatous dispersal
ments found in most moist terrestrial habitats. also emerged during the Upper Silurian. Zosterophyllopsida
Spores from vascular plants can be traced back to the up- with fertile strobili are known from the lowermost Devonian
permost Ordovician whereas the plant bodies themselves (Lochkovian epoch). During the Upper Silurian and Lower
can only be identified in Silurian fossils. The primordial land Devonian, plants with real roots emerged, including Barag-
plants were dichotomously branched and creeping, with only wanathia. As a result, plants increasingly began to influence
their terminal branches bent upward and featuring terminal the structure of the soil as well as weathering patterns. At
sporangia. During the Middle Silurian (Wenloch epoch), the the same time, the complexity of the sporophyte increased
height of plants and the size of sporangia began to grow; during the Upper Silurian and Lower Devonian.
dichotomous: (Grk.: dichotomos = in two parts) splitting of a lateral: sideways or a side part of something
shoot axis into two parts Palaeo-Tethys Ocean: ancient ocean between Laurussia and
fertile strobili: fertile cones Gondwana; it began to form in the Upper Silurian, was most
Hun-Superterran: 1.2 billion-year-old fluvial sedimentary for- expansive in the Lower Carboniferous (Mississippian) and closed
mation in Canada (Summerset Island, Nunavut, Canada) in the Triassic
Iapetus: early Palaeozoic ocean between Baltica and Laurentia sporophyte: spore-producing diploid generation in the alterna-
between 700 and 400 million years ago tion of generations in land plants
See also: Liverwort: 4.4.3.2

Phylogenetic analyses place genus Jamoytius (below) with the ancestors The genus Cooksonia (left, arrow) is one of the oldest land plants. Its leaf-
of gnathostomata. During the Silurian, the first jawed and armored (pla- less axes were forked and possessed stomata and terminal sporangia. The
coderms) fish emerged from this lineage. The seas were still dominated genus Cosmoclaina (right) is considered to be a multicellular tissue-form-
by jawless fish ing algae belonging to the Nematophytales
Panthalassic Ocean
Siberia
Laurentia
Baltica
ne
e rra Gondwana
rt
pe
Iapetus Su
Rheic Ocean n-
Ocean Hu
Sahara India
Cape Siberia
The extinct Eurypteridae (here: Eurypterus remipes) lived from the Silurian to Persian Gulf Ruhr area
the Devonian and are considered to be arthropodes. They are characterised by Great Lakes South China
the last prosomal (‘head’) extremity-pair serving as a swim organ
Mexico Australia
The echinoderm Paracrinoidea were, along with Tabulate corals (tabulata) were among the most Rugose corals (rugosa) were the second major
the corals, important representatives within the important Silurian reef-builders Silurian coral group
marine benthic fauna
2.3.3.6
Colonisation of terrestrial environments

Many groups of organisms independently colonised the change. Adaptations to the challenges of life on land evolved
terrestrial environment. At first, prokaryotes appeared on independently – convergently – across different organismal
land likely around 2,600 million years ago, with confirmed groups.
microfossils dating back to 800–1,200 million years. The Importantly, these include the development of respiratory
formation of the ozone layer, which reduced UV radiation, organs and systems that are able to breathe air, including the
was vital in the colonisation of land by higher eukaryotes. lungs of vertebrates and terrestrial snails, the book lungs of
Apart from prokaryotes and protists, various groups inde- spiders, and the tracheal system of other arthropods. Plants,
pendently colonised the terrestrial habitat, specifically the on the other hand, developed stomata and intercellular sys-
Platyhelminthes, Nemertea, Nematoda, Annelida, Mollusca tems for conducting gases.
(Pulmonada and Prosobranchia), Crustacea (Amphipoda, Different land-colonizing groups of organisms also devel-
Isopoda, Decapoda), the Chelicerata, Onychophora, Myr- oped a range of tissues serving to reduce evaporation and
iapoda, Hexapoda, and the Vertebrata. It remains unclear reduce the risk of dehydration. At the same time, these tis-
whether the ancestor of all land plants colonised land at sues usually also offer protection from the sun’s UV radia-
a singular occurrence or whether the splitting-off of some tion, which is higher on land. Such tissues include the epi-
bryophyte lineages, specifically of the liverworts, occurred dermis, cuticle, bark of seed plants, and waxes. Life on land
before colonisation of terrestrial habitats and these groups also had to develop water-independent ways to reproduce,
came ashore independently. often by the formation of protective outer shells around their
Terrestrial life is fundamentally different from life in wa- propagules (seeds or eggs) or the relocation of fertilisation to
ter; survival on land requires a variety of physiological ad- within the parental organisms themselves
justments to characteristics of the terrestrial environment, Finally, supportive tissues and structures, such as wood or
which include the lowered buoyancy in air compared to wa- skeletons, also developed differently on land across organis-
ter, the risk of dehydration, and the requirements of gas ex- mal groups.
In general, terrestrial primary producers and terrestri- ship involves the evolution of detoxifying enzymes in ani-
al food webs are a prerequisite for the colonisation of land mals as well as an increase in the presence of sporopollenin,
by animals. Nevertheless, it is possible that arthropods col- and thus in the thickness of spore walls in plants. Thus, fungi
onised terrestrial habitats before the vascular plants. Rep- and herbivores were only able to efficiently exploit plant bio-
resentatives of the first terrestrial fauna probably lived as mass by the end of the Carboniferous period
detritivores on the basis of the biomass produced by algae, The colonisation of terrestrial habitats was made most-
lichens, and mosses. ly from fresh water (vertebrates, land plants, Annelida [Oli-
The first vascular plants were hardly eaten by animals: gochaeta]). Some organismal groups were able to reach the
lignin and the toxic by-products of lignin synthesis led to a terrestrial environment by way of interstitial habitats (for ex-
decoupling of terrestrial primary production and the deg- ample, nematodes), or directly from marine habitats such as
radation of organic material until the Carboniferous. The the marine littoral, salt marshes, or mangroves (for example,
lignin-synthesizing peroxidases of fungi arose only in the Pulmonata, Isopoda, Chelicerata). Most waves of terrestri-
uppermost Carboniferous. In addition, vertebrate and insect al colonisation by animals were correlated with periods of
herbivory also developed in the Carboniferous: these early elevated atmospheric oxygen, allowing for the survival of
herbivores were initially specialised to consume the mostly organisms with yet underdeveloped breathing organs. This
non-toxic plant parts (young shoots, seeds, spores) and broke holds particularly true for the terrestrial colonisation by ar-
down their plant food with the help of symbiotic fungi and thropods during the Silurian, but also for the diversification
bacteria. To that end, the coevolution between plants and of terrestrial tetrapods during the Carboniferous.
herbivorous insects arose in the Carboniferous: this relation-
detoxification: process of detoxifying lignin: (Lat.: lignum = wood) various phenolic macromolecules
detritivore: feeding on organic detritus and decomposing which are stored in the cell walls of plants and which make them
plant and animal matter woody
herbivores: (Lat.: herba = plant, vorare = to eat) plant-eaters: sporopollenin: main component of the exospores in the spores
animals subsisting exclusively on plants of spore-producing plants (bryophytes, ferns) and the external
interstitial: fluid-filled porous spaces in aquatic sediments wall (exine) of pollen grains
See also: Amnion: 2.3.4.2; Adaptation to terrestrial habitats: 2.3.4.2; Co-evolution: 4.4.3.9, 4.4.3.8; Cormus: 2.3.3.10
The colonisation of the terrestrial environ-

Neogene ment is a still ongoing process. Through-
23 Ma out the planet’s history, terrestrial species
have evolved in a number of different or-
ganismal groups. Other lineages have de-
Palaeogene veloped adaptations to an only temporary
terrestrial lifestyle. Deserts, in particular,
form physical boundaries for the colonisa-
66 Ma tion of land by certain organismal groups Sand dunes in the Sahara
Land snails (Pulmonata) and also terres-

trial annelids may have emerged as early
Cretaceous as in the Devonian or the Carboniferous
periods. The exact time of transition to
terrestrial life remains controversial within
the academic literature
145 Ma Land snail fossils
After plants and animals had colonised

Jurassic
terrestrial habitats the interaction be-
tween both groups was initially decou-
pled. Herbivory began during the Carbon-
201 Ma iferous. Since this period feeding traces
can be found on fossilised parts of plants.
The radiation of insects was connected to
Triassic the coevolution of insects and plants
Fossilised feeding damage (Neogene) Fossilised lacewing (Cretaceous)
252 Ma The Ichthyostega lived in the Upper Devo-

nian represented one of the first tempo-
rarily terrestrial tetrapods. These species
Permian are characterised by a number of special
features, such as seven toes, a very rigid
chest with overlapping ribs, and – unusual
298 Ma for tetrapods – very long forelimbs rela-
tively to their hindlimbs
Limb of Ichthyostega Skull of Ichthyostega
Carboniferous It is possible that arthropods colonised

the terrestrial environment before the
land plants. With the advent of liverworts,
the early relationships between microbial
359 Ma
mats and fungi were replaced by associa-
tions between liverworts and myriapods
or other terrestrial arthropods
Devonian
Fossilised spiders (Cretaceous)
The oldest fossil fungal spores can be

419 Ma
dated back to the Ordovician. During this
Silurian period and the Silurian, plants colonised
terrestrial habitats. The first land animals
443 Ma were detritivores, feeding on microbial
mats and organic materials recycled by
fungi and bacteria
Ordovician
Fossil fungal spores (Ordovician)
485 Ma
Microbial mats appeared on land around
1.6 billion years ago. Since the late Pre-
cambrian or early Palaeozoic, these ter-
Cambrian restrial microbial mats likely comprised cy-
anobacteria and heterotrophic bacteria, as
well as various eukaryotic algae and fungi
541 Ma
Microbial mat from the Lower Cambrian Shiynatou-formation

2.3.3.7
The Devonian period

The Devonian period ranges from 419 to 358 million years the same time, trilobites were in decline, perhaps due to the
and is divided into the Lower (419–393 million years), Mid- emergence of fish with jaws. The Placodermi (armored fish)
dle (393–382 million years), and Upper Devonian (382–358 emerged as the most diverse vertebrate group, including the
million years) epochs. largest living predatory fish of the time, growing to around
The Caledonian orogeny, between the former continents 10 m in length. The Placodermi died out by the end of the
Baltica and Laurentia, continued into the Devonian. The Devonian. Spiny sharks also reached their greatest diversity
Rheic Ocean was subducted as a result of micro-continents during the Devonian, though they went extinct by the Per-
(Hun-Superterrane, Armorica) drifting from Gondwana to- mian.
wards Laurussia, opening up the Palaeo-Tethys. The Rhe- During the Devonian lungfish and coelacanths developed;
noherzynic Ocean, which emerged from the Rheic Ocean, from the latest Upper Devonian the first tetrapoda (land ver-
formed within the collision area between the micro-conti- tebrates) are known. These include the genera belonging to
nents and Laurussia. It began to close again during the De- the Labyrinthodontia Ichthyostega and Acanthostega. On land
vonian as a result of the collision between Laurussia and the first winged insects emerged in the Devonian.
Gondwana. The rocks of the Rhenish Massif were formed During the Devonian, primordial fern-like and lyco-
within these sedimentary basins. The Devonian climate was pod-like vascular plants further spread out. From the De-
warm and dry and the temperature difference between the vonian period, the first secured findings of mycorrhizal are
equatorial and polar regions was lower than it is today. The recorded. The plants increased in size During the Devoni-
sea level remained high. During the Upper Devonian tem- an period. In the Upper Devonian first forests with tree-like
peratures cooled down. As a result, a further glaciation event ferns and lycopods developed in tropical swamps. For the
occurred at the polar regions. This cooling may have been first time flat leaves and flowers developed. True seeds first
the cause of the Upper Devonian extinction events; in par- emerged in the Upper Devonian. Atmospheric carbon diox-
ticular, marine fauna has been affected, including trilobites, ide concentration decreased and the oxygen concentration
corals, brachiopods, and fish. The heavily armored early Pal- strongly increased due to the increasing primary production
aeozoic fish species were increasingly replaced by sharks and by land plants and increased weathering processes associated
bony fish. Terrestrial taxa were less affected. with the spread of land plants. Terrestrial food webs had to
The Ammonoidea, which were important macro in- arise. Therefore, a large proportion of plant biomass was not
dex-fossils for the Middle Devonian to the Upper Mesozo- initially decomposed, but deposited.
ic, developed during the uppermost Lower Devonian. At
The first land plants were still missing megaphylls (flat er hand, were less prone to overheating during the Lower
leaves). Lower Devonian plants still had no leaves, with the Devonian. Levels of atmospheric carbon dioxide strongly
exception of, for example Eophyllophyton, which carried very decreased during the course of the Devonian as a result of
small (< 5 mm wide) leaves. Although flat leaves would pro- plant photosynthesis and, on the other hand, indirectly as a
vide a higher photosynthetic capacity, large flat leaves did result of stronger chemical weathering by plant roots: More
only develop during the course of the Upper Devonian ions entered the oceans forming, above all, calcium and mag-
The relatively late appearance of flat plant leaves can be nesium carbonates.
attributed to the high concentrations of atmospheric car- Levels of atmospheric carbon dioxide therefore dropped
bon dioxide and otherwise generally unfavourable climatic as plants increased their presence in the terrestrial environ-
conditions during the Devonian. The number of stomata is ment. Consequently, the size of plant leaves suddenly began
correlated with carbon dioxide concentrations: lower levels to grow and the up-to-eightfold increase in stomatal density
lead to many stomata, higher levels of atmospheric carbon ensured a volume of transpiration sufficient to prevent over-
dioxide lead to plants possessing fewer stomata. During heating. As a consequence of the increased leaf size and as-
the course of the Devonian plants developed only few sto- sociated rates of transpiration, Devonian plants also devel-
mata. As a result, transpiration was characteristically low oped improved vascular bundles.
and leaves would often overheat; leafless stems, on the oth-
stomata: pore in a plant which serves to regulate gas exchange

with the environment; the resultant transpiration cools the tissue
See also: Vascular bundles: 4.4.3.4; Telome: 2.3.3.10

The bones in the pectoral fin of the Devonian fish Eusthenopteron (left: Land plants in the Devonian featured the first tree-like plants as well as
Sarcopterygii) are likely homologous to the arm of tetrapods, such as that the first flat (two-dimensional) leaves. The genus Archaeopteris grew to
shown here in the amphib Acanthostega (right). The number of fingers over 30 m in height and had flat but slit fronds. Since this species was
and toes deviated from the typical tetrapod body plan: Acanthostega had deciduous, their fronds were frequently observed in the fossil record
eight fingers and seven toes
humerus
radius
ulna
digiti (finger)
Panthalassic Ocean
Siberia
Palaeo-Tethys
Ocean
Baltica
Laurentia
n
cea
e ic O
Rh
Gondwana
Sahara India
Cape Siberia
Palaeozoic reef formation reached a climax during the Devonian. Corals of the Persian Gulf Ruhr area
genus Hexagonaria (above) were widespread within Devonian reefs. Following Great Lakes South China
the mass extinction event at the end of the Devonian, reefs only recovered
Mexico Australia
again during the Mesozoic
Brachiopods were a significant component Nautiloidea emerged during the Devonian; it The Goniatitida emerged during the Devonian.
of the Devonian marine benthic fauna. Broad remains the only extant group of Nautiloidea They were the most common group of Ammo-
shells were typical of the Devonian brachiopods, (here: member of family Rutoceratidae) noidea until their extinction at end of the Permi-
typified in the species Plicathyris ezquarrai (top) an. The surface of their shell features a series of
and Mucrospirifer thedfordensis (bottom) narrow, wavy sutures
2.3.3.8
The Carboniferous period

The Carboniferous period ranged between 358 and 298 a result, carbon dioxide was progressively withdrawn from
million years ago. The Carboniferous is divided into two the atmosphere and atmospheric oxygen concentrations rose
epochs, the Mississippian (358–323 million years ago) and to around 35 % during the Carboniferous. These changes
the Pennsylvanian (323–298 million years ago), which are reduced the greenhouse effect and cooled the planet, lead-
further divided into the Lower (Tournaisian, 358–346 mil- ing to several cooler periods and partial glaciations around
lion years ago), Middle (Visean, 346–330 million years ago), the South Pole. The strongest cooling event and climax was
and Upper Mississippian epochs (Serpukhovian, 330–323 the Permo-Carboniferous glaciation that covered much of
million years ago) and the Lower (Bashkirian, 323–315 mil- Gondwana with ice. Traces of this glaciation can be seen in
lion years ago), Middle (Moscovian, 315–307 million years the fossil record of glacial sediment (tillites) found, for exam-
ago), and Upper Pennsylvanian (Kasimovian + Gzhelian, ple, in the present-day Sahara.
303–298 million years ago) epochs. Following the late-Devonian mass extinction, the oceans
During this time, the mega-continents Laurussia and were likely relatively oxygen-poor for a long period. This
Gondwana drifted towards each other. They collided already timeframe is characterised by a sparse fossil record, and is
during the Devonian with the smaller continents lying in be- referred to as the ‘Romer Gap’ after palaeontologist Alfred
tween. These collisions were the starting point of the Var- Romer. Marine animal diversity and radiations of different
iscan orogeny (upfolding of mountains), which continued animal groups only recovered in the middle of the Lower Car-
through the Lower Carboniferous and led to the upfolding of boniferous. Ray-finned fish and ammonoids developed into
mountains in large areas of Central Europe, North America, the major components of the pelagic fauna. Foraminifera,
and Asia. The collision between Laurussia and Gondwana especially Fusulinida, and bryozoans were prominent with-
led to the super continent Pangaea, which in turn was finally in benthic ecosystems. On land, high oxygen concentrations
formed by Siberia‘s collision with this continent during the promoted animal gigantism, including in the dragonfly Meg-
Permian. aneura, which had a wingspan of 70 cm and the spider-like
During the Carboniferous, extensive tropical and subtrop- extinct Eurypterid group comprising genus Megarachne, with
ical forests fixed large volumes of carbon dioxide. Much of a body length of 60 cm. Land snails and land-dwelling anne-
the Upper Carboniferous biomass was deposited as coal. As lids also emerged at the latest in the Carboniferous.
Erosion rates intensified as a result of the orogeny caused rope and eastern North America ultimately filled the coastal
by the collision between Laurussia and Gondwana, increas- marshes (coal forest habitats) with rock debris. Lycophytes
ing ionic deposits in the oceans. This process led to further dominant in the coal forests of the Lower and Middle Car-
carbonate deposition and subsequently to a further reduction boniferous significantly declined. Carbon dioxide fixation by
in atmospheric carbon dioxide concentrations. Extensive gla- photosynthesis also decreased and the Upper Carboniferous
ciers were formed in the mountains of southern Gondwana, climate became increasingly drier and warmer.
contributing to, on the one hand, climatic cooling (ice and The cool, temperate areas of Gondwana became increas-
snow reflected a large portion of sunlight) and, on the other, ingly dominated by the species-poor Glossopteris-flora during
to a lowering of the sea level – paving the way for the forma- the Upper Carboniferous; this became the typical vegetation
tion of the coal forests in tropic regions. of southern Gondwana until the Triassic period. The genus
Extensive fern and club moss forests grew in the subtropi- Glossopteris possessed annual rings indicating seasonal cli-
cal swamps, especially in the molasse basins of the Variscan mates and winter frost.
orogeny. The dominant representatives of the coal swamp The typical coal forests existed only in areas not under
flora were the scale trees (Lepidodendron) and the Sigillaria, the influence of orogenic processes until the Permian (for
both belonging to the Lycopodiopsida and reaching heights example, southern China). In Europe and North Amer-
of over 40 m. Horse tails (Equisetopsida) and Calamites also ica, Lycopodiopsida were increasingly replaced by more
thrived, growing to over 20 m in height. Seed ferns were drought-resistant conifers, cycads, and seed ferns in the Up-
widespread at drier locations per Carboniferous.
Driven by the collision between Laurussia and Gondwa-
na, the formation of mountains in the area of present-day Eu-
radiation: rapid diversification of a taxon giving rise to an array Variscan Orogeny: a mountain-building event in the Palaeozoic
of new forms caused by the collision of Gondwana and Laurussia
supercontinent: large landmass formed from several conti-
nents or cratons
See also: Carbonates: 2.1.2.3; Gymnospermae: 4.4.3.5

Hyolomenus, which lived in the Upper Carboniferous around 312 million In the Carboniferous, ferns, club moss, and Seed ferns formed the first
years ago, was one of the first vertebrates to be fully-adapted to terrestrial extensive forests (left: bark fossil of a Sigillaria sp.; right: leaf fossil of
life. Individuals were around 20 cm long with an anapsid skull and its eggs Linopteris sp. seed fern within Ruhr Carboniferous)
had an early amnion
Panthalassic Ocean
Siberia
Laurussia
Palaeo-Tethys
Ocean
Gondwana
Sahara India
Cape Siberia
Fungi and herbivorous insects developed the ability to degrade lignin and other Persian Gulf Ruhr area
complex organic molecules only during the course of the Upper Carboniferous,.
Thus, plant biomass accumulated, forming the now vital global coal reserves
during the Upper Carboniferous (here: coal seam beneath a sandstone layer) Mexico Australia
Bryozoans were important reef-builders during The Fusulinida were a significant group of During the Carboniferous, Goniatitida remain the
the Palaeozoic, particularly in the Ordovician, foraminifera during the Upper Palaeozoic most important and widespread ammonoidea
Carboniferous, and Permian periods (here a member of the Goniatitida from the
Mississippian). Goniatites were characterised by
the smooth sutures on their shell
2.3.3.9
The Permian period

The Permian period ranged between 298 and 252 million endured four global evaporation cycles: Progressively, car-
years ago and was divided into the Cisuralian (298–272 mil- bonates, gypsum (calcium sulfate), halite (rock salt, NaCl)
lion years ago), Guadalupian (272–259 million years ago), and, finally, potassium and magnesium chlorides, precipi-
and the Lopingian (259–252 million years ago) epochs. tated in each cycle. As a result, the richest Phanerozoic salt
During the Lower Permian, Siberia collided with the al- deposits emerged during the Permian, up to 1,500 m thick.
ready-united continents Laurussia and Gondwana, which The Permian is also characterised by the extensive radia-
led to the creation of the Ural mountains. At that point, all tion of the Amniota. Many reptile-like groups thus emerged,
major land masses were connected as the super continent several of which became extinct already by the end of the
Pangaea. Near the equator, the Tethys Ocean opened to the Permian. During the Permian, the Anapsida (including
East and, in the Upper Permian, Pangaea began once again various extinct lineages as well as likely also the turtles),
to disintegrate. The Permian-Carboniferous glaciation per- the Diapsida (lizards, dinosaurs, birds), and the Synapsida
sisted in the Lower Permian and the global climate warmed (mammals and extinct lineages, such as the therapsids) had
sharply in the later Permian. Due to the large Pangaean con- already separated. About 90 % of animal species became ex-
tinental land mass the climate was dry. tinct during the Permian-Triassic transition, including many
The upper Permian was the most volcanically active time major groups which disappeared completely, including the
of the entire Phanerozoic and was based around the Siberi- trilobites and the eurypterids.
an plate. This volcanism contributed to the global warming During the Permian, gymnosperms (naked-seeded plants)
trend, dramatically heating the atmosphere by up to 10 °C displaced the ferns and club moss as the dominant group
and, along with its geochemical consequences, resulting in of plants, in part because of the dry climate characteristic
the largest Phanerozoic mass extinction event. Intraconti- of this era. During this time, Glossopteris flora spread across
nental and coastal areas with shrinking access to the oceans Gondwana’s circumpolar regions.
The oldest fossils belonging to major tetrapod lineages a heterodental dentition, with incisors, canines, and fangs
(amphibians and amniotes) are 338 million years old, re- as molars. The Sphenacodontoidea (Pelycorsauria: Upper
covered from East Kirkton, Scotland. Early tetrapods were Carboniferous to Upper Permian) had still further differen-
carnivorous and likely insectivores. Herbivory developed tiated teeth and were also characterised by the mammalian
only during the Upper Carboniferous. Early tetrapods likely gait, with legs placed underneath the body rather than spread
breathed using buccal pumps, like extant amphibians, which towards the sides as in reptiles). Therapsids emerged in the
means they presumably had to eventually pause during late Upper Permian, with Tetraceratops as the first known rep-
breathing. Breathing with the ribs developed later on with resentative lineage. Compared with the earlier Pelycosauria,
the emergence of Amniota. Around 310 million years ago, therapsids possessed an enlarged temple fenestrae, a forward
the Synapsida (the lineage comprising mammals and their facing jaw joint, reduced dentition at palate, as well as chang-
ancestors) separated from the ancestral lineages of the Anap- es to the shoulder and pelvis girdle. Sex chromosomes also
sida and Diapsida, in other words from the lineages includ- emerged around 320–240 million years ago.
ing reptiles and birds. The oldest known ancestral reptiles The transition from Pelycosauria to therapsids also al-
were the small insectivorous anapsids Cotylosauria (Family tered the structure of ecosystems and food chains. Early
Romeriidae, Upper Carboniferous to Middle Permian). terrestrial ecosystems were dominated by insectivorous tetra-
One of the oldest Pelycosauria was the 50 cm tall predator pods. However, by the Upper Permian, a relatively large and
Archaeothyris (Pelycosauria: Ophiacodonta, Upper Carbonif- diverse group of herbivores became the nutritional founda-
erous to Middle Permian). The emergence of Pelycosauria tion for a small number of carnivores. Likely as a result of a
was an important time point in the evolution of dental dif- heightened pressure on their terrestrial niches by therapsids,
ferentiation: Archaeothyris had uniformly sharp teeth accom- amphibians became increasingly aquatic during the Upper
panied by larger canines. Higher Pelycosauria had already Permian.
buccal pumping: (Lat.: bucca = cheek) a form of breathing thoracic respiration: inhalation by expanding the rib-cage and
using the cheeks only (in amphibians) in which the animal raises increasing the volume of the chest cavity; in contrast to buccal
and lowers the floor of its oral cavity and contracts its trunk mus- respiration, thoracic respiration takes place through an open
culature in order to pump air between the lungs and oral cavity mouth
while its mouth is closed
See also: Anapsidic skull, Heterodont, Temple fenestrae: 4.2.1.9

Dimetrodon (Pelycosauria) was the largest carnivore during the Lower The southern gondwanan Permian flora was dominated by the seed fern
Permian. The characteristic large sail on its back allowed a rapid increase Glossopteris (left: stem cross-section; right: leaf), known as collectively
of its body temperature by sunlight as the Glossopteris-flora. The growth rings of Glossopteris‘ stem cross-
section prove a seasonal climate
Panthalassic Ocean Siberia
Laurussia
Tethys
Pangaea Ocean
Gondwana
Sahara India
Cape Siberia
Gymnosperms began to dominate the forests during the Permian. In addition to Persian Gulf Ruhr area
the seed ferns, conifers also thrived during that time Great Lakes South China
Mexico Australia
The Proetida (here: Ditomopyge decurta- Brachiopods (here: Hercosestria cribrosa) were an important The early Actinopterygii (ray-finned fish,
ta) was the only trilobite order to survive group of Permian reef-builders and benthic filter-feeders. Most here: Palaeoniscus sp.) possessed primi-
until the Permian brachiopod species went extinct by the end of the Permian and tive airbags associated with their mouth.
they never again fully recovered These served as primitive swim bladders
2.3.3.10
Development of the cormus

Early land plants were mostly creeping shoots, undiffer- light shines from above and therefore, in order to maximise
entiated into the roots, shoots, and leaves characteristic of light exposure, especially in competition with other organ-
the cormus plants. The typical architecture of land plants isms, plants ensure that their photosynthetically active struc-
represents an adaptation to life in the terrestrial habitat. This tures are as high up and away from the ground as possible.
fundamentally different organisation of land plants and al- Consequently, terrestrial life requires a spatial separation
gae can largely be explained by the different availability of between nutrient uptake and light absorption; the distance
nutrients and light in water and on land: between specialised structures able to supply with nutrients
In water nutrients are dissolved and can be absorbed (roots) and ones used for photosynthesis (leaves) must be
throughout the entire body surface. A smaller body size, bridged. Therefore, structures are required that serve both
in other words a larger surface-to-volume ratio, is therefore nutrients transport between the roots and leaves whilst at the
well-suited for the absorption of nutrients. Light was stream- same time supporting the weight of the plant under terrestri-
ing into the aquatic habitat from above. The simultaneous al gravitational conditions (shoot axis).
supply of nutrients and light required locomotory or sus- In addition to the structuring of the plant into the organs,
pension mechanisms to keep these usually small organisms shoot, leave and root, plants developed a number of other
within the upper regions of the water column. adaptations to the terrestrial environment, including the for-
On land, nutrients are bound to soil solution or to soil mation of a vascular bundle, the growth of a cuticle for pro-
particles. As a result, plants have developed root structures tection from evaporation and UV radiation, as well as the
which maximise contact between the roots and the soil. The formation of lignin, already previously established in some
growth of roots typically excludes mobility. As in water, sun- green algae.
Leaves optimise gas and light supplies to plants and thus es, enations). Vascular bundles grew secondarily into these
enable higher photosynthesis. However, large, flat leaves structures.
emerged only during the Devonian. Both the small leaf-like However, telome theory, on the other hand, posits that
outgrowths characteristic of club moss and fern-like plants, as the formation of true leaves occurs from stems (telomes) in
well as true leaves, originally developed from leafless shoots. a series of distinctive stem-growth processes also known as
However, these structures developed in different ways. elementary processes: planation (the ordering of sprouts in a
Enation theory posits that small outgrowths, or enations, plane), overtopping, and fusion (as well as reduction, incur-
characteristic of many club mosses and emerging from vation and longitudinal differentiation). Since they too arise
multicellular formations of the outer cell layers (emergenc- during the earliest sprout stages, vascular bundles are present
within the leaves from the onset of their growth.
cormus: (Grk.: kormus = stump) plant body divided into root, planation: relocation in one plane
leaves and shoot axis telome: axial plant structure in land plants
enation: (Lat.: enatere = float out) formation of outgrowths on
the surface of leaves
See also: Early land plants: 4.4.3.2; Colonisation of terrestrial environments: 2.3.3.6
In water, organisms can only receive an optimal supply

of light by swimming into the upper layers of the water
column. On land, plants get an optimal supply of light by
overgrowing competing plants
fusion
formation of leaves overgrowing

from telomens
Rhynia
(fossil, Silurian)
planation
On land, sources of nutrients (soil) and light (from
above) are often physically separated. This discrepancy
was basic to the evolution of transport structures and
supporting tissues
formation of leaves from club moss

emergences (enations)
In water, sources of nutrients and light are generally not spatially

separated. As a result, smaller body sizes optimise nutrient absorp-
tion due to the relatively large surface-to-volume ratio.
The roots of land plants also increase their surface-to-volume area
through the formation of root hairs
2.3.3.11
Towards a smaller and shorter-lived haploid generation (gametophyte)

Many organisms undergo an alternation of generations sis happens for each syngamy and the recombination rate
(also known as alternation of phases or metagenesis) be- remains relatively low whereas the rate of propagation is
tween a haploid and a diploid generation. This type of life relatively high with four meiospores – and thus four new in-
cycle decouples meiosis (reductive division resulting in dividuals – per syngamy.
daughter cells with half a chromosome set), from syngamy Diplonts achieve a high rate of recombination since many
(the fusion of two cells) during reproduction. The haploid cells per organism can undergo meiosis. On the other hand,
generation forms sex cells (gametes) by mitotic division, the propagation rate, with a production of just one individu-
which fuse after fertilisation to become a diploid zygote, and al per syngamy, is relatively low.
eventually grow into a diploid generation. The diploid gener- In addition to the rates of recombination and propaga-
ation, in turn, forms haploid cells, by meiotic division, which tion, water dependence also plays a central role within these
are distributed (usually as spores) and grow into a haploid reproductive processes: the processes of fertilisation are de-
generation. pendent on an aqueous environment in which male gametes
The significance of the haploid and diploid generations can swim towards the female gametes (ovum). As a result,
respectively varies greatly in different organismal groups. In the gamete-forming generation, the gametophyte, is highly
the case of land plants and their evolution, however, most water dependent. Whereas this gametophyte is the dom-
striking is the increasingly reduced state of the haploid, gam- inant, long-lived generation in mosses, it is already greatly
ete-forming generation (= gametophyte). The high recombi- reduced in ferns. In seed plants, on the other hand, the game-
nation rates of the diploid generation seems to have been ad- tophyte consists of only a few cells and must be nourished by
vantageous for the transition to life on land, perhaps because the sporophyte.
the terrestrial habitats are less stable than those found in the Because of the water dependency of gametes and with
aquatic environment. that of the gametophyte, this generation must remain rela-
In order to better understand this development in land tively small according to the substrate. Bryophytes (gameto-
plants, it is important to note the advantages and disadvan- phyte is the dominant generation) are physically smaller than
tages of being haploid (haploid organisms, only zygotes dip- ferns and seed plants (sporophyte is the dominating genera-
loid) and diploid (diploid organisms, only gametes haploid). tion).
In haplonts, haploid organisms arise directly from diploid
zygotes as a result of meiosis. As a result, only one meio-
Bryophytes undergo an anisomorphic alternation of gen- ated than the sporophyte. Gametophytes reach a maximum
erations. Here, the photoautotrophic gametophyte is clearly size of only a few centimetres and show similarities in shape
both morphologically and anatomically differentiated. The with the thalloid liverworts. The anatomically simple, green
gametophyte develops from aprotonema (prothallus) and can thallus is attached to the substrate by way of unicellular, tu-
be a thallos (little differentiated, flat, lobed, and with rhizoids bular rhizoids. Antheridia and archegonia, morphologically
attached to the substrate) with high tissue differentiation (as- more simple than in bryophytes, are often found on the un-
similation and storing tissue) or be foliose (differentiation of derside of the body. Fertilisation only takes place in water.
stems, leaves, and rhizomes). Male gametangia (antheridia) In seed plants, the gametophyte is even more strongly re-
are club-shaped and short-stalked structures within a sterile duced. The male gametophyte, a multicellular pollen grain,
membrane. The female gametangia are bottle-shaped with a is made up of only three cells in the angiosperms: two sperm
neck canal and a swollen base. cells and one vegetative cell. The female gametophyte, the
The short-lived (a few weeks) gametophyte spores of vas- embryo sac, remains on the sporophytic mother plant and
cular spore plants, including ferns and club moss, is called forms the ovum.
the prothallus. It is significantly smaller and less differenti-
diploid: (Grk.: di = two) double set of chromosomes meiospores: spores produced by meiosis
garnet: haploid reproductive cell mitosis: (Grk.: mito = thread) process in which the chro-
gametangium: (Grk.: gamos = wedding, marriage) organ in mosomes double in number before a cell nucleus is divided,
which the gametes are formed in sexual reproduction the ploidy (number of chromosomes) therefore remaining un-
haploid: (Grk.:haploeides = simple) a single set of chromosomes changed
meiosis: (Grk.: meiosis = lessening) cell division in which the syngamy: sexual reproduction through the fusion of two gam-
number of chromosomes is halved etes
See also: Sporophyte: 2.3.3.12

In mosses, the gametophyte is the dominant perennial generation. The gametophytes of liverworts are either thallose (left: Metzgeria sp.) or foliose
(middle left: Lophocolea sp.). The gametophytes of mosses are foliose (centre-right: Polytrichum sp.; right: antheridium of Polytrichum sp.)
In ferns, both the sporophyte and gametophyte generations are independently viable. The gametophyte is thallose, remains small, and is attached to
the substrate. This way of living increases the likelihood of fertilisation , since the gametes formed by gametophytes require freely available water for
fertilisation to take place. Featured here are the prothallium of Dicksonia sp. (Polypodiopsida, left) and Equisetum hyemale (Equisetopsida, right)
In the Pinaceae (gymnosperms), the male gametophyte is made up of five cells: two prothallium cells and one antheridium cell which divides into one
pollen tube cell and one generative cell. The generative cell is subsequently divided into two sperm cells. The female gametophyte consists of several
hundred cells and forms rudimentary archegonia. In angiosperms, the gametophytes, as shown below, are even further reduced: in what is known as
double-fertilisation , one angiosperm sperm cell fertilizes an egg cell, with the nucleus of the other sperm cell fusing with the other central binuclear cell
of the embryo sac, forming the triploid endosperm
The male gametophyte of angiosperms (pollen grain) is re- The female gametophyte of angiosperms (embryo sac) is re-
duced to three cells: a vegetative cell, which forms a pollen duced to seven cells: a central, binucleate cell, one ova accom-
tube, and two forming sperm cells panied by two synergid cells, and three antipodal cells
core of vegetative
cell
sperm cells
Pollen grain of Light microscopic cut showing an ovule

Epilobium angustifolium
Gametophytes are most strongly reduced in angiosperms
2.3.3.12
Towards an increasingly dominant diploid generation (sporophyte)

Most terrestrial organisms are either entirely diploid or, dominant generation is the gametophyte, the sporophyte is
for those with alternating generations, undergo dominant dominant in vascular plants. Furthermore, within the con-
diploid generations. Plants with alternating generations have text of the evolutionary history of land plants the sporophyte
a diploid generation characterised by the presence of a sporo- has had an increasingly more prominent role compared to
phyte, which forms haploid spores from which gametophytes the gametophyte. This trend towards the more dominant role
emerge. In protists (algae) with alternating generations, the of the diploid, spore-forming generation (= sporophyte) has
sporophytes and gametophytes are often alike (isomorphic). two advantages: it maintains a high recombination rate and,
In mosses and vascular plants, however, the two generations at the same time, reduces the water-dependence of processes
are markedly different (heteromorphic). While in mosses the to better accommodate terrestrial living.
The diploid sporophyte of bryophytes is not independent- ample, the gametophyte of Derbesia marina was previously
ly viable and is nourished by the gametophyte, to which it designated as another species (Halicystis ovalis).
remains connected. Hornworts represent a rare exception, Rhodophyta are characterised by a tripartite generation-
where the sporophyte remains relatively long-lived and al alternation, involving a haploid gametophyte, a diploid
reaches a certain state of independence from the gameto- carposporophyte, and yet another diploid sporophyte gen-
phytes. The sporophytes of mosses consist of the spore cap- eration (often tetrasporophyte) generations. In most red
sule (sporogon) and a stem (the seta). algae the three generations develop on two different vege-
In extant vascular spore plants, including ferns and club tative bodies (diplobiontic development). The gametophyte
moss, the sporophyte generation is dominant and long-lived. (haploid) and the tetrasporophyte (diploid) are often alike.
It is divided into an axis, leaves, and roots (cormus). The fur- The carposporophyte, however, is inconspicuous consisting
ther development of the sporophyte, including lignification, of smaller cell filaments, developing after fertilisation of the
transport of water and assimilates, as well as the develop- carpogonia (female gametangium) and remaining on the ga-
ment of roots, as well as its gradual independence from the metophyte. After mitotic nuclear division, the carposporo-
gametophyte enabled plants to survive in a range of new phyte forms diploid carpospores (mitospores), from which
niches. the autonomous diploid tetrasporophyte develops. In genus
In seed plants, the sporophyte is many times larger and Batrachospermum, all three generations occur on a single in-
has a more complex structure (tree, shrub, or herb). At the dividual (haplobiontic development). Here, the tetrasporo-
same time, the gametophyte is greatly reduced. phyte grows on the carposporophyte.
The alternation of generations is also found in many algal The Phaeophyceae undergo a diplobiontic generational
groups: some feature predominantly or exclusively haploid alternation involving a haploid gametophyte and a diploid
generations, whereas others feature predominantly or ex- sporophyte. The sporophyte of the primitive brown algae,
clusively diploid generations, yet others exhibit alternating such as Ectocarpus, forms single-chambered (unilocular) spo-
generations. rangia in which meiotic nuclear division lead to the forma-
Green algae are either haplobiontic (haploid generation, tion of meiospores. These develop to form gametophytes,
only the zygote remains diploid), or diplobiontic, as in land which form multi-chambered (plurilocular) sporangia within
plants, where haploid and diploid phases alternate. The two which mitotic gamete division takes place. A zygote emerges
generations can be either isomorphic, as in the genus Ulva, through the fusion of two gametes of different mating types.
or heteromorphic. Morphological differences between the The zygote subsequently develops into a sporophyte. Unlike
generations can be so strong that can be – without further in Ectocarpus, where the gametophyte and sporophyte are
knowledge – mistakenly assigned to separate species. For ex- alike, the sporophyte of larger brown algae is significantly
more developed compared with the gametophyte.
carposporophyte: formed by the fusion of haploid gametes in haplobiontic: organisms with either one haploid or one diploid
the three-stage lifecycle of red algae generation, but not both
diplobiontic: organisms with two generations (a haploid and tetrasporophyte: the second sporophytic generation in red al-
diploid generation) gae formed from a carpospores
See also: Gametophyte: 2.3.3.11

The sporophytes of bryophytes are short-lived and do not carry out photosynthesis, with the exception of hornworts. Instead, they obtain their nutrients
from the maternal organism. Left: sporophyte of the liverwort Calypogeia which opens its spore capsule (second from the left); middle: sporophyte of
the leafy liverwort Lophocolea sp.; second from the right: sporophyte of the moss Dicranoweisia sp.; right: sporophyte of the moss Brachythecium sp.
Sporophyte of true ferns (left: the tree fern Dicksonia antarctica) and horsetails (centre: mature strobilus; right: enlarged view of the sporangia). The
sporotrophophyll of the tree fern fulfills both the function of the sporophyll (dispersal) and of the trophophyll (photosynthesis). In club moss, these
functions are often separated into sterile trophophylls and fertile sporophylls
Sporophytes of seed plants: all visible plant components, with the exception of pollen grains, are
formed from the sporophyte (top: beech at different ages; left: cut Crocus flower). The stamens
and carpels also emerge from the sporophytes; these are the equivalent of sporangia stands in
spore plants
2.3.4
The Mesozoic era

The Mesozoic era followed the Palaeozoic, spanning from The Cretaceous period is divided into two epochs, the
252.2 to 66 million years ago. It is divided into the Triassic, Lower and Upper Cretaceous, which in turn comprise twelve
Jurassic, and Cretaceous geologic periods. ages. Spanning around 80 million years, the Cretaceous is
In turn, the Triassic is divided into three epochs: the Low- the longest period within the Phanerozoic. It is character-
er, Middle, and Upper Triassic. These are further divided into ised by its distinctive chalkstone deposits (e.g. at Dover or
seven ages. The end of the Triassic is characterised by anoth- Rügen) of widespread fossil calcium carbonate skeletons of
er mass extinction event, possibly related to the breakup of various organismal groups (such as haptophytes). These are
super continent Pangaea. also found in other rock formations, such as the equally com-
The Jurassic period is divided into the Lower, Middle, and mon Cretaceous sandstones. The end of the Cretaceous was
Upper Jurassic epochs, which in turn comprise eleven ages. also characterised by a large mass extinction event, probably
The terms Lower Jurassic, Middle Jurassic, and Upper Ju- associated with a meteorite impact and associated volcanic
rassic denote internationally recognised chronostratigraphic activity.
epochs.
When it comes to the Triassic and Jurassic periods, Cen- such as gypsum, anhydrite, and halite dominate. Sandstones
tral European time scales sometimes differ from those adopt- and mudstones dominate Keuper rocks.
ed more internationally. The Jurassic is regionally subdivided into the Black,
The Triassic is divided into Buntsandstein, Muschelkalk, Brown, and White Jurassic, or into the Lias, Dogger, and
and Keuper within the sedimentary environment of the Malm. These classifications do not necessarily match in-
Germanic Basin (present-day western and central Europe). ternationally recognised divisions but they are still used as
Since this stratigraphic division is only pronounced in the regional lithostratigraphic units. While the various terms
Germanic Basin, and deposition started at different times in (Lower Jurassic-Black Jurassic-Lias; Middle Jurassic-Brown
different areas, its classification system is not in line with the Jurassic-Dogger; Upper Jurassic-White Jurassic-Malm) were
internationally recognised system of classification. Region- often used synonymously, these are today conceptually dif-
ally, however, this division remains in use. ferent. The terms Black, Brown, and White Jurassic are most
Buntsandstein rocks are predominantly made of con- often used for the description of lithostratigraphic units in
glomerate, sandstone, and mudstone. Muschelkalk is dom- southern Germany, where names are given to the prevailing
inated by calcareous rock, where mussels and brachiopods weathering colours of the rock layers. The terms Lias, Dog-
are commonly found fossils. Fewer calcareous deposits are ger, and Malm are used for corresponding lithostratigraphic
found in Middle Muschelkalk deposits, where evaporites units in northern Germany.
biostratigraphy: a branch of stratigraphy assigning relative conglomerate: hardened clastic sediment with clasts >2 mm,
ages of rock strata using fossils fragments usually rounded
chronostratigraphy: the geological discipline that classifies the lithostratigraphy: spatial and temporal classification of rock
age of rocks according to time and in relation to their absolute strata based on the characteristics of the rock; subdiscipline of
age; subdiscipline of stratigraphy stratigraphy
See also: Haptophyta: 4.7.1; Mass extinction: 2.3.1

The Phanerozoic eon: the Mesozoic era 125
66.0 Ma Stratigraphic time scale of the Mesozoic

Maastrichian
72.1 Ma
Campanian
Upper Cretaceous
83.6 Ma
Santonian
86.3 Ma
Coniadian
89.8 Ma
Turonian
93.9 Ma
Cenomanian
100.5 Ma
Cretaceous Albian
113.0 Ma
Aptian
Lower Cretaceous
125.0 Ma
Barremian
129.4 Ma
Hauterivian
132.9 Ma
Valanginian
139.8 Ma
Berriasian
145.0 Ma
Tithonian
152.1 Ma Callovian
Upper Jurassic Kimmeridgian
157.3 Ma 166.1Ma
Oxfordian Bathonian
163.5 Ma
168.3 Ma
Middle Jurassic Bajocian

170.3 Ma
Jurassic 174.1 Mio
Toarcian Aalenian
182.7 Ma
Lower Jurassic Pliensbachian

190.8 Mio
Sinemurian
Hettangian 199.3 Ma
201.3 Ma
Rhaetian
208.5 Ma
Upper Triassic Norian
Triassic 227.0 Ma
Karnian
237.0 Ma
Olenekian
Ladinian
Middle Triassic 242.0 Ma
Anisian
247.2 Ma 251.2 Ma
Lower Triassic Induan
252.2 Ma
2.3.4.1
The Triassic period

The Triassic period lasted from 252 to 201 million years. vived in other organismal groups, of which some underwent
ago It is divided into the Lower (252–247 million years ago), a more profound radiation during the Triassic. For example,
Middle (247–235 million years ago), and Upper Triassic only two ammonoid genera survived the Permian-Triassic
(235–201 million years ago) epochs. mass extinction event, but over 100 genera had evolved again
During the Triassic, all major land masses were connected already in the Lower Triassic.
to each other as the supercontinent Pangaea. Elements from Alongside sharks, bony fish, and aquatic reptiles (Notho-
the northern edge of the eastern side of the Gondwana plate sauria, Pleiosauria, Ichthyosauria, and crocodiles), ammo-
detached (Cimmerian Terranes) and drifted northward. The noids and belemnites were important constituents of ecolog-
Palaeo-Tethys was subducted under these terranes, opening ical communities in the open sea. Brachiopods played only a
the (Neo-) Tethys between Gondwana and the Cimmerian minor role after the mass extinction event, whereas mussels
terranes. In the Upper Triassic, a rift valley developed be- dominated benthic habitats since the Triassic. Scleractinia
tween the subsequent North America and Europe, thus were important as reef-building corals.
forming the origins of the North Atlantic. The Triassic cli- The Upper Triassic featured another mass extinction
mate was dry and warm, with an almost uniform climate event. Conodonts and Placodonts were completely wiped
across latitudes between the equator and the poles. The Up- out, as well as most species of mussels, ammonoids, plesi-
per Triassic climate was slightly cooler and wetter. osaurs, and ichthyosaurs. On land, many mammal-like rep-
The Fusulinida (Foraminifera), rugose corals, trilobites, tiles went extinct.
and other major Palaeozoic organismal groups became ex- Gymnosperms, particularly Cycadopsida and Ginkgoop-
tinct at the Permian-Triassic boundary. Only a few taxa sur- sida, dominated the forests of the Triassic.
The largest Phanerozoic mass extinction event occurred were more affected by the changing conditions compared to
at the boundary between the Permian and Triassic periods. motile species. After the mass extinction event, the Lower
The event, which took place around 252.5 million years ago, Triassic was characterised by continued low levels of diver-
occurred during the most volcanically active period of the sity with predominantly cosmopolitan species in the oceans.
Phanerozoic, the Siberian Trapp Volcanism: at this point, 2.3 Lower Triassic marine reefs were predominantly microbial;
million km³ of flood basalt covered most of the continent metazoan reef-building lineages only recovered in the Mid-
Siberia with an up to 3 km thick layer. dle Triassic
During this time, increases in atmospheric greenhouse gases On land, seed plant populations also dropped. Algae and
caused global temperatures to rise which, in turn presumably, fungi (thriving by removing decaying biomass) reached peak
led to a collapse of ocean currents, and subsequently local an- abundances immediately after the Permian-Triassic bounda-
oxia in many marine habitats. The volcanic gases (carbon di- ry, followed shortly by spore plants, such as club mosses and
oxide, sulfides, hydrogen chloride) also led to an acidification ferns, and subsequently by the regeneration of herbaceous
and local poisoning of the seas; only H2S-producing bacteria plants. Only terrestrial vertebrates with distinctly efficient
grew in anoxic areas whereas phytoplankton populations de- breathing systems were able to survive the harsh environ-
clined worldwide. Decaying biomass exacerbated the marine mental conditions; for example, the Archosauria managed to
anoxia, ultimately triggering a general marine mass extinction. survive due to their efficient airbag breathing system.
Warming oceans also increased the release of methane clath- In a phenomenon known as the Lazarus effect, many
rates and, as a result, rising atmospheric methane concentra- surviving taxa are not detectable in the fossil record from
tions led to further climatic warming and a strong decrease in immediately after the extinction event, but reappeared later
atmospheric oxygen concentrations to levels of around 13 % in on. In contrast, some taxa spread quickly in the temporarily
the Lower Triassic. At higher altitudes, land animals died from unoccupied niches and their abundances increased rapidly
a lack of oxygen whereas near coastlines they were exposed to (‘catastrophe taxa’) until they were displaced again by the
toxic hydrogen sulfide emissions from the marine. more specialised taxa. The planet’s biodiversity only fully re-
Ecological equilibria shifted in the wake of these cata- covered by the Middle Triassic.
strophic events; for example, in the sea, sessile filter feeders
anoxia: the total depletion of oxygen expansive in the Lower Carboniferous (Mississippian) and closed
basalt: volcanic, finely crystalline rock of mafic composition in the Triassic
cosmopolitan: found all over the world peak: the highest point or level
epibenthic: on the bottom of a body of water (in contrast to Tethys: ocean that existed between Laurasia and Gondwana be-
endobenthic: in the sediment at the bottom of a body of water) tween the Permian and the Tertiary
Palaeo-Tethy Ocean: ancient ocean between Laurussia and
Gondwana; it began to form in the Upper Silurian, was most
See also: Diapsidae: 4.2.1.9; Rugose corals, Tabulate corals: 4.2.1.3; Subduction: 2.1.1.2
The Cynodontia were closely related to early mammals. Genus Cynogna- Gymnosperms dominated the Triassic, especially ginkgo, cycads, and co-
thus lived in the Lower and Middle Triassic and, with a skull length of up nifers. The seed ferns (bottom: leaf of Dicroidium sp.) show early charac-
to 40 cm, was one of the largest Triassic carnivores teristics of seed plants
Siberia
Palaeo-Tethys Ocean
Kim
mer
ian
Pangaea terr
ane
s
Tethys Ocean
Gondwana
Sahara India
Cape Siberia
After the Permian-Triassic mass extinction event, mussels increasingly began Persian Gulf Ruhr area
to dominate the shallow marine benthic fauna. In particular, digging mussels
were better able to escape predation by starfish compared with epibenthic
brachiopods Mexico Australia
Triassic sea cucumbers (Holothuroidea), which After the Permian-Triassic mass extinction event, the ammonoids, and in particular the Ceratitida,
belong to the echinoderms, were represented by enjoyed an explosive radiation, in the end making up the majority of Ammonoidea during the Triassic
Strobylothyone rogenti (here: Ceratites nodosus and Monophyllites aonis). These lineages usually had ceratitic sutures, in
other words anteriorly smooth and posteriorly frilly sutures
2.3.4.2
Reproductive adaptations to terrestrial life

Terrestrial life requires a number of adaptations, which Since water is denser than air, the shift towards terrestri-
have been evolved independently in all land-living organ- al life also required developing stronger supporting tissue
isms. Microorganisms are perhaps the only exception (cy- and skeletal elements. Exoskeletons (which also protected
anobacteria, bacteria, protists, and some small metazoans), against predation) or internal skeletons (e.g. in vertebrates)
because they are able to live in pore water or other perma- that had already been formed in aquatic organisms were able
nently moist terrestrial microhabitats. to fulfil this function. In organisms with a cell wall, the sup-
Terrestrial organisms have to secure their water supply porting role was often taken up by the cell wall itself (e.g. in
whilst at the same time reducing the rate of evaporation fungi and plants).
across their body surface. As a result, they developed epithe- Most aquatic organisms sexually reproduce by releasing
lial tissue that would restrict diffusion rates from the body sperm (spermatozoa) directly into the water body, which in
outwards into the environment. Since the body surface is turn swim freely to the female reproductive organs. Thus, re-
also important for the absorption and exchange of nutrients production is heavily dependent on the presence of water.
and gases, alternative ways of carrying out these vital tasks During the colonisation of terrestrial environments, sexual
had to develop. The same applies to excretion: increasing- reproduction had to increasingly take place internally within
ly sealing off the inside of the body required organs which the bodies of the parents, in order to gain independence from
would specialise to take care of excretory functions. Since the water. Embryonic development also became increasingly
water is often a limited resource for terrestrial organisms, water-independent, taking place within an embryo surround-
newly developed excretion mechanisms also specialised in ed by protective layers such as a seed coat (testa) or amnion.
limiting the loss of water. Specifically, these included mecha-
nisms concentrating salts in excretions (e.g. in urine).
In order to remain viable, terrestrial organisms had to terrestrial amphibians generally needed to return to water to
restrict evaporation of water through the body surface, de- reproduce, since the fertilisation of their eggs can only occur
veloping epithelial tissue in order to fulfil this function. In in water by way of free-swimming sperm. Similarly, the sper-
plants, this role is taken up by the epidermis and the cuticula; matozoids of mosses float freely in aquatic habitats towards
similarly, the same function is carried out by the skin in ver- the female archegonia, fertilizing the eggs there. At least a
tebrates. In many organisms, protection from evaporation is thin film of water – for example, after rainfall – is therefore
simultaneous with support functions – this is especially true a prerequisite for fertilisation. Also within other organismal
for organisms with an exoskeleton. groups, sexual reproduction is usually more water depend-
In many aquatic organisms, most gas exchange takes ent than the adult life. A complete water-independence of
place through the surface of the skin. With increasing imper- reproduction became possible in numerous lineages through
meability of the skin and/or the epithelial tissues, powerful a shift of the fertilisation process toward the inside of indi-
respiratory systems (e.g. lungs) specializing in gas exchange viduals. Such a shift happened in, for example, the amniotes,
functions were required. The terrestrial colonisation and ra- seed plants, and also many arthropods. However, both the
diation by so many species during the Carboniferous was gametes and the developing embryo are threatened with de-
facilitated by high levels of atmospheric oxygen (over 30 %). hydration within the terrestrial habitat. In many terrestrial
Under such conditions, the relatively weak lungs of early tet- groups, dehydration of the embryo is avoided because it is
rapods already allowed for successful colonisation of terres- surrounded by numerous protective layers (e.g. testa or the
trial habitats. More powerful respiratory organs became only amnion). However, these protective layers also restrict the
necessary when oxygen concentrations dropped towards the supply of nutrients from the environment. For this reason,
end of the Carboniferous. the formation of the protective layer around the embryo is
The first terrestrial organisms were often highly water de- always accompanied by a system of storage or supply of nu-
pendent, at least in terms of reproduction; for example, even trients (e.g. an egg yolk or endosperm).
allantois: embryonic urinary bladder suspensor: connection between endosperm and embryo in
chorion: outer membrane around the amniotic sac surrounding seed plants; formed by asymmetrical division of the zygote
an embryo in vertebrates
mikropyle: canal between the integuments at the tip of the
ovulum in seed plants
See also: Colonisation of terrestrial environments: 2.3.3.6; Carboniferous 2.3.3.8; Ovule 2.3.3.11
egg shell yolk

suspensor chorion
endosperm mikropyle
embryo
amnion allantois
internal Integument amnion liquid

seed coat embryo
external Integument
In terrestrial organisms, the dissemination and reproduction units must be protected against dehydration. As a result, these are often surrounded by
thick, waterproof casing. This separation from the outside world is only possible when nutrients allowing for the growth and development of the embryo
can be stored within these dispersal units. The principle of isolation (through a seed coat in plants or the amnion and/or egg shell in vertebrates) and
storage of nutrients (through an endosperm in plants or the yolk in animals) from the environment is of fundamental importance within the colonisation
of the terrestrial environment
pollen
pollen tube
stigma
pistil
testicles
spermatic duct
ovary
fallopian tube
cloaka
ovary
In order to survive in a terrestrial environment, the transfer of the sperm (spermatozoa) had to be water-independent in sexual organisms. Several
mechanisms of internal fertilisation have thus developed
In aquatic organisms, the fertilisation of oocytes

and the development of embryos takes place in
the water. In early terrestrial organisms, as with to-
day’s mosses (left: Plagiopus oederianus) and am-
phibians (right: Midwife toad Alytes obstetricans),
reproduction is still highly water-dependent and
gametes are barely protected against dehydration.
At the same time, nutrients can be absorbed from
the environment and, as a result, a storage of nu-
trients or steady supply to the embryo is not at all,
or only weakly expressed
2.3.4.3
The Jurassic period

The Jurassic period spans a time period from 201 to 145 During the Jurassic, populations of organisms that sur-
million years ago. It is divided into the Lower (201–174 mil- vived the Upper Triassic mass extinction event began to
lion years ago), Middle (174–163 million years ago), and Up- rebound. Following on from the extinction of many mam-
per Jurassic (163–145 million years ago) epochs. mal-like reptiles, the dinosaurs grew to become the dominant
During the Jurassic period, the super continent Pangaea group of terrestrial vertebrates. The break apart of the su-
further disintegrated and the Tethys transgressed on the in- percontinent Pangaea resulted in a markedly increased ende-
land, eventually leading to the separation of Gondwana from micity of terrestrial fauna. The ‘primaeval bird’ Archaeopteryx
South America as well as between North and South Amer- also emerged during the Jurassic. In the sea, the Dinophyta
ica. The North Atlantic began to form between the Eura- experienced a stronger radiation.
sian and North American plate (Laurasia). First, three major The Polypodiceae, the most diverse family of present-day
continents emerged: North America, Eurasia, and Gondwa- ferns emerged during the Jurassic.
na. Rift systems initially experienced marine transgressions. Glossopteris went extinct during the Jurassic, whereas
Salts were precipitated by evaporation and salt deposits are Cycadopsida experienced a strong radiation. Many extant
recorded on both sides of the Atlantic. The Jurassic climate gymnosperm groups, including Thuja (Cypressaceae), Taxus
was steady and warm, but cooler than in the Permian. Al- (Taxales), Pinus and Picea (Pinaceae), emerged for the first
though the seasons were pronounced, there were no big tem- time in the Jurassic. Tree records from the Jurassic are large-
perature gradients between the equator and the poles. ly characterised by clear annual growth rings, indicating a
seasonal climate and spells of winter frost.
Following the Permian-Triassic mass extinction event and ischium faces backwards. The ornithischian pelvis is bidirec-
the recovery of diversity throughout the Triassic, the Upper tional and the pubis lies parallel to the ischium.
Triassic was characterised by yet another mass extinction The Saurischia include the Theropoda and the Sauropo-
event. Modern-day tetrapod groups emerged during the Up- domorpha: the carnivorous, bipedal Theropoda (e.g. Herrera-
per Triassic and the Jurassic, including turtles, crocodiles, saurus, Allosauroidea, and birds) were the dominant preda-
Lepidosauria (snakes, lizards, and the extinct aquatic Sau- tors of the Jurassic and Cretaceous periods. The herbivorous,
ropterygia), Ornithodira (with pterodactyles [Pterosauria] quadripedal, very large Sauropodomorpha (e.g. Brachiosau-
and dinosaurs [including birds]), and mammals. Increased ridae) were the dominant large herbivores of the Upper Ju-
predation by sauropods likely exacerbated the radiation of rassic and Cretaceous. Finally, the Ornithischia (e.g. Stego-
conifers, particularly those with hard needles. The first angi- sauria, Ankylosauria, Iguanodontidae, Ceratopsia) had been
osperm fossils originate in the Lower Jurassic. purely herbivorous and very diverse organismal group.
Early dinosaurs were carnivorous; herbivores emerged With the increasing break apart of Pangaea, the diversi-
only later. From their common ancestor, which is thought ty of dinosaurs grew strongly. Only 7 % of known dinosaur
to have resembled the approximately 1 m tall Eoraptor, the genera are from the Triassic, whereas 28 % are from the
dinosaurs diversified into the Saurischia and Ornithischia. Jurassic and, finally, 65 % are from the Cretaceous (mostly
The two groups are characterised by the arrangement of from the Upper Cretaceous).
their pelvic bone: in Saurischia, the pelvis is three-rayed, the
pubic bone (pubis) faces downwards and forwards, and the
bipedal: locomotion by means of two legs quadruped: an animal which has four feet
Glossopteris: dominant plant genus on the Gondwana conti-
nent during the Permian period
See also: Amniota 4.2.1.9; Angiosperms and dinosaurs 4.2.1.8; Dinosaur, Sauria 2.3.4.4
The Archaeopteryx, which belonged to the Archosauria (Theropoda, Di- The Jurassic vegetation was dominated by gymnosperms. Cycads were
nosauria), had typical bird features – for example, asymmetric pinion especially common (left: leaves from Zamites feneosis; right: leaves of
feathers, clavicles fused to a wishbone and a posteriorly-oriented first Zamites gigas)
toe, but it also had primitive features, such as teeth, cervical ribs, and a
long tail spine
Laurasia Siberia
Tethys Ocean
Pangaea
Pacific Ocean
Gondwana
Sahara India
Cape Siberia
Rising nutrient-rich currents promoted high plankton production in the tropical Persian Gulf Ruhr area
continental shelf areas of the Tethys. Biomass partly sank and was deposited Great Lakes South China
under anoxic conditions, making up the modern-day’s oil fields in the Persian
Mexico Australia
Gulf
The Ammonoidea were significant marine pred- Clypeus ploti, a sea urchin from the Jurassic The Trigoniidae (cockles) underwent a period of
ators also during the Jurassic. Within Ammo- rapid diversification during the Jurassic, reaching
noidea the Ceratitida were increasingly replaced their highest level of diversity in the Lower Creta-
by the Ammonitida during the Jurassic (here: Ko- ceous (here: Trigonia interlaevigata)
smoceras jason)
2.3.4.4
Sauria
The term ‘saurian’ summarizes large fossil amphibians • Fossil discoveries of dinosaurs from the (at that time) po-
and especially reptiles of the Mesozoic. More specifically, the lar regions
term is applied to the Ichtyosauria, the Sauropterygia, which • Evidence for the presence of insulating feathers on many
together with lizards and snakes make up the Lepidosauro- small dinosaurs
morpha, and the Pterosauria (flying dinosaurs) which belong • Isotope analyses of dinosaur teeth (carbon and oxygen)
to the Ornithodira (Archosauromorpha), as well as the di-
nosaurs. The dinosaurs evolved in the Middle Triassic, most However, it remains unclear whether the likely dinosaur
likely from the Archosauria, occupying terrestrial niches left warm-bloodedness was simply a result of their size – in large
vacant after the Permian-Triassic mass extinction event. Con- animals, heat dissipation is low due to a low surface-to-vol-
temporary theories suggest that dinosaurs were most likely ume ratio – or whether it actually indicates endothermy, that
warm-blooded for a number of reasons, including: is, an active regulation of body temperature, such as that ob-
• Skeletal build and construction of vasculature, hinting to served in birds.
a high activity
The dinosaurs are divided into the Saurischia (‘liz- (including distinctive prominent canine-like teeth), the ar-
ard-hipped’ dinosaurs) and the Ornithischia (‘bird-hipped’ moured Ankylosauria and Stegosauria, together summarised
dinosaurs). as the Thyreophora, the Pachycephalosauria, characterised
The Saurischia include the Herrerasauria, early bipedal by their thickened calvarium, as well as the Ornithopoda
dinosaurs from the Upper Triassic, the Sauropodomorpha and the Ceratopsia. The Ornithopoda and Ceratopsia were
(sauropods), and the Theropoda (theropods). The sauropods likely able to chew their (vegetable) food, whereas other her-
mainly include large herbivores with often very long necks, bivorous dinosaurs crushed their food using stomach stones,
such as the Brachiosauridae or Titanosauria. The theropods known as gastroliths. The adaptation allowing for the chew-
include various groups of mainly bipedal carnivorous dino- ing of food likely was influential in these two groups gaining
saurs, including Ceratosauria (smaller and larger theropods ecological importance towards the end of the Cretaceous pe-
from the Lower Jurassic to the Upper Cretaceous), and the riod, at the same time that angiosperm and grass populations
Carnosauria (large theropods such as Allosaurus) but not also flourished.
Tyrannosauridae, with their different bone struture. Coe- The collision of the continents into the super continent
lurosauria are also theropods and are characterised by thin- Pangea favoured the global spread of the Dinosauria and led
walled bones and therefore a lighter physique. Most Coe- to a globally similar dinosaur fauna. With the break apart
lurosauria ran on strong hind legs and had arms equipped of Pangaea in the Upper Jurassic and Cretaceous, the dino-
with claws, well-suited for grasping prey. The group notably saurs diversified on each continent. In the Upper Cretaceous,
included the Tyrannosauridae (including Tyrannosaurus rex), North America was dominated by the herbivorous Hadro-
the Dromeaeosauridae (including Velociraptor spp. and other sauria, Ceratopsia, Ankylosauria, Pachycephalosauria, as
raptors) as well as Aves (birds) as the only extant dinosaurs. well as the carnivorous Tyrannosauria. At the same time,
Birds evolved in the Middle Jurassic. Archaeopteryx, which Europe was dominated by the herbivores Iguanodontia (Or-
displayed a number of avian but also reptilian features, can nithopoda), Nodosauria (Ankylosauria), Titanosauria (Sau-
be observed in fossils from the Upper Jurassic Solnhofener ropodomorpha), as well as the carnivorous Dromaeosauria.
limestone. The southern continents were likely dominated by the her-
The Ornithischia are a morphologically variable group of bivorous Titanosauria, with Ceratosauria as the dominant
primarily herbivorous dinosaurs, including the Heterodonto- carnivores.
sauria, which are characterised by their heterogeneous teeth
anapsids: monophyletic group of amniotes with skulls which endothermic: regulation of body temperature from within
have no temple fenestrae; extinct group of reptiles (such animals are usually warm-blooded (homeothermic))
diapsids: amniotes that have developed two fenestra in the gastroliths: hard objects, usually rocks, which are swallowed by
cheek and temple regions; includes most recent reptiles as well vertebrates to help them grind food in their stomach
as dinosaurs and birds
See also: Amniota: 4.2.1.9; Ornithodira: 2.3.2.8

The dinosaurs dominated terrestrial ecosystems since the Middle Triassic until the end of the Upper ilium
ilium Cretaceous. Around 530 genera have been described, whereas the estimated total number of dino-
saur genera is 2,000–3,500. The dinosaurs include all descendants of the common ancestor of birds,
as well as of Triceratops. They are divided into the orders Saurischia (‘lizard-hipped’), which originally
pubis ischium
were characterised by a pelvic structure featuring a protruding pubis and ischium bone (left), and the pubis
Ornithischia (‘bird-hipped’), characterised by their parallel and diagonal posteriorly extending pubis and
ischium ischium bone (right). The birds, however, belong to the Saurischia
Saurischia (lizard-hipped dinosaurs) Ornithischia (bird-hipped dinosaurs)
The Theropoda (left: Allosaurus) comprise mainly bipedal carnivores, The Ornithischia are a diverse group of mainly herbivorous dinosaurs
whereas the Sauropodomorpha (right: Brachiosaurus) comprise mainly (left: Triceratops; right: Stegosaurus)
large herbivores
Coelurosauria: e.g. Dromaeosauridae (Middle Heterodontosauridae: Upper Triassic to Lower
Jurassic to Upper Cretaceous, 168–66 mya, e.g. Cretaceous (228–113 mya). Small (0.5–2 m), bi-
Velociraptor) and Aves (birds) pedal, herbivorous or omnivorous dinosaurs (Het-
erodontosaurus)
Basal Coelurosauria: e.g. Compsognathidae (Up- Stegosauria: Middle Jurassic to Lower Cretaceous
per Jurassic to Lower Cretaceous, 157–100 mya, (170–100 mya). 3–9 m large, herbivorous dino-
usually < 1 m), Tyrannosauroidea, (Middle Jurassic saurs with a double row of bony plates and spines
to Upper Cretaceous, 168–66 mya, over 12 m tall (Stegosaurus)
Carnosauria: Lower Jurassic to Upper Cretaceous Ankylosauria: Middle Jurassic to Upper Cretaceous
(199–66 mya). Large, bipedal, carnivorous Dino- (166–66 mya). Medium (3–6 m) to large (9 m)
sauria (Allosaurus: 12 m; Sinraptor: up to 8 m; Gi- quadruped, herbivorous dinosaurs with character-
ganotosaurus: 13 m istic armor
Ceratosauria: Lower Jurassic to Upper Cretaceous Ornithopoda: Lower Jurassic to Upper Cretaceous
(191–66 mya). Morphologically variable group of usu- (201–66 mya). Medium to large, bipedal but also
ally bipedal, carnivorous dinosaurs. Small (Ligabuei- secondarily quadrupedal, herbivorous dinosaurs,
no, 70 cm) to larger species (Carnotaurus, up to 9 m) e.g. Hadrosaurus and Iguanodon
Herrerasauria: Upper Triassic (235–208 mya). Pachycephalosauria: Middle Jurassic to Upper Cre-
They belong to the earliest dinosaurs, around taceous (166–66 mya). 1–6 m tall, bipedal, likely
3–5 m tall, bipedal, carnivorous species (Herrera- herbivorous dinosaurs with thickened skullcap, e.g.
saurus, Staurikosaurus) (Pachycephalosaurus)
Sauropodomorpha: Upper Triassic to Upper Cre- Ceratopsia: Upper Jurassic to Upper Creta-
taceous (235–66 mya). Very large (up to 40 m long ceous (163–66 mya). 1–8 m large herbivores,
and 17 m high) dinosaurs, primarily herbivorous, often with a neck shield and/or horns, e.g. Tri-
including Brachiosaurus ceratops
Some groups of large reptiles from the Mesozoic are colloquially referred to as saurian, but do not belong to the dinosaurs. This applies to the Sau-
ropterygia (Lepidosauromorpha), mainly aquatic ‘finned saurian’ (top-left), the Ichthyopterygia, the also aquatic ‘fish lizards’ (bottom-left), as well as
a number of basal Diapsida groups and the Pterosauria, the flying saurians (right). The pterosaurs ruled the skies long before birds appeared but their
populations became increasingly displaced when birds appeared, surviving as gigantic gliders along the coasts
Pterosauria
Sauropterygia
Ichthyopterygia
2.3.4.5
The Cretaceous period

The Cretaceous covers the period from 145 to 66 million whilst larger and more specialised lineages were repeatedly
years ago and is divided into the Lower (145–100 million more vulnerable during different smaller extinction events.
years ago) and Upper (100–66 million years ago) Cretaceous Mammals had a decisive advantage over the archosaurs be-
epochs. During the Cretaceous, Gondwana began to break cause of their highly developed teeth. However, mammals
apart: the South Atlantic formed between Africa and South dominated the fauna only after the disappearance of the
America, and Australia separated from Antarctica. At the dinosaurs at the Cretaceous-Palaeogene boundary. Major
same time, India split from Africa and began to drift north- groups of social insects also evolved during the Cretaceous,
wards. The Cretaceous climate was still warm and balanced, including termites and ants. Snakes also emerged in the Mid-
characterised by atmospheric decreases in carbon dioxide dle Cretaceous, becoming important not before the Cenozoic
and increases in oxygen. as their preferred prey, i.e. mammals.
Giant Sauropodomorpha became less important at the be- Angiosperms appeared in the Lower Cretaceous (the
ginning of the Cretaceous (except, perhaps, in South Amer- Hauterivian) and spread widely in the upper Lower Cre-
ica) and were increasingly replaced the Ornithischia. The taceous (Albian). In lowlands until 90 million years ago,
Theropods remained the dominant carnivores. angiosperms made up already approximately 70 % of all
The diversity of species grew as a result of increasing isola- plant species. Their spread may have been enabled by the
tion of faunal provinces. In the Upper Cretaceous, small pred- activities of fruit- and seed-specialised pterosaurs. Angio-
atory dinosaurs (troodontids, elmisaurids, avimimids) lived sperms flowers of the Middle Cretaceous were pollinated by
alongside giant species, such as Tyrannosaurus, Tarbosaurus, the activity of pollen-eating insects. Flowers specialised on
and Albertosaurus. The birds, which also belonged to the thero- nectar-collecting insects appeared later. The spread of angi-
pods, also diversified throughout the Cretaceous, increasingly osperms correlated with a change in dominant herbivores,
displacing the pterosaurs from their ecological niches. from sauropods to Ornithischia. In parallel, modern conifer
Mammals were diverse and adapted to a number of differ- populations (Pinus, Picea, Larix, Cedrus, Metasequoia) spread,
ent ecological niches. However, they evolved from relative- whereas seed ferns and Bennettitopsida died out in the upper
ly unspecialised, shrew mouse-like animals, which thrived Lower Cretaceous.
Unlike in mammals, the evolution of size in pterosaurs giant fish-eating or water-filtering gliders along coastlines.
during their first 70 million years was not restricted by com- Pterosaurs subsequently died out around the Cretaceous-Pal-
petition with other animal groups. During the Jurassic, the aeogene boundary, while around 20 different bird lineages
typical pterosaur wingspan was around 1.2 m, doubling in survived
size around the border at the Lower Cretaceous and increas- The ability to fly seems to be selected for small genomes:
ing further to around 7 m during the Cretaceous period itself. modern birds have relatively small genomes compared to ex-
The enlargement of the pterosaurs was not correlated with tant mammals and reptiles. In addition, flightless birds have
the increase in size of the sauropods, but occurred in parallel a slightly large genome. A similar trend is observed in bats,
with the appearance of the ancestors of modern-day birds, which also carry a smaller genome than their flightless sister
the gliding or nonvolant Maniraptora groups (e.g. insectivores). This trend is explained by the fact
Presumably, birds were competitively stronger than the that genome size is correlated with cell size and hence also
pterosaurs and increasingly suppressed them from the niche to metabolic demand.
spectrum of smaller flyers. As a result, during the Creta- Grasses first appeared in the Upper Cretaceous, first in
ceous only very large pterosaurs were able to successfully damp habitats and then, from the Miocene onwards, also in
outcompete other lineages within their niche, in particular significantly drier habitats.
faunal provinces: a term similar in meaning to fauna kingdoms;

regions that differ markedly from other regions due to their
endemic taxa
See also: Haptophyta: 4.7.1; Co-evolution: 2.3.4.6, 4.4.3.9

Todays dominating vertebrate groups became dominant in the Cenozoic. Plants which dominated during the Cenozoic began to spread wider in the
Specifically this included the mammals and the birds (here: Longipteryx Cretaceous. This was particularly true for the grasses (here: grass frag-
chaoyangensis) ment from dinosaur coprolites)
Eurasia
tic
an
h Atl n
r t a
No Oce
Tethys Ocean
Pacific Ocean
South Atlantic
Ocean
Sahara India
Cape Siberia
Haptophyta, which form calcareous scales, dominated the phytoplankton dur- Persian Gulf Ruhr area
ing the Cretaceous. The fossil remains of these organisms, known as cocco-
liths, are a major component of eponymous cretaceous marine sediments – the
chalkstone Mexico Australia
During the Cretaceous, the Ancyloceratina The Belemnitida (belemnites) were widespread During the Cretaceous, diatoms (Bacillariophyce-
(Ammonoidea) appeared (here: Aegocrioceras cephalopods of the Jurassic and Cretaceous ae) became increasingly important within marine
spathi), an organismal group characterised by plankton populations. The plankton composition
their heteromorph morphology (irregularly, in- at that time began resembling what it is today
completely coiled shell)
2.3.4.6
Evolution of pollination
Pollination can be either wind- (anemophilous) or ani- For example, they usually produce a very high number of
mal-driven (zoophilous). The first seed plants were anemo- pollen and, in addition, their surface area is enlarged in or-
philous, with zoophilous flowers having evolved from der to increase chances of contact between pollinators and
anemophilous ancestors. This development was likely done pollen grains. This increased surface area is achieved by the
relatively early, since all extant angiosperms are pollinated excretion of a pollination drop. This drop contains sugar, in-
either by animals or derived from animal-pollinated ances- creasing stickiness and reducing rates of evaporation. Early
tors. insects with mouthparts designed for licking or sucking prob-
Zoophilous pollination evolved through associations ably developed a habit of eating this pollination drops and
of flowers and insects, which used specialised structures the excretion of the stigma of early angiosperms. Finally, the
or excretions located in or near the (originally anemophil- morphology of pollinators evolved in parallel with that of
ous) flower as a source for food. Pollen from wind-polli- flowers, which developed specialised flower morphologies
nated plants is dispersed randomly by the wind. However, and structures, such as nectar leaves, to facilitate the pollina-
wind-pollinated plants have a number of specialised adap- tor-flower interaction.
tations that increase the likelihood of successful pollination.
Beetles or flies were the most likely pollinators of early an- plex system and is therefore likely not regarded as primordi-
giosperms, whereas todays flower-pollinating Hymenoptera al. In addition, and also in contrast with earlier assumptions,
groups, especially the social insects, evolved only later. From robust and therefore well-protected flower structures (e.g. in
the Mesozoic, associations of beetles as well as of insects the magnolia) are not older than other flower types: the first
with leaking-sucking mouthparts (particularly flies) with angiosperms originated around 140 million years ago. Her-
flowers are known. maphrodite flowers with many floral organs (similar to to-
Earlier theories assumed that the first pollinating insects day’s magnolias) and flowers with few floral organs (similar
were beetles with biting mouthparts and that consequently to pepper plants) emerged at around the same time.
more robust flower architecture as well as integuments (and It is believed that the first flower-pollinating insects had
with that angiospermy) evolved as a response for the protec- specialised leaking-sucking mouthparts. The evolution of
tion of the ovules. However, closed carpels and integuments zoophilous pollination started likely from associations with
likely did not evolve in order to achieve better protection of flies. These unspecialised opportunist pollinators did not
the ovules from grazing. The formation of closed carpels show flower constancy. Nevertheless, they probably visited
supports an efficient development of the pollen tube and flowers of the same species regularly, as wind-pollinated
therefore likely developed independently. It is unclear wheth- plant species usually occur in high densities. The develop-
er zoophilous pollination arose before or after the evolution ment of stronger flower constancy likely took place later in
of closed carpels. However, cantharophily, the cross-pollina- the evolution of angiosperms.
tion of flowers by beetles that feed on the pollen or on some
of the juicy tissues in the flower, is a highly evolved and com-
carpel: (Grk.: karpos = fruit) organs of a flower with one or flower constancy: flower constancy: preference of individual
more ovules pollinators for the flowers of specific plant species
Coleoptera: order of beetles Hymenoptera: order of flying insects (bees and wasps)
Diptera: order of two-winged insects (flies and mosquitoes) Lepidoptera: Insect order which includes butterflies and moths
See also: Angiosperms: from 4.4.3.6 to 4.4.3.9

Many anemophilous plants increase their likelihood of fertilisation by producing a pollination drop at their stigma, a part of the pistil (top-left: pollina-
tion drop of Ginkgo). Pollination drops contain sugars and thereby become ‘sticky’ to ensure that pollen grains stick more readily to the stigma. Early on
in their evolution, insects began using these sugars as a food source, thus contributing to the targeted dissemination of pollen (top-right). Insect-polli-
nation likely developed from such associations between wind-pollinated plants with nutrition-seeking insects. (left-bottom: stigma strewn with pollen;
centre-bottom: bee on a winter aconite flower Eranthis hyemalis; right-bottom: nectar gland of the winter aconite
Monokotyle Dikotyle Coleoptera Diptera Lepidoptera Hymenoptera
Cenozoic
Gymnospermae
Mesozoic
Palaeozoic
50,000 plant species 20 insect families
The diversity of many insect groups increased sharply during the Mesozoic. The great diversity of insect groups, especially those with the habit of visiting
flowers for nutrition, provided the foundation for the radiation of the flowering plants in the Cretaceous. After the radiation of flowering plants, insects
diversified further in the Cenozoic
2.3.5
The Cenozoic era

The Mesozoic was followed by the Cenozoic era, begin- The formation of these high mountain areas led to increased
ning around 66 million years ago and is still ongoing. The levels of erosion and thus higher influx of calcium and mag-
Cenozoic is divided into the Palaeogene, Neogene, and Qua- nesium ions in the oceans. In turn, this caused increasing
ternary periods. lime precipitation, consequently leading to the withdrawal
In turn, the Palaeogene comprises the Palaeocene, Eo- of carbon dioxide from the atmosphere. At this point, the
cene, and Oligocene epochs, which can be further subdivided carbon dioxide concentration of the atmosphere dropped
into nine ages. The Neogene includes the Miocene and Pli- from 1,000 ppm to around 500 ppm, significantly cooling
ocene epochs, which include eight ages. Finally, the Quater- the climate. This phase characterised by a sharp drop in car-
nary includes the Pleistocene, which comprises four ages, as bon dioxide concentrations corresponds approximately with
well as the Holocene, which is not further divided. the evolution of more efficient carbon dioxide fixation mech-
In the early Palaeogene, the climate was warm and hu- anisms in plants, especially C4 photosynthesis. Yet another
mid. During this period, the Indian and Asian tectonic plates sharp decline in carbon dioxide levels to under 300 ppm was
collided resulting in the upfolding of the Himalayas. At the experienced during the upper Miocene and Pliocene, final-
same time the African plate pushed the Adriatic and the Eu- ly resulting in the Cenozoic Ice Age. The period comprising
ropean plates together resulting in the upfolding of the Alps. these glaciations is known as the Quaternary.
The Cenozoic was previously divided into the Tertiary importance of anthropogenic activity. As a result, the Gela-
and Quaternary periods. In this paradigm, the Tertiary com- sian was shifted to the Quaternary after being the youngest
prised the Palaeocene, Eocene, Oligocene, Miocene, and Pli- age within the Pliocene, lengthening the Quaternary period
ocene epoch. The Gelasian age, which is now assigned to the from 1.8 to 2.588 million years. As a result, all glacial strata
Quaternary, was previously listed as the youngest age within now belong to the Quaternary.
the Pliocene, and thus within the Tertiary. Due to this strong The Cenozoic in general, and especially its youngest pe-
imbalance in length between the Tertiary (~63 million years) riod, the Quaternary, comprises relatively short geological
and the Quaternary (~2.5 million years), the Cenozoic was time frames. This is often justified by the relatively important
reorganised into the Palaeogene (43 million years) and Ne- influence of its constituent ice ages within the development
ogene (23 million years). This new proposed organisational of the planet. However, ice ages within older eras were not
structure has been widely accepted internationally. However, divided into their own periods. The exceptional position of
a recognition of the Quaternary was also increasingly prop- the Quaternary as the youngest period is therefore more like-
agated and finally accepted as a result of its strong climatic ly motivated by its exceptionally good remaining physical re-
(Ice Age) and ecological differences, as well as the increasing cord as well as its importance with respect to hominisation.
anthropogenic: (Grk.: anthropos = man, gen = cause) caused, of physical and mental characteristics such as the ability to walk
influenced, brought about by human beings upright and an enlarged brain
hominisation: the evolution of modern man, particularly in ppm: parts per million
the last five to seven million years, including the development
See also: C4 photosynthesis: 2.3.5.3, 2.3.5.4; Carbon dioxide concentration: 2.3.1.1

The Phanerozoic eon: the Cenozoic era 139
Holocene 0.0117 Ma
Quaternary Pleistocene Calabrian
1.806 Ma
Gelasian 2.588 Ma
Piacenzian
3.600 Ma
Pliocene Zanclean Upper Pleistocene
5.333 Ma
Messinian
7.246 Ma 0.126 Ma
Tortonian
11.62 Ma
Neogene Serravallian
13.82 Ma
Miocene
Langhian
15.97 Ma
Burdigalian
20.44 Ma
Aquitanian
23.03 Ma
Chattian
Middle Pleistocene
28.1 Ma
Oligocene
Rupelian
33.9 Ma
Priabonian
38.0 Ma
Bartonian
41.3 Ma
Palaeogene Eocene
Lutetian
0.781 Ma
47.8 Ma
Ypresian
56.0 Ma
Thanetian
59.2 Ma
Selandian
Palaeocene Stratigraphic time scale of the Cenozoic
61.6 Ma The Holocene is an epoch within the Quater-
nary. It is too short to be shown to scale and
Danian therefore only shown at the level of stages
66.0 Ma
2.3.5.1
The Palaeogene period

The Palaeogene is the oldest period within the Cenozoic, in a mostly temperate climate. The air temperature was so
lasting from 66 to 23 million years ago. It is further subdi- moderate during this time that even the poles were not glaci-
vided into the Palaeocene (66–56 million years ago), Eocene ated and climate at the poles was temperate.
(56–33.9 million years ago), Oligocene (33.9–23 million Only in the Oligocene were the continents far enough
years ago) epochs. apart that a circumpolar oceanic current could form. Dur-
At this time, the Atlantic was initially not fully developed. ing this time, the climate cooled by around 5 °C and glaciers
By the end of the Palaeocene, Greenland and Europe had began to expand. As a result of the increased glaciation, sea
drifted apart, but a land bridge still existed between Eurasia, levels dropped by up to 150 m, drying out a number of shal-
Greenland, and the North American continent. In addition, low seas and, among other things, connecting the Iberian
during the Palaeocene, Africa and India were already sep- Peninsula to Europe and Europe, in turn, to Asia. At this
arated from the other southern continents, but Antarctica, time, the Tethys Ocean was separated into the Mediterrane-
Australia, and South America were still connected with each an Sea and the Para-Tethys Ocean in eastern Europe. During
other. They remained relatively close together, even when the the Oligocene, the African continent was still largely isolated
southern continents finally did separate, during the Eocene. from Europe and Asia. At the same time, the folding of the
The early Palaeogene was slightly cooler than the Cretaceous, Alps and the uplift of the Rocky Mountains reached their
but it warmed slightly as the period progressed. The Palae- climax during this epoch.
ocene-Eocene boundary itself was marked by a temperature The early Palaeogene was also characterised by a radia-
rise of around 5–6 °C, possibly as a result of the release of tion and diversification of birds and mammals. Towards the
carbon dioxide or methane hydrate, before declining again to end of this period, proboscideans were the largest land mam-
their previous values over a period of approximately 200,000 mals. The fauna on each continent initially developed large-
years. The Palaeocene and Eocene epochs were overall hu- ly in isolation. However, a land bridge between Africa and
mid and warm. The position of the continents resulted in Eurasia, which formed around 27 million years ago, allowed
warm water moving southwards along the coasts, resulting animals to once again spread themselves further.
The Alpine orogeny refers to the last global mountain Europe while Africa drifted further to the northeast causing
building phase in Earth’s history, during which the Alps were the uplift of the Western Alps and the Apennines. At the
formed. The process of this orogeny lasted from the Cre- same time the older Variscan mountains of middle and west-
taceous through the strongest uplift phase of the Miocene ern Europe, began to rise over the sea surface of the Para-Te-
around 20 million years ago until present days. In total, the thys once again. At the end of the Palaeogene, the Alps were
Alpine orogeny encompassed a time frame of around 100 largely upfolded. The Para-Tethys Ocean closed except for
million years, fading since around 5 million years. The ice a few residual basins (such as the Black and Caspian seas).
ages of the Pleistocene in the last 2 million years significant- The formation of mountains (Alps, Himalayas) and the
ly influenced the appearance of the mountains in existence increased precipitation of carbonates led to a reduction of
today. As part of the alpine orogeny, the Atlas, Pyrenees, carbon dioxide concentration, thus contributing to climat-
Balearic Islands, Alps, Carpathians, Apennines, Rhodopes, ic cooling. Later in the Oligocene, the climate cooled even
Balkans, Anatolia, Caucasus, Hindu Kush, Karakoram, and more, until Antarctica was finally glaciated roughly 30 mil-
the Himalayas all the way to the western mountains of Indo- lion years ago. Through the cooler and drier climate, the de-
china and Malaysia had been formed. sert stretched out across the subtropics, and increasing glaci-
In the early Palaeogene, the Adriatic micro-plate, which ation rates caused lowering of sea levels over extensive land
segregated from the African plate, collided with pre-Alpine areas along the margins of continental shelves.
trunked mammals: order Proboscidea, the only living family is

the Elephantidae (elephants)
See also: Magnoliopsidae: 4.4.3.6

Ancestors of the horse alive during the Eocene and Miocene (here: In the Cenozoic, as the climate became cooler and drier, open grasslands
Mesohippus) displayed various adaptations to an increasingly drier spread further across the planet. Grasses and herbaceous angiosperms
steppe-like habitat: their legs were significantly lengthened and their became more common. The mutualistic relationship between insects
incisors facilitated the consumption of relatively harder grasses (as and flowers caused a further diversification of both insects and flowers
compared to foliage)
Atlantic
Ocean
Pacific Ocean
Indian Ocean
Sahara India
Cape Siberia
The diversity of insects exploded during the Palaeogene. The fossil record of Persian Gulf Ruhr area
insects in in tree resins (amber) from the Cenozoic is much better than from Great Lakes South China
previous chronostratigraphic systems
Mexico Australia
More modern marine taxa also developed during the Palaeogene, including the whales, The importance of snails as index fossils increased during the
emerging in various intermediate forms during this time. The Basilosauridae (here: Palaeogene. The moon snails shown here (Crommium wil-
Dorudon atrox), which lived around 35 million years ago, were among the first whales lemeti – Naticidae) fed on mussels, scaphopods, and other
living exclusively in water. Their hind legs were greatly reduced, but still complete snails, drilling through their shells and consuming them using
their radula and acidic excretions of their boring gland
2.3.5.2
The Neogene period

The Neogene period spans from 23 to 2.6 million years periods, the polar ice caps melted completely and the result-
ago and is divided into the Miocene (23–5.3 million years ing rise in sea level flooded parts of Europe with shallow seas
ago) and the Pliocene (5.3–2.6 million years ago) epochs. and caused the continent to disintegrate into smaller islands.
The Miocene epoch is characterised by the Alpine oroge- The Rhone and Tagus basins were, at that point, large shal-
ny. The African plate pushed the Adriatic plate as an indent- low seas on the European continent.
er into the Eurasian plate, causing the folding of the Alps. At that time, Europe’s flora was dominated by subtrop-
At the same time, the folding of the Himalayas, caused by ical species, such as evergreen deciduous forests of oak, as
the collision of the Indian and Eurasian plates proceeded. well as members of the laurel family, magnolias, pines, figs,
In North America, the Rocky Mountains rose during the and rattan palms. Mangroves grew along Europe’s coast-
Miocene. During the Pliocene, global mountain building lines. However, the climate started cooling and drying again
has come to a standstill, but the mountains are still being around 15 million years ago during the Middle Miocene.
uplifted. In addition, the Pliocene is characterised by the for- Finally, in the Pliocene, the climate was relatively stable
mation of a land bridge between North and South America. and warm, with annual average temperatures of around 5 °C
The Miocene was an epoch of climatic warming. Already higher than they are today. A further cooling period occurred
in the Lower Miocene, warm temperate to subtropical cli- during the end of the Pliocene, the start of an impending ice
mates prevailed even in northern latitudes. During certain age.
Savannah grasslands became widely distributed during Vast moors and forests could be seen during the Palaeo-
the Miocene. The land bridge (isthmus) between North and gene and the Neogene periods. These habitats are responsi-
South America did not yet exist during the Miocene and, as ble for formations of lignite currently found in the Lusatia
a result, the South American fauna was still isolated. On the and Rhenish lignite mine district. The sedimentary rocks
other continents, the ancestors of today wolves, cats, horses, from the Miocene are therefore of great importance to the
deer, and camels developed. Proboscideans flourished dur- hydrocarbon production and energy industry. Specifically in
ing the Miocene and several currently-extinct groups were the areas around the Para-Tethys Ocean, oil and natural gas
also prevalent, including Barbourofelidae (false saber-tooth deposits are bound to Miocene sandstone.
cats) and Chalicotheres, a group of browsing odd-toed un-
gulates.
transgression: marine transgression takes place when the sea

advances rapidly into continental regions and is caused by a drop
in the sea floor or a rise in sea level
See also: Hominisation: 2.3.5.7

Early ancestors of humans developed during the Neogene, including The monocots and, in particular, the grasses, began to spread further
Sahelanthropus tschadensis (left). Later on, the australopithecines (right: during the Neogene (here: leaves from a monocot). The increasingly cool-
Australopithecus afarensis) populated different habitats and began to dry climate favored the spread of grasslands
diversify
Atlantic
Ocean
Pacific Ocean
Indian Ocean
Sahara India
Cape Siberia
In the Neogene, much of the flora already resembled modern-day species. The Persian Gulf Ruhr area
forests were populated by pines (top: Pinus brevis) and maples (bottom: Acer Great Lakes South China
sp.) amongst others. From these forests, by repeated transgressions of the North
Mexico Australia
Sea, the lignite deposits of the ‘Rhenish lignite mine district’ were formed
Foraminifera Elphidium sp., which belongs to the The snail Bivetiella cancellata, belonging to the Mussels were dominant filter feeders in marine
Rotaliida, from the Pliocene Cancellariidae benthic habitats. Above: Glycimeris sp. from the
Miocene; Below: Dentalium solidum from the
Lower Pliocene
2.3.5.3
Evolution of C4 photosynthesis
In the Oligocene, 35–30 million years ago, the carbon di- synthesis is particularly advantageous under hot-dry climatic
oxide concentration of the atmosphere decreased to below conditions. Although only around 3 % of extant plant species
500 ppm. As a result, the global climate became cool and carry out C4 photosynthesis, the process contributes around
arid. The first C4 plants arose during this period and per- 23 % to terrestrial primary production. Most types of C4
haps slightly earlier. During the Miocene, C4 photosynthesis plants – around 60 % – are grasses living in subtropical and
evolved in many different plant lineages. At first, these plants tropical climates. The high productivity within these eco-
played a quantitatively minor role. The more arid conditions systems is a prerequisite for the high densities of herbivores
were initially reflected in the shift from forest to C3 grassland. found there.
The diversification and propagation of many succulent plant The shift from forest to grassland on the one hand (be-
groups, such as cacti, occurred in parallel to the spread of fore 30–10 million years), and from C3 to C4 grassland on
grasslands around 10 million years ago. the other (mainly in the last 10 million years), were therefore
Before around 10 million years, the CO2 concentration of temporally separate events. This fundamental change within
the Earth’s atmosphere dropped further below 300 ppm and tropical and subtropical ecosystems created the foundations
the climate became increasingly arid. As a result, C4 plants for the spread of large herbivores and thus contemporary Af-
spread quickly across the savannas and grasslands, coming to rican savanna food webs around 1.8 million years ago as well
dominate the lower latitudes since at least 2–3 million years. as for the evolution of hominids and humans.
C4 photosynthesis arose as a consequence of the reduced
availability of carbon dioxide in the atmosphere. C4 photo-
C4 photosynthesis is particularly important in warm cli- Therefore, C4 photosynthesis is more important in warm-
mates because photorespiration plays a greater role at higher er and drier habitats and a higher proportion of C4 plants is
temperatures. One reason for this dependence on tempera- found in dry subtropical climate zones. This is particularly
tures for photorespiration is due to the differential temper- evident in the distribution of vegetation in Africa and Aus-
ature dependence of oxygen and carbon dioxide solubility tralia. Within a climatic zone, the proportion of C4 plants
in water. Carbon dioxide solubility in water decreases more increases with increasing aridity. For example, low rainfall
strongly with increasing temperature compared to oxygen. areas in mountain lees, such as for example to the west of the
As a result, under high temperatures, RubisCO converts Himalayas or east of the Rocky Mountains, are particularly
more oxygen. densely populated with C4 plants.
The importance of C4 photosynthesis also depends on In Central Europe, as a result of climatic changes, the
the availability of water: in a dry climate, plants come under moist and warm lignite swamplands were replaced by grass-
increased water stress and, in order to reduce evaporation, lands adapted to drier and cooler conditions. However, due
stomata are shorter or open for a shorter time. Consequently, to the cooler temperatures compared with tropical and sub-
less carbon dioxide moves into the cells and the ratio of oxy- tropical habitats, photorespiration played a smaller role and
gen to carbon dioxide is therefore unfavourable. the flora is therefore dominated by C3 plants.
arid: dry stomata: pore in a plant which serves to regulate gas exchange
ppm: parts per million with the environment; the resultant transpiration cools the tissue
RubisCO: RubisCO (ribulose-1,5-bisphosphate carboxylase/oxy- succulent: (Lat.: sucus = juice, suculentus = juicy) having thick
genase); act as centres of carbon dioxide enrichment fleshy leaves or stems adapted to storing water
See also: Savannah: 3.2.2.10; Evergreen tropical forests: 3.2.2.11; PEP-carboxylase: 2.3.5.4
In North America, precipitation coming In Europe, C4 photosynthesis is only signifi- Southern Asia lies in the catchment area of
from the West is blocked by the Rocky cant in areas around the Mediterranean. In eastern to northeastern trade winds. Conse-
Mountains and precipitation from the East the continent’s cooler regions, in Northern quently, regions to the West of the Himala-
becomes sparse towards the West. As a and Central Europe, photorespiration plays a yas lie in the lee of mountains and receive
result, C4 photosynthesis is relatively more minor role in C3 plants and, as a result, these relatively low levels of precipitation. These
important to the South (warmer) and to the species remain strongly competitive hot-arid regions are dominated by C4 plants
West (drier) of the continent
100
50
C4 plants dominate the arid subtropical sa-

vanna and semi-desert areas of Africa. They
0 are less prevalent in the humid tropical for-
ests and rainforest areas
Present-day distribution of C4 photosynthesis
History of climate and vegetation The first C4 plants appeared around 30 mya.
The folding of the Himalayas started around Since then, C4 photosynthesis has developed
49 mya. Around 34 mya, the Himalayas were independently approximately 70 times
so high that they heavily influenced climatic
conditions: the accompanying weathering C4 ecosystems become more widespread
of silicates led to the release of calcium and Great Plains, USA around six million years ago, especially C4
subsequently to the formation of limestone grasslands
from calcium and carbonate.
The equilibrium reaction between carbon
dioxide and carbonic acid (which, in turn,
Pakistan Climatic changes since the Oligocene led to a global ex-
dissociates into carbonate) removes large
amounts of carbon dioxide from the at- pansion of arid habitats. Water stresses favoured the
mosphere; as a result, atmospheric carbon spread and diversification of succulents and of C4 and
dioxide concentrations fell sharply around CAM-plants. The forests (green) were replaced by grass-
Kenya lands (yellow). With the further spread of arid habitats,
35–30 mya to below 500 ppm, decreasing
the greenhouse effect and leading to a gen- C4 plants spread increasingly (red line) from the upper
eral global cooling Miocene
Carbon dioxide concentrations fall

below 300 ppm and the warm-
Estimated development moist climate of the Miocene is The evolution and spread of C4 photosynthesis was linked
of global temperatures replaced by the cool-dry climate of to declines in atmospheric carbon dioxide. As a result, Ru-
the Pliocene BisCO became increasingly inefficient on the one hand as
a direct consequence of decreasing carbon dioxide con-
centrations, on the other hand oxygen became increas-
1,000 ppm ingly used as a substrate (photorespiration). Compared
with RuBisCO, PEP-carboxylase can operate at lower car-
bon dioxide concentrations, since it uses hydrogen car-
bonate. At neutral pH, in equilibrium bicarbonate is 50
500 ppm times more concentrated than carbon dioxide; in sum, C4
photosynthesis is still efficient at lower substrate concen-
trations, and photorespiration is suppressed
Estimated development of
carbon dioxide concentrations
Eocene Oligocene Miocene Pliocene

50 40 30 20 10 0 million years
2.3.5.4
Physiological efficiency of C4 and CAM photosynthesis

C4 photosynthesis has likely developed independently pre-fixation) by the enzyme PEP carboxylase forming a
approximately 70 times. This multiple evolution of C4 pho- C4-sugar (oxaloacetate).
tosynthesis in a geologically relatively short period of time Within the ‘normal’ form of C4 photosynthesis, the prefix-
indicates a strong selection pressure in favour of photosyn- ing is achieved via PEP carboxylase that occurs in the mes-
thetic pathways that reduces the impact of photorespiration. ophyll cells; but they do not contain RubisCO. The resulting
The basic advantage of C4 photosynthesis is the mainte- oxaloacetate is transported into the bundle sheath cells. Here,
nance of a high carbon dioxide partial pressure for the Cal- carbon dioxide is released from the oxaloacetate, which is
vin cycle. In this way photorespiration, that is the use of ox- then used as a substrate by RubisCO. The same principle is
ygen in place of carbon dioxide, as a substrate by RubisCO, found in the CAM photosynthesis. However, the separation
is substantially suppressed. This high carbon dioxide partial of the pre-fixation via PEP carboxylase and the fixation via
pressure is achieved by a spatially separated pre-fixation (in RubisCO is implemented in CAM photosynthesis within the
the case of a CAM photosynthesis this is a time separated same cells.
Solar radiation is steadily increasing since the forma- Basically, the C3-photosynthesis is more energy efficient.
tion of the solar system. A uniform climate is achieved by Only three molecules of ATP and two molecules of NADPH
geochemical and biological feedback of greenhouse gases are spent for the fixation of a carbon atom. In the C4 photo-
(mainly carbon dioxide concentration). The carbon dioxide synthesis five ATP and two NADPH molecules are needed;
concentration has accordingly decreased in the course of in CAM photosynthesis 4.8–5.9 ATP molecules and 3.2–3.9
Earth’s history. C4 photosynthesis became evolutionarily sig- NADPH molecules. The benefits of C4 photosynthesis (in-
nificant only with a decrease in atmospheric carbon dioxide cluding CAM) are the reduction of photorespiration and
concentrations below about 500 ppm. the efficient use of carbon dioxide. This allows for efficient
The enzyme PEP carboxylase uses the hydrogen car- photosynthesis with little water loss through transpiration.
bonate anion as a substrate, while RubisCO uses carbon The water use efficiency, i.e. the dry weight formed by pho-
dioxide. Under physiological conditions, the concentration tosynthesis in relation to the loss of water by transpiration is
of hydrogen carbonate in cytoplasm is significantly higher 1.0–2.2 g dry weight per ml of water in C3 plants, 2.8 to 4 g/
than of carbon dioxide. The efficiency of C4 photosynthesis, ml in C4 plants and 8–55 g/ml in CAM plants. CAM plants
therefore, is mainly due to the higher substrate availability can even maintain metabolism with closed stomata for a
for the PEP carboxylase (hydrogen carbonate) compared to while, by using carbon dioxide produced during respiration.
RubisCO (carbon dioxide).
ATP: adenosine triphosphate – transporter of energy within cells hydrogen carbonate anion: HCO3–
bundle sheath cells: cells surrounding the vascular tissue of NADPH: reduced form of nicotinamide adenine dinucleotide
plants phosphate (NADP)
Calvin Cycle: a series of reactions during photosynthesis in partial pressure of carbon dioxide: the degree of pressure
which carbon dioxide is converted into carbohydrates exerted by carbon dioxide in a mixture of gases
CAM (Crassulacean Acid Metabolism): temporal division be- PEP-carboxylase: phosphoenolpyruvate carboxylase
tween carbon fixation and the Calvin cycle
See also: Carbonate, Hydrogen carbonate: 2.1.2.3

The mesophyll of C4 plants is, in contrast to C3 plants, not subdivided into spongy and palisade parenchyma. The
mesophyll cells have plastids with grana and two photo systems (I and II). Here, the full light reaction occurs,
forming the reducing equivalents (NADPH/H+) as well as hydrolysis of water forming oxygen at the photo sys-
tem II. Hydrogen carbonate is bound by the enzyme PEP carboxylase to phosphoenolpyruvate in the mesophyll
cells. The first product of carbon fixation, the oxaloacetate, is composed of four carbon atoms. However, the
mesophyll cells do not contain RubisCO
PEP-carboxylase: PEP-carboxylase uses hydrogen carbonate
as a substrate and forms a C4 body
3 HCO3–
3 phosphoenolpyruvate 3 oxaloacetate
3 NADPH/H+
3 AMP + 3 Pi
3 NADP+
3 ATP
3 pyruvate 3 malate
3 pyruvate 3 malate
3 NADPH/H+ 3 NADP+
RubisCO: RubisCO
uses carbon dioxide as 3 CO2
substrate and forms a
6 3-phosphoglycerate 6 ATP
C3 body
In C4 plants, the diffusion of carbon dioxide through 6 ADP + 6 Pi
cell walls of the bundle sheath cells is generally limit-
ed by suberin depositions. The plastids of the bundle 6 NADPH/H+
sheath cells do not have any grana and almost only 3 ribulose-1,5-bisphosphate
photosystem I. This has two consequences: 6 NADP+
1. There is no NADP+ reduction. Reducing equiva- 3 ADP + 3 Pi
lents occur via the reduction of malate on the one
hand, on the other phosphoglycerate is imported
from the mesophyll cells and reduced in the plastids 3 ATP 6 glycerinaldehyde-3-phosphate
of the bundle sheath cells
2. The lack of activity of photo system II, the pho-
tolysis of the water and thus the oxygen evolution 3 ribulose-5-phosphate
is suppressed. High CO2 concentrations and low O2 glycerinaldehyde-3-phosphate
concentrations suppress the oxygenase activity of
Pi
RubisCO
2 H2O 5 glycerinaldehyde-3-phosphate
CAM plants bind hydrogen via PEP carboxylase to

3 HCO3–
phosphoenolpyruvate. In contrast to the C4 plants,
pre-fixation and Calvin cycle are not spatially dis- PEP-carboxylase
tributed on different cells, but separated in time. At
night, carbon pre-fixation takes place. The formed 3 phosphoenolpyruvate oxaloacetate
malate is stored in the vacuole. The phosphoe- NADPH/H+
nolpyruvate required is provided by breakdown of NADP+
carbohydrates, usually of starch
day
starch
malate
night malate
phosphoenolpyruvate
During the day, carbon dioxide is split off from AMP + Pi vacuole cytoplasm
malate within the chloroplasts and the resulting ATP
pyruvate is stored as starch. Carbon dioxide is fed to
the Calvin cycle. In contrast to C4 photosynthesis the
site of photolysis of water (oxygen formation) is not pyruvate malate
NADPH/H+ NADP+
separated from the site of the Calvin cycle in CAM
photosynthesis. However, the oxygenase activity of RubisCO
RubisCO is greatly reduced by the high carbon diox-
ide concentration.
The CAM photosynthesis allows plants at closed sto- Calvin cycle
mata to survive for days until weeks, by recycling the
carbon dioxide formed by respiration
chloroplast
2.3.5.5
The Quaternary period

The Quaternary lasts from 2.6 million years ago until the nary are relatively well developed and can be easily identi-
present day. It is divided into the Pleistocene (2.6 million to fied. In addition, the Quaternary terrestrial environment was
11,700 years ago) and the Holocene (11,700 years ago until heavily overprinted by the multiple advances of glaciers.
the present). During the Quaternary, flora and fauna are also strong-
The Quaternary is the period of the Cenozoic (or Quater- ly influenced by the advances of glaciers and associated
nary) Ice Age. During this period hominisation took place, sea level variations. Especially in Europe, due to different
in other words, the evolution of humans. Although Antarc- mountain chains, a fragmentation of previously contiguous
tica was already glaciated in the late Palaeogene, beginning populations took place and consequentely, a biogeographical
around 30 million years ago, ice settled over the Arctic dur- differentiation. In contrast, the land bridges formed during
ing the Quaternary. As such, the Cenozoic Ice Age began cold phases facilitated the spread of animal and plant species
already in the Palaeogene, but the onset of glaciation in the across continental borders, a trend that has been increasingly
northern hemisphere marked the beginning of the Quater- reinforced during the Holocene by the anthropogenic spread
nary. During the Quaternary, glacial (cold phases) periods al- of animal and plants species.
ternated with interglacials (warmer phases). The last warmer An extinction event as big as the previous big five mass
phase of the Quaternary Ice Age is known as the Holocene. extinction events is thought to have been triggered by the
The continents reached their present-day position during dispersal of humans and increased industrialisation. The
the Quaternary. The Quaternary is relatively short in com- biological, geochemical, and climatic consequences of this
parison with other geological periods. As the Quaternary current species extinction remain unclear.
reaches up to the present day, sediments from the Quater-
The Cenozoic era was formerly divided into the Tertiary The Quaternary was once again recently introduced as
and Quaternary periods. Despite the sometimes thick Qua- the most recent geological period, extending over the older
ternary geological layers, the Quaternary period is relatively definition into the Gelasian age, which is now known as the
short compared with the Tertiary. Therefore, the Cenozoic oldest age within the Pleistocene. According to older defini-
was recently newly divided into the Palaeogene and Neo- tions, the Gelasian was known as the youngest age within
gene. the Pliocene. Definitions of geological history found in old-
The Neogene originally stretched until present day and er works may vary greatly compared with those used today,
included the Quaternary, which in the most recent definition especially in light of the redefinition of the Quaternary, a
has again been separated. factor that must be always be considered when consulting
older literature.
hominisation: the evolution of modern man, particularly in the mental characteristics such as the ability to walk upright and an
last 5–7 million years, including the development of physical and enlarged brain
See also: Erosion: 2.1.2; Hominisation: 2.3.5.7; Cenozoic mass extinction event: 3.2.1.8; Neobiota: 3.2.1.7
During the Quaternary, hominins spread across the whole planet (left: Fossil leaf collection from the Upper Pliocene near the Pliocene-Pleisto-
skull of Homo neanderthalensis from 50,000 years ago; right: cave paint- cene boundary from the lignite mine Garzweiler II
ing from Cueva de las Manos in Argentina)
Atlantic
Ocean
Pacific Ocean
Indian Ocean
Sahara India
Cape Siberia
The increasing importance of diatoms (top) within marine plankton was Persian Gulf Ruhr area
brought on by the increased release of silicate into the oceans. This phenome-
non is thought to have been caused by increased erosion due to the Cenozoic
formation of mountains (Himalayas, Alps) and the propagation of grass and the Mexico Australia
consequent changes in erosion behaviour Amazon Basin Antarctica
Giant armadillos of the genus Glyptodon were widespread in The saber-toothed cats of the genus Smilodon were common in North America dur-
South America, reaching a size of up to 3 m. They died out at the ing the Pleistocene. The up to 20 cm long teeth were likely used for hunting large
end of the Pleistocene mammals. Smilodon fatalis (top) was found in North America and in South America
west of the Andes. It is thought to have gone extinct around 12,000 years ago
2.3.5.6
The Cenozoic Ice Age

The Quaternary period corresponds to the Cenozoic Ice the climate around Antarctica cooled leading to further gla-
Age, which is characterised by changes between glacial (cold) ciations.
and interglacial (warmer) periods. Between long glacial pe- The closure of the Isthmus of Panama and thus the con-
riods and the considerably shorter interglacials temperatures nection of North and South America around 4.6 million
varied by around 10 °C. Overall, the climate was cooler even- years ago resulted in major changes to ocean currents in the
during the warmest interglacial periods of the Quaternary Northern Hemisphere. Warm tropical water was transport-
Ice Age than during the Palaeogene and Neogene. ed to the North, activating the Gulf Stream. The change of
During interglacial periods, ice remained on land masses ocean currents led to a warming up of the Northern Hemi-
near the poles as well as at high mountain regions. The Ce- sphere. The increased supply of warmer water led to higher
nozoic Ice Age lasts around 2.58 million years. levels of atmospheric moisture in the Arctic, leading to the
The Cenozoic glaciation arose from the drift of continen- further spread of glaciers since around 2.7 million years.
tal landmasses and the associated changes in global ocean In addition, decreasing volcanism caused greenhouse gas
currents. During the Oligocene, Antarctica shifted enough concentrations to fall in the atmosphere, causing a general
of a distance from Australia and South America to allow for cooling of the atmosphere and leading to further glaciation
a circumpolar oceanic current to form, blocking out warmer at the polar regions.
water masses from penetrating near Antarctica. As a result,
The general cooling of the Earth’s poles and thus the on- cles are called Milankovitch cycles. The associated changes
set of the Cenozoic glaciations is tightly linked to changes in in solar radiation and its distribution across the Earth are
plate tectonics. However, changes between glacial and inter- thought to drive the fluctuations between glacial and inter-
glacial periods during the Ice Age are driven by cosmic fac- glacial periods.
tors: Quaternary glacials last around 90,000 years compared An ice age is mainly divided by deposits caused by ad-
to the 15,000 years of interglacials. The triggers for fluctua- vances of glaciers. The comparison and the temporal cor-
tions between cold and warm periods are thought to be var- relations of glaciations in different regions are problematic.
iations in the position of Earth’s axis (obliquity of the eclip- It is therefore unclear whether, for example, the deposits of
tic) and changes in Earth’s orbit around the sun. The mutual Northern European Saale glaciation and the Riss glaciation
gravitation of the sun, moon, and Earth caused changes in in the Alps arose simultaneously. Quaternary stratification
the elliptical orbit of the Earth with a periodicity of around analyses are therefore regional and, depending on the re-
100,000 years. The skewness of the planet’s axis is affected gion, the last major ice advance is known as the Weichselian
at a period of around 40,000 years, and the relative position (Northern Central Europe), the Würm (Alpine region), De-
of the sun at the equinox (beginning of spring and autumn) vensian (British Isles), Valdai (Northern Russia), or the Wis-
alters with a periodicity of around 25,800 years. These cy- consin (North America) glaciation.
equinox: point in time at which the sun stands directly above interglacial: interglacial period; warm period between two gla-
the equator when day and night are of equal duration cial periods
See also: Plate tectonics: 2.1.1.2

The Holocene is the current interglacial within the Cenozoic Ice Age. Humans settled and
learned to use metals during this interglacial
11,700 years
The Weichsel glaciation (the Würm glaciation in the
Alps) is the most recent glaciation event, lasting from
around 115,000 to 11,700 years ago. During this time,
Scandinavia, the Baltic region, and much of the UK
were glaciated. As a result, the sea level fell by about
12 m, drying out the English Channel and opening up
a land bridge for the recolonisation of the British Isles
by European fauna for a short time. The Channel filled
up again with the continued retreat of glaciers and the
associated sea level rise, once again restricting the
exchange of many terrestrial species
Maximum extent of ice coverage during the

Weichsel and Würm glaciations
115,000 years
The Eemian interglacial (Northern Central Europe) is not precisely syncronal with the Riss-
Würm interglacial (Alps) and the Sangomonian (North America)
130,000 years
The Saale complex includes the Saale glaciation,
separated from the Fuhne glaciation by the Dömnitz
warm period. The Saale complex corresponds to the
Riss glaciation in the Alps
Maximum extent of ice coverage during the

Saale and Riss glaciations
300,000 years
The Holstein interglacial (Northern Central Europe) is not precisely syncronal with the
Mindel-Riss interglacial period (Alps) and the pre-Illinoian interglacial (North America)
320,000 years
The Elster glaciation advanced further southwards
than the Saale and Weichsel glaciations in eastern
Europe. The exact history of glaciation in the West
of Germany and further to the West is unclear, since
the Saale glaciation advanced further southwards
flattening the moraines of the Elster glaciation. In the
Alpine region, the Mindel glaciation correspond to the
Elster glaciation
Maximum extent of ice coverage during

the Elster and Mindel glaciations
400,000 years
Temperature development of the last

420,000 years
2.3.5.7
Hominisation
Hominisation refers to the biological and cultural devel- that remained in Africa. These four species of the genus
opments of humans (Homo). At the very earliest, based on Homo likely lived simultaneously and it is likely that the
fossils from Chad and East Africa, upright hominins evolved different lineages crossbred at times during the development
around 6–7 million years ago in Africa. Phylogenetically the of modern humans.
ancestors of chimpanzees diverged from the ancestors of hu- Homo sapiens has the largest skull and smallest masticatory
mans around 6.5–5.5 million years ago. apparatus of all primates and is distinguished from other
The australopithecines are an extinct group of hominins species of great apes through their bipedalism, a large
from around 3.5 to 1.8 million years ago. They lived for the neocortex (a region of the cerebral cortex), reduced incisors
most part in savannah and bush lands, specifically in gallery and canines, and by its sexual and reproductive behaviour
forests along watercourses. Although most australopithecines and distinctly material culture.
walked upright, they still regularly held onto or clung to trees. The Palaeolithic Age began around 2.6 million years with
The first representatives of the genus Homo (Homo the use of simple stone tools. In the Lower (early) Palaeolithic,
habilis and Homo rudolfensis) developed presumably from hominin populations learned to master fire and in the Middle
the australopithecines around 2–3 million years ago. Palaeolithic they were able to improve their development of
The skulls of these species are lighter than those of the tools, such as hand axes. Finally, blades and artworks were
australopithecines, with smaller upper and lower jaws, but produced since the Upper Palaeolithic. With the beginning
a larger brain volume. Homo erectus developed from Homo of reforestation after the onset of the Holocene warm period
rudolfensis and became the first member of the genus to around 11,700 years ago, new hunting techniques were
master fire and to leave the African continent. A further required, leading to the development of, in particular, bows
enlargement of the brain developed from Homo erectus and arrows. Stock farming and agriculture arose during the
leading to Homo heidelbergensis, roughly 800,000 years ago, Neolithic, in Mesopotamia around 13,000 years ago and in
and subsequently Homo neanderthalensis in Europe. Homo Europe around 7,500 years ago. The increased use of metals
sapiens developed from members of the Homo erectus lineage led to the Bronze Age, which started roughly 4,200 years ago.
The ancestors of modern humans evolved in Africa under open prey and gain access to the marrow of longer bones.
initially hot and humid climatic conditions. As a result of cli- Presumably, the targeted use of tools arose from this initial
matic change in connection with the dawn of the Cenozoic development. Probably the most important evolutionary
Ice Age, desertification spread across many parts of Africa step for early humans was the development of hunting and,
and the soft fruits and leaves that sustained hominid pop- linked to this, improvements in communication. Together,
ulations became increasingly scarce. As a result, australo- these changes led to the development of a larger brain.
pithecines split into two main lineages. The first was a more That eventually became a problem because the female pel-
‘robust’ lineage, with enlarged teeth and strongly developed vis could not enlarge itself sufficiently to accommodate the
masticatory muscles, specializing in fibrous, cellulose-rich growing head circumference of new-borns. For humans, this
food (grasses and seeds). The jaw muscles were hinged upon eventually led to the evolution of a shorter gestation period
a clearly visible bony crest on the vertex of the skull. The sec- and earlier birth, coupled with a longer brooding phase and
ond lineage became increasingly omnivorous, adding meat a prolonged childhood and adolescence.
to its diet likely after sharp stones were first used to break
gallery forest: a forest which forms a corridor along a river,

bordering on a landscape with markedly different vegetation, a
different type of forest, or no vegetation
See also: Climate development: 2.3.5.3

Lower Palaeolithic Middle Palaeolithic Upper Palaeolithic Bronze Age Iron age Skull of Homo sapiens
Increased tool use in Homo sapiens
The modern human Homo sapiens originated in Africa around 200,000 years ago. This species is morphologically different from its ancestors, in par-
ticular by its increased brain size of around 1,500 cm³, and is also distinguished by its improved use of tools. The Palaeolithic Age was characterised
by the use of stone tools. In the early (Lower) Palaeolithic, these were simple stone tools but in the Middle Palaeolithic these were already improved
bifaces, or hand axes. Finally, blades and artworks were found left by H. sapiens from the younger Stone Age. The Mesolithic began with the onset of
the current interglacial and was characterised by human adaptations in hunting based on the emergence of forests. Finally, the Neolithic was char-
acterised by stock farming and agriculture. The Bronze (since around 4,200 years ago) and Iron (since around 3,200–2,800 years ago) followed, as
humans developed the ability to exploit and work on metals
The genus Homo: The first representatives of the genus Homo, the species Homo rudolfensis (left) and Homo habilis (middle-left) evolved from the
more ‘gracile’ australopithecines around 2–3 million years ago. The phylogenetic relationships of these species remain controversial. In H. erectus
(middle-right) and later in H. heidelbergensis the brain volume increased significantly from 650 cm³ (similar to that of H. habilis) to over 1,200 cm³. H.
erectus is considered to be the first hominid species to have left Africa and spread to Europe and Asia
‘Gracile’ australopithecines – the genus Australopithecus ‘Robust’ australopithecines – the genus Paranthropus
Representatives of genus Australopithecus sensu stricto generally ate Representatives of genus Paranthropus had a diet specialised in hard,
more meat. Stones were increasingly used as a tool in order to force open fibrous grasses, seeds, and roots. Their specialisation was enabled by en-
their prey, in particular in order to open long bones. Left: skull of the ‘Dik- larged chewing surfaces on the molars and the formation of a skull crest
ika child’ (Australopithecus afarensis); Right: fossil footprints of the same as an anchor point for powerful jaw muscles (left: P. robustus; right: P.
species from Laetoli in East Africa aethiopicus). With the spread of large herbivores and tool-using homi-
nins these australopithecines were displaced and subsequently became
extinct
Australopithecines
Australopithecus anamensis – is now considered to be the earliest certain species of hominini. As Southern Africa became increasingly drier and cooler,
forest land disappeared and savannah habitats expanded. As a result, the supply of soft fruit and leaves dwindled and consequently the australopith-
ecines split into two lineages, namely, the ‘robust’ and ‘gracile’ type
The 6–7 million years old Sahelanthropus tchadensis is considered to

likely be the oldest upright-walking species of hominins. In contrast,
molecular data suggest that humans and chimpanzees split only 5–6
million years ago
2.3.5.8
The future
The future development of life on Earth depends on the Declines in carbon dioxide concentrations will favour C4
planet’s future temperature development and, therefore, on photosynthesis in future.
long-term variation of solar radiation. In this context, the C3 plants will likely not be viable in about 100 million
current anthropogenically-induced climatic warming is rele- years. However, due to further rising surface temperatures,
vant for the current development of biodiversity. For the long- C4 plants are also predicted to go extinct in around 800–900
term development of biodiversity, however, i.e. in geological million years. At that point, the planet’s average surface tem-
time periods, changes in the sun’s radiation are critical. perature will exceed 30 °C and, as a result, higher-level eu-
Solar radiation comes from the continuous fusion prokaryotes will likely go extinct. All surviving eukaryotic line-
cesses within the sun and is therefore highly dependent on ages will eventually go extinct in around 1,200 million years,
changes in the sun’s material composition which continuous- when surface temperatures are set to surpass 50 °C. Some
ly changes resulting in increasing solar radiation. The temper- prokaryotes will survive at these high temperatures, though
ature on Earth is currently stabilised by the carbonate-silicate even these lineages are predicted to die off in around 1,300–
cycle: at higher temperatures, silicate weathering patterns are 1,600 million years, leaving behind only extremophiles living
stronger and more prevalent, with the released ions leading deep within Earth’s crust for a short time period. In 6.5 bil-
to greater carbonate precipitation – the atmosphere thus is lion years the sun will develop into a red giant and will likely
increasingly deprived of carbon dioxide, a greenhouse gas. swallow the Earth in roughly 7.6 billion years.
In addition to climate change, the position of continents the next 100–250 million years. The arrangement of current
is a significant factor in the development of Earth’s biodi- continents within such a super continent can be predicted
versity in the next 100– 200 million years. However, predict- within several scenarios.
ing continental drift is difficult, as it is driven by convection Assuming a continuous broadening of the Atlantic and
currents in the Earth’s mantle; in other words, if convection continued subduction of the Pacific plate under the Eurasian
cells change location, so too does the direction of plate drift. and North American plates, America will eventually collide
It is possible, however, to predict continental drift over the with Northeast Asia and form the super continent Amasia
next 50 million years with a relative certainty due to present- or Novopangaea. If we assume a slowing opening of the
day plate tectonic processes. To that end, it is predicted that Atlantic and the formation of a subduction zone in the
the Atlantic continues to widen, with North and South Atlantic Ocean, a counter-push and subsequent closure of
America on the one hand and Eurasia and Africa on the other the Atlantic is conceivable. This scenario would lead to a
drifting further apart from each other. Africa will continue continental arrangement similar to that of the Pangaea – as
to drift towards Europe, closing the Mediterranean. Further a result, this potential super continent is referred to as the
on, it is likely that another super continent will form within Pangaea Ultima or Pangaea Proxima.
extremophile: organisms which thrive in extreme environmen-

tal conditions
See also: Convection: 2.1.1.2

7,590 Ma In about 6 billion years, the sun is predicted to turn into a ‘red giant’ and eventually swallow up the Earth in around 7.59
billion years. Already in around 3.5 billion years, the temperature of the Earth will be so high that rocks begin to melt
6,500 Ma
1,300 Ma In about 1.3 billion years the temperature on Earth is predicted to be so high that even cyanobacteria and many prokaryotes
can no longer survive. The extinction of cyanobacteria will also lead to the collapse of prokaryotic food webs. Only extremo-
phile organisms would then be able to survive. In around 1.6 billion years there will be no live on Earth anymore
1,200 Ma In about 1.2 billion years, the surface temperatures on Earth will rise to around 50 °C and most unicellular eukaryotes will
go extinct
The rate of global carbon dioxide fixation will decline with the disap-
pearance of C3 photosynthesis. As a result, the decline in carbon dioxide
concentration in the atmosphere will slow. Global warming will therefore
accelerate. For some time, C4 photosynthesis will remain possible, but
will become increasingly inefficient as carbon dioxide concentrations con-
tinue to decrease.
850 Ma In around 850 million years, Earth’s surface temperatures will reach
30–35 °C and most higher eukaryotes will then likely die out, especially
higher plants. This process will eventually lead to a collapse of terrestrial
ecosystems. For the following 400 my, microbial mats will radiate and
dominate Earth’s ecosystems
Microbial mat
Australia Australia
Eurasia Eurasia Africa Eurasia
North America North America
North America
Africa Amasia Africa Novopangaea Pangaea Ultima
South America
Antarctica South America South America Australia
Antarctica Antarctica
Assuming that the widening of the Atlantic and subduction of the Pacific plate continues to progress, the East Asian and
American plates will collide. This event is predicted to lead to the formation of a super continent. Depending on assumptions
in the model, Antarctic may remain at the South Pole (super continent Amasia) or may becoming included in the super
250 Ma continent Novopangaea. An alternative scenario assumes the formation of a subduction zone in the Atlantic resulting in the
closure of the Atlantic Ocean, ultimately leading to the formation of super continent Pangaea Ultima
The long-term carbon dioxide concentration of the atmosphere will drop

below 150 ppm in around 100 million years. Under this level, C3 photo-
synthesis is no longer effective and, as a result, C3 plants are predicted to
100 Ma go extinct in around 100 million years. C4 plants will subsequently domi-
nate the ecosystems, as they can operate to a lower threshold of around
10 ppm of carbon dioxide
C4-plants: Zea mays, Amaranthus caudatus

157
3. Distribution of present-day biodiversity

Biodiversity is unevenly distributed across the planet. A and, on the other, into faunal and floral kingdoms. In con-
range of factors contribute to this distribution, including trast with the ecologically-defined biomes, faunal and floral
the global climatic gradient, the current and historical dis- kingdoms are characterised by phylogenetically related taxa.
tribution of land masses, and geographical barriers, such as Faunal and floral kingdoms are defined by the occurrence
mountains. of many plant and animal taxa within the particular area.
In addition, our perception of the diversity of life is fur- This distinction is aimed at phylogenetic relationships, i.e.
ther influenced by the results of biodiversity surveys and the endemic species, genera and families, and not the adaptation
choice of suitable measurement units, as well as by the spe- of these organisms to specific environmental conditions.
cies concept used in each study. The biome was originally understood as a basic unit of bi-
This introductory chapter covers the basic principles be- ocenosis, and thus used as a synonym for the formation of a
hind the measurement of biodiversity, including concepts climax community. Indeed, the term ‘biome’ is derived from
and indices relevant for the description of biodiversity as the term bioformation, which refers to biocenosis across a
well as the theoretical and practical foundations for the de- vast area of the Earth and is defined in terms of the climax
scription of species. For some organismal groups, the species vegetation found in this area.
concept is problematic. These groups will be briefly present- The term ‘biome’ is now used more specifically in an
ed here, including viruses, which are subject to Darwinian ecological sense for ecosystems bearing vegetation which
evolution but are not able to replicate autonomously. To that appears to be the same or is constructed in the same way.
end, the concept of the ‘sub-species’ was established for the Biomes are strongly tied to climatic factors; their distribu-
description of molecular diversity within a host. Lichens are tion is, therefore, not a chance occurrence but, rather, occurs
symbioses of a fungal and one or several algal species. A li- in parallel with global climate zones and climate-driven soil
chen is thus composed of several other species. types.
The second chapter introduces the biogeographic regions The biome concept was previously used as a synonym for
and deals with the climatic and geographical factors contrib- bioformation; today, however, it is viewed as more closely
uting to the differentiation of these areas. This includes a related to the geoscientific ‘ecozone’ term. Ecozones are vast
discussion about the generalisability to other organisms of areas on Earth containing largely similar climate, vegetation,
key biogeographic concepts derived primarily from plant and soil, and agricultural land. Ecozones closely correspond to
animal case studies, as well as of anthropogenically influ- biomes, though their definition is more strongly driven by
enced global biodiversity trends. abiotic factors.
The regions of the world can be grouped ecologically and
biogeographically on the one hand into biomes (or ecozones)
3.1 Basics of biodiversity

This chapter introduces concepts in the measurement and description of biodiversity. This includes an explanation
of the most frequently used biodiversity indices. This chapter also introduces practical implications and challenges
around species description, especially related to exclusively molecular approaches
3.2 Biodiversity distribution

This chapter covers the distribution of Earth’s extant biodiversity, including estimates of total species counts and the
factors responsible for species biogeography. This chapter also introduces trends in global biodiversity and the forma-
tion of biogeographical habitats

158 Distribution of present day biodiversity
3.1
Basics of the biogeographical distribution of taxa

Biogeography is concerned with the distribution of spe- several individuals, by definition, exist over a wider distribu-
cies, which range from the punctiform to the global. A rat, tion known as their range.
for example, is globally distributed. Most species ranges lie in Species often have local or regional distributions. Integrat-
between these extremes. ing range of several species, as is the case when consider-
Species distributions depend on ecological tolerance (the ing genera and other higher-level taxonomic units, results
range of tolerated environmental conditions), competition in more extensive distribution areas. This type of analysis
levels, geographical factors (mountain ranges or oceans), and would simultaneously consider the ranges of all of the spe-
historical circumstances. Historical factors influencing species. This relationship appears trivial at first, but it is of fun-
cies distribution are related, in part, to the historical develop- damental importance for the understanding of biodiversity
ment of the natural habitat, including plate tectonics and cli- patterns. This is especially true for comparative analyses
matic history, as well as to the ‘age’ of the individual species. examining the range of different species: both the species
To that end, ‘young’ species, which only recently evolved, concept itself and the definition of the individual species are
often have a narrower distribution than do the ‘older’ ones fraught with problems. As a result, the species boundaries of
since they have only had the chance to colonise potential many organisms are not completely clarified.
natural habitats close to their region of origin. Furthermore, the definition of ‘species’ differs with the
The distribution of organisms is also linked to the taxo- taxonomic group. As a consequence, species with broad defi-
nomic resolution of the observation: individuals, for exam- nitions should be expected to have a wider distribution range
ple, have a defined, localised distribution. Groups containing as compared to species that are narrowly defined.
Considering the relationship between the taxonomic reso- unknown to what extent species correspond to the under-
lution and the species distribution patterns is of practical rel- standing of species in higher organisms. Species in micro-
evance in a number of ways. organisms are possibly more comparable with the higher
Many conservation measures depend on both the number taxonomic units in metazoan and land plants. In addition,
of individuals in question and the size of their distribution relatively few microorganisms have been characterised taxo-
area. Both the number of individuals and the distribution nomically, and their distribution patterns remain largely un-
area depend on the study’s taxonomic resolution and the known.
particular species concept used. Molecular analyses show Depending on the interpretation and on the species con-
that many morphological species, for example, are actually cept used, microorganisms can be understood to have very
distinct species complexes comprised of a number of bio- wide or very narrow distributions. A popular viewpoint
logical species. Although the actual distribution remains the regarding the distribution of microorganisms is the ‘Every-
same, the distribution range of the morphological species is thing is Everywhere’ hypothesis, which claims that species
broken up into several different distribution areas of the bio- under a certain size are found globally and that only the
logical species. As a consequence, common and widespread ecological conditions of the habitat in question determine
morphological species may actually be a species complex whether a species occurs locally. Opponents of this view pos-
comprising rare, endemic taxa. In these cases, the knowledge it that microorganisms and higher organisms are both largely
or use of a different species concept would be highly relevant comprised of endemic organisms and therefore have similar
for planning future conservation strategies. distribution patterns.
The complexities of species definitions are even more
pronounced in the case of microorganisms, where it remains
endemic: occurrence of organisms within a defined geographi- punctiform distribution: only in one place or at a point, little
cal area spatial distribution
See also: Biogeography of microorganisms: 3.2.1.6

Basics: biogeographic distribution of taxa 159
At the family level, distribution patterns span almost the entire planet. Corvids (Corvidae) are commonly found across Earth, with the exception of
southern South America and some tundra areas. The following representative species are shown here: Pica pica (magpie, top-left), Corvus monedula
(daws, top-centre), Corvus cornix (or Corvus corone cornix, hooded crows, top-right), Garrulus glandarius (jays, bottom-left), Corvus corax (raven,
bottom-middle), Corvus corone (or Corvus corone corone, carrion crow, bottom-right)
At the genus level, distribution patterns are often extensive. The magpies (Pica spp.), comprised of the Pica pica (left), Pica hudsonia (black-billed
magpie, top-right), and Pica nuttalli (yellow-billed magpie, bottom-right), inhabit a large part of the temperate zone of the Northern Hemisphere
Species have limited distribution areas. The range of the yellow-billed magpie (Pica nuttalli) extends across a small strip along the west coast of the
United States
Individuals exist at a precise location and time

3.1.1
Species descriptions
The description of a species relies upon a number of disci- Central to the description of any species is a species di-
plines within biology, including systematics, taxonomy, and agnosis; that is, the exact description of the new species, es-
nomenclature. Systematics includes the determination and pecially in light of its distinguishing features compared to
reconstruction of the phylogenies, or trees of life, of living closely related species. The species diagnosis commonly con-
organisms. Taxonomy, on the other hand, aims to provide a tains a morphological description and, in more recent work,
hierarchical classification system for species. Finally, nomen- a DNA sequence description. The initial species description
clature pertains to the naming of organisms. Species descrip- is commonly carried out on an individual specimen with
tion is carried out differently across organismal groups. species-specific characteristics, which is ideally subsequently
However, certain elements of the description are present archived as a holotype in research collections of museums or
in all species: the genus and species name should be unique other scientific institutions. A picture or a drawing of char-
and chosen according to the described organism in question. acteristic features of the holotype should accompany the spe-
References to a particular distinctive feature of the location cies diagnosis within the initial publication. A DNA sample
the species was first observed are common. New species de- is often also deposited in a DNA bank.
scriptions are regulated by a recognised, corresponding no-
menclatural code.
Species description methodologies change with the devel- assignment has been invalidated, species may remain in the
opment of novel scientific methods. For example, the rise of literature under a number of names, specifically if the names
PCR and sequence analyses increasingly led to the use of have become popular and are in common use.
molecular data within species descriptions. To that end, new A large number of species have, therefore, been indepen-
species are sometimes even designated based on molecular dently described two or more times for a number of reasons,
features alone, though such an approach is problematic spe- including the existence of intraspecific variants, sexual di-
cifically in light of taxonomic revisions due to the lack of morphism, or clear generational change within a species.
data to compare with other similar species. Therefore, it is Even ignorance of an existing description can lead to double
helpful when all of the underlying theoretical underpinnings descriptions. Species descriptions may also be considered in-
of the species delimitation – specifically the applied species valid because they do not apply rules specific to a particular
concept – are stated for the comparative assessment of differ- discipline.
ent species descriptions. As a result of all of these factors, it is vital to make a dis-
As a result of new findings, many species have been tinction between the number of published species names and
shifted into other or novel genera. Though the ‘old’ species the number of valid species that may exist in nature.
DNA bank: institution in which DNA samples extracted from or- Polymerase Chain Reaction (PCR): laboratory technique used
ganisms can be stored for future testing to make multiple copies of a segment of DNA
holotype: a single individual organism which was used as the sexual dimorphism: (Lat.: sexus = gender; Grk.: dimorphos =
name-bearing type when a species or sub-species was first de- having two forms) differences in appearance between male and
scribed female individuals of the same species
intraspecific: occurring or existing within a species or between
individuals of the same species
See also: The species concept: 3.1.2; Taxonomic resolution and biogeography: 3.1, 3.2.1.6
Basics: definition of species 161
Chlorella pulchelloides C. Bock, Krienitz et Pröschold, sp. nov. 2011 Scientific names are comprised of the genus and species epitheton
put together. The complete name also comprises the surname of
Diagnosis. Cells colonial, planktonic, with mucilaginous envelope. Colonies the describing authors and the year of publication
4–32 celled, diameter of colonies 25–35 μm. Adult cells spherical 4.5–6.5 μm,
connected via mucilaginous stalks. Young cell oval to ovoid, 3.5–4.5 × 4–6
μm, attached to the stalks at their broader side. Chloroplast single, parietal, The species diagnosis should include all of the distinguishing char-
cup- or saucer-shaped with ellipsoid to spherical pyrenoid, covered by two acteristics of the type species and, in particular, how they differ
starch grains. Reproduction by 2–4 autospores. Release of autospores after from related species. In the field of plant science, the species di-
rupture of mother cell wall horizontally or slightly obliquely. Differs from agnosis must be in English or Latin, whereas in zoology it must be
other species of this genus by the order of nucleotides in ITS-1 and ITS-2 and written in an established language of science
the barcoding signatures
Species descriptions increasingly also contain sequence data, i.e.
the sequenced sections of specific marker genes. Often, these se-
quences code for DNA segments coding for ribosomal RNA, or for
other DNA ‘barcode’ regions established for the respective group
of organisms
Species descriptions often include drawings or photographs of the

new species, especially for smaller organisms. The diagnosis must,
where applicable, define which image or which individual deter-
mines the type
As a rule, newly described type species must be deposited. They

Holotype: Material of the authentic strain CCAP 211/118 is cryopreserved at may be stored as herbarium sheets, as a live culture or as a cryopre-
the Culture Collection of Algae and Protozoa, Oban, Scotland. served sample, depending on the organism in question
Isotype: An air-dried as well as a formaldehyde-fixed sample of strain CCAP
211/118 was deposited at the Botanical Museum at Berlin-Dahlem under the
designation B40 0040664.
Type locality: Lake Feldberger Haussee, Brandenburg, Germany Species descriptions also include locality information, i.e. where
(53°20’27,35’’N; 13°26’10,89’’E). the sample was taken
Etymology: from Latin: pulchella = nice
Authentic strain: CCAP 211/118
3.1.2
The species concept

Delimitating species is different from defining the concept In contrast with biology, which considers only extant (liv-
of species, though the two are often mistakenly taken as the ing) species, palaeontology also accounts for the change of
same thing. For example, according to the biological species species over time. Palaeontologists only have the morpho-
concept, species are defined by their reproductive isolation. logical features of fossils at their disposal, whereas biologists
In practice, however, the examination of this criterion is can examine the molecular, behavioural, and phylogenetic
complicated, and the recognition of different species is most- features. Therefore, palaeontology almost always uses a
ly on morphological and molecular dissimilarity. ‘morphological’ species concept, delimiting species based on
Biology most commonly uses the biological species con- physical differences. The often-applied ‘chronological’ spe-
cept, where species are groups of actual or possibly compat- cies concept is basically a morphological species concept,
ible natural populations isolated from other such groups by but it allows for the variation of species over geological time
reproductive isolation. Since hybrids may occur after the periods. Strictly speaking, it is not an alternative concept but,
mating of two different species, a refined definition requires rather, it is a differential practice of species delimitation.
that only descendants within a species are fertile but descend- The different practices of species delimitation in biology
ants of two different species are not. and palaeontology are, therefore, largely a matter of the pos-
On the other hand, the ‘recognition’ species concept is sibilities of species identification and delimitation rather
based on species that are defined as sex partners – be it at the than a matter of deviating species concepts.
level of gametes, sex apparatus, or of individuals – that can
recognise each other as sex partners.
A number of species concepts have thus far been pro- In addition to the biological and typological concepts are
posed. Common to all of these is the demarcation of inde- the evolutionary and phylogenetic definitions of the species:
pendently evolving populations within a larger metapopula- the evolutionary species concept is based on a common evo-
tion. Yet, different species concepts vary in their reliance on lutionary fate with common evolutionary roles and devel-
particular features. opments. Similarly, a phylogenetic species concept defines
Typological species concepts use morphological, physi- monophyletic lineages as separate entities. Finally, the geno-
ological, or ethological properties to classify organisms. typic cluster concept, which hinges on a low frequency of
The morphological and chronological (historical) species clusters of intermediate forms (not their complete absence),
concepts are both typological, as is the physiological species is sometimes also used.
concept, as applied in prokaryotes. The ecological species concept can be seen as a variant of
In contrast, the biological species concept hinges on fertil- the evolutionary species concept, defining species according
ity, a property that can only be observed in living species. to their occurrence in the same ecological niche or adaptive
zone.
adaptive zone: the combination of environmental conditions metapopulation: group of several individual populations be-
and ecological niches respectively, which are occupied by species tween which gene flow is restricted
that exploit the same resources in a similar way reproductive isolation: a set of barriers impeding the gene
Horizontal Gene Transfer (HGT): the transfer of genes be- flow between two populations; examples of such barriers might
tween organisms without reproduction; also between species be geographical separation, genital incompatibility, or behav-
ioural differences
See also: Ecological niche: 3.2.1.2

Species are defined differently between major organismal groups and by the different species concepts used. Microorganism species are often defined
based on genetic variations that may already indicate genus or family level in higher animals and plants
species 2 Prokaryotes pose a major challenge in delineating species, since different

species can show similarities to each other as a result of lateral gene
transfer across large parts of their genome. As a result, distinct organisms
would belong to different species at the same time. In this figure, the single-
species 1
coloured rings represent the genome of the individuals. Multi-coloured
rings represent genomes where lateral gene transfer has created a ‘mixed’
genome
species 3
Speciation is usually a continuous process occur-

phylogenetic species ring over a longer period of time. Various species
monophyletic lineages concepts apply different criteria for the definition
of species, represented at different points within
biological species the speciation process. Thus, genotypic clusters
hybrids not fertile are often observed when gene flow between two
sub-populations is still high. The ecological spe-
cies concept, which is based on niche differentia-
ecological species tion, requires a stronger restriction of genetic ex-
niche differentiation change, despite niche differentiation. However,
genetic exchange is minimal between biological
species and non-existent between monophyletic
genotype clusters lines
beginning of shifts in
allele frequencies
3.1.3
Molecular diversity and OTUs

The determination and identification of species requires versity studies, the majority of sequences obtained from the
expert knowledge and is very time consuming. In addition, environment do not belong to the known species that are ge-
it is increasingly clear that a vast majority of existing species netically characterised. It is, therefore, difficult to determine
will not be described in the near future. As a result, DNA how different these sequences are from those of related spe-
sequencing methods have been developed to allow for the cies and how big the intraspecific diversity is, in other words,
relatively quick identification of organisms based on snippets how much genetic diversity there is within a known species.
of their genetic code, a strategy superficially resembling the Ideally, using OTUs should contribute to the accuracy of
barcoding of products by way of scanners in a supermarket. estimations of species richness by broadening the threshold
This is known as DNA barcoding. of sequence variability within a species. OTUs should not
DNA barcoding is a taxonomic method of species deter- be formed based on variation as a result of sequencing error,
mination based on the DNA sequence of a specific target yet this often contributes to selection of OTU cut-off-levels
marker gene. For many organisms, and especially for meta- in practice. OTUs determined through an environmental se-
zoans, DNA barcoding targets the cytochrome c oxidase quencing study often have little to do with the precise species
subunit 1, often referred to as COI or cox1. in nature. Still, they can be useful for measuring diversity by
A fundamentally different way of detecting biodiversity allowing for an approximate assignment of organisms to a
using molecular techniques is to group sequences into op- kinship group.
erational taxonomic units, or OTUs. In most molecular di-
Finding a uniformly applicable concept of a single bar- DNA barcoding elicits further problems, most important-
code, in other words, a unique sequence section for the identi- ly because its purpose clashes with the requirements of other
fication of species is both difficult and controversial. For one, molecular diversity studies.
the portions of sequences selected for barcoding are them- In many studies, DNA sequence segments are used as
selves subject to evolution. Mutations and intraspecific vari- phylogenetic markers, i.e. as sequences that will allow for
ation are also common within such barcode regions. There- the phylogenetic classification of organisms via the calcu-
fore, a ‘barcoding gap’ is often applied, a standard sequence lation of phylogenetic trees. However, the requirements for
threshold used to differentiate species, where intraspecific such makers are different from those of a barcode. Highly
variability (within one species) of a genetic sequence should conserved sequence segments should flank phylogenetic
be much smaller than the sequence divergence between dif- marker genes used in diversity studies in order to make sure
ferent species. that PCR primers target a broad variety of organisms. The
A second problem is that the extent of sequence variabil- requirement for sequence variability within the marker re-
ity of a distinct gene differs between organismal groups. As gion itself also differs between the different applications. For
a result, the original idea of creating a single barcode that is phylogenetic studies, they need to allow for phylogenetic as-
applicable to all groups is therefore not feasible. Most meta- signment across the whole target group, e.g. for eukaryotes.
zoan cells are targeted at the mitochondrial DNA regions. These sequences are usually too conserved to reliably differ-
Plastid DNA is targeted in plants, whereas, in fungi, the in- entiate between closely related species. The ribosomal RNA
ternal transcribed spacer 1 (ITS1) region of the ribosomal of the small ribosomal subunit, known as the SSU rRNA
DNA is often used as a barcode. There is still great debate (hereafter referred to as the 16s rRNA in prokaryotes and the
about the feasibility and potential target regions for barcod- 18S rRNA in eukaryotes), are frequently used as markers for
ing in protists. such molecular phylogenetic studies.
16S: the small subunit of prokaryotic ribosomes, as well as plas- bind onto, thereby serving as the starting point for polymerase
tids and mitochondria with a sedimentation coefficient of 16 enzymes to catalyse the polymerase chain reaction (PCR)
Svedberg (S) units Small Subunit (SSU): the small subunit of ribosomes; the term
18S: the small subunit of eukaryotic ribosomes with a sedimen- refers to both the 16S subunit of prokaryotic ribosomes as well
tation coefficient of 18 Svedberg (S) units as the 18S subunit of eukaryotic ribosomes
primers: primers are short strands of nucleic acid with comple-
mentary reverse sequences directed at a target sector which they
See also: Phylogenetic trees: 4.1.1.6

The term ‘barcode of life’ (BOL) is based on the idea of barcodes for goods. Barcodes are designed to allow for the clear identification of organisms
based on DNA sequence segments. Barcodes should enable non-specialists to identify species and, ideally, at the same time, allow for phylogenetic
placement in molecular diversity studies. On the one hand, the requirements of taxonomic distinctiveness and on the other, as phylogenetic markers in
diversity studies of known groups are usually not compatible
sequence variability
within the species
Euastrum oblongum
between both species
Euastrum oblongum
within the species
Euastrum crassum Euastrum crassum
A ‘barcode gap’ is used to define the difference between intraspecific and interspecific variability, where the difference in sequence variation should be
significantly less within a species compared to variation between species that are closely related. As a result, effective barcodes have only been estab-
lished for organismal groups where the majority of species have already been described, in particular, in higher plants and animals
3.1.4
Biodiversity indices
Biodiversity is complex. In research, and perhaps even The most widely used diversity index, the Shannon in-
more so for the communication of science to the public, it dex (H), is comprised of both the species richness and the
is often necessary to break down biodiversity information to uniformity of the species distribution within an area. It is
one or a few key numbers, or indices. sometimes mistakenly referred to as the Shannon-Weaver or
The term biodiversity is often taken as a synonym for spe- Shannon-Wiener index. The Shannon index of uniformly
cies richness, though these terms are subtly different. Species distributed species is equal to the logarithm of natural spe-
richness denotes the number of species found in a particular cies diversity (or H = ln S). This index is unlimited and,
habitat. It is not comprised of information about structural therefore, can even take large values.
dominance or the distribution of species within that habitat. The Simpson index (D), similar to species evenness, pro-
The term biodiversity, on the other hand, includes both vides information about species dominance within a habitat.
the number of species present in a habitat (species diversity, This index ranges from 0 to 1 and offers the probability that
or species richness [S]) and the degree of uniformity of their two randomly sampled individuals in a population belong to
distribution (evenness [E])). A variety of measurements and the same species. Conversely, the Gini-Simpson index (1–D)
indices has been developed to describe biodiversity on the refers to the probability that two randomly selected individu-
basis of these two dimensions. Both do not consider the ab- als do not belong to the same species. Compared with the
solute abundance of species or the total biomass within an Shannon, the Simpson index is less prone to shifts in biodi-
area. versity.
Each diversity index characterises diversity in a different exponents and underweighted for high exponents (e.g. Simp-
manner by variations in how they integrate the number of son index).
species present and the degree of evenness of their distribu- In a biological context, the species number is usually in-
tion (the uncertainty, similar to the concept of entropy from tuitively considered as the basis for measuring biodiversity:
physics). Most indices consider species richness as well as when two communities show the same distribution, for in-
the evenness of their distribution. stance, when all species have the same abundance, diversity
Most diversity indices are proportionate to the sums of should be proportionate to the number of entities (i.e. spe-
the power functions of the relative abundances (∑pq) of the cies). A community with eight species would be considered
distinct species (p: relative abundance of the species; q: expo- twice as diverse as a community with four species. This rela-
nent, different for the different indices). tionship is reflected by the species richness. In contrast, both
For the special case of q = 0, the formula returns the spe- the Shannon index and the Simpson index, as the most com-
cies richness (p0 = 1, therefore ∑p0 = number of species). For mon diversity indices, do not increase proportionately to the
the case q = 2, the formula returns the Simpson-index (∑p2). number of species. If, for instance, a meteor causes half of
While species richness (q = 0) does not consider the rela- an area’s 200,000 species to go extinct (i.e. 100,000 species),
tive abundances of species – species are simply summed up these two indices would hardly change. For evenly distrib-
– high values of q (as for the Simpson index with q = 2) uted species, the Shannon index would decrease from 12.2
will result in a disproportionately high weight of the rela- to 11.5, corresponding to 5.6 %, and the Gini-Simpson-Index
tive abundance. Thus, the different indices mainly differ in would decrease from 0.999995 to 0.99999, corresponding to
the weight of these two measures, i.e. species richness and 0.0005 %. This negligible decrease does not correspond to
evenness. As a result, rare species are overweighted for low the intuitive expectations for measures of biodiversity.
dominance structure: frequency distribution (dominance) of relative frequency: the number of individuals in a given spe-
the various species in a habitat cies relative to all the individuals of all species living in that habi-
tat
See also: α-, β-, γ-diversity: 3.1.5

Basics: cataloguing biodiversity 167
species p ln (p) p*ln(p) p2

magpie 3 / 15 = 0.20 (20 %) ln (0.20) = –1.6 –0.32 0.040
pheasant 2 / 15 = 0.13 (13 %) ln (0.13) = –2.0 –0.27 0.017
bee-eater 2 / 15 = 0.13 (13 %) ln (0.13) = –2.0 –0.27 0.017
hoopoe 2 / 15 = 0.13 (13 %) ln (0.13) = –2.0 –0.27 0.017
oriole 2 / 15 = 0.13 (13 %) ln (0.13) = –2.0 –0.27 0.017
woodchat shrike 1 / 15 = 0.07 (7 %) ln (0.07) = –2.7 –0.19 0.005
daw 1 / 15 = 0.07 (7 %) ln (0.07) = –2.7 –0.19 0.005
nutcracker 1 / 15 = 0.07 (7 %) ln (0.07) = –2.7 –0.19 0.005
jay 1 / 15 = 0.07 (7 %) ln (0.07) = –2.7 –0.19 0.005
sum 1 (100 %) –2.16 0.128

The Shannon index (H) is the negative sum of the product
of the proportion of individual taxa in a community and the
natural logarithm of this value (here 2.16)
The Simpson index (D) is the sum of the square of relative abundances of individual
taxa (in this case, 0.128). The inverse Simpson index (1/D, here 1/0.128 = 7.8) and the
Gini-Simpson index (1–D, here 0.872) are most commonly used
Calculation of common diversity indices: the community shown here is comprised of 15 individuals belonging to nine different species. The species
richness is therefore nine. The Shannon index is calculated, as shown above, to be 2.16. Likewise, the Simpson index is 0.128
The trend of diversity indices along a gradient of an increasing

number of uniformly distributed species: species richness is
(linearly) proportional to the number of species present. The
species richness Simpson and derived indices (inverse Simpson and Gini-Simpson)
as well as the Shannon index are not proportional to the number
of species. For uniformly distributed species within a community,
the Shannon index corresponds to the logarithm of species richness
(In S), whereas for unevenly distributed communities that value is
less. While species richness and the Shannon index increase with
Shannon index increasing diversity, the Simpson index decreases. Therefore the
inverse Simpson index or the Gini-Simpson index is more commonly
diversity index
used
Gini-Simpson index
species number (uniform distribution)
The influence of uneven distribution on biodiver-

sity indices: both communities here consist of 15
individuals, each belonging to one of three species.
Here the number of different species (species rich-
ness) or, more generally, the number of different
types or units (richness), is three in each case.
Aside from species richness, the extent of uniform-
ity of the distribution of the units (evenness) is usu-
ally part of the diversity indices. In this example, the
left panel shows the three species as being evenly
distributed, so evenness is high, whereas the right
panel shows the magpie individuals outnumbering
their counterparts, illustrating a low evenness. The
distribution of species is taken into account by the
Shannon and Simpson indices
3.1.5
Spatial distribution of biodiversity

Assessing of biodiversity always targets a specific spatial the variability of comparisons between a single entity with-
area (habitat, region) or the comparison between two areas. in a greater whole. While α- and γ-diversity can be directly
α-diversity (Alpha diversity) describes the diversity of measured by counting species and their relative abundances,
a habitat and is therefore referred to as ‘local’ diversity. In the β-diversity is always calculated.
contrast, γ-diversity describes the diversity of a landscape, or The Jaccard index is commonly used for the direct com-
an area. It is therefore similar to α-diversity but at a larger parison of diversity between two habitats. It compares how
spatial scale. α- and γ-diversity are qualitatively identical and closely the species composition of two habitats matches an
can both, therefore, produce a species richness value for a inventory of species. The Jaccard index is therefore similar to
particular area. species richness indices, though it only takes species presence
β-diversity describes the difference between α- and into account and does not incorporate species distribution
γ-diversity, characterising the difference between the diver- or dominance. In addition to comparing spatially separated
sity of a single habitat (α-diversity) and an entire landscape habitats, the Jaccard index and β-diversity may also be used
(γ-diversity). Therefore, β-diversity is a qualitatively different to analyse the development of habitats over time.
measurement compared with α- and γ-diversity; it describes
Diversity indices do not always reflect the intuitive basic β-diversity would be minimal, even in a mass extinction situ-
assumptions regarding biodiversity. These assumptions in- ation.
clude, for example, that diversity should be proportional to A useful tool for the comparison of different diversity in-
the number of species, if the species are evenly distributed; dices is the number of taxa (assuming an evenly distributed
for example, if half of the species go extinct, the diversity community) corresponding to the respective index value, i.e.
in a habitat with uniformly distributed species should drop the number of taxa that would, given that all taxa have the
by half. In addition, the different levels of diversity should same abundance, result in the respective index value. This
relate to each other – depending on the scientific viewpoint – equivalent number of species is also known as the ‘true di-
either by addition (α-diversity + β-diversity = γ-diversity) or versity’. It is not the diversity indices themselves, but rather,
multiplication (α-diversity x β-diversity = γ-diversity). How- it is their equivalent number (true diversity), which follows
ever, most diversity indices display a limited compliance to the intuitive assumptions for diversity measures. Both the
these relationships. Particularly in species-rich communities, equivalent numbers for the Shannon index and for the Gini-
both the Shannon and Gini-Simpson indices only minimally Simpson-index would correctly reflect the above described
comply with these assumptions. Thus, calculated changes in fictitious extinction event.
α-diversity: punctual diversity, diversity in a habitat habitat: area inhabited by a particular species
β-diversity: difference between α- and γ-diversity, that part true diversity: term describing the number of species that ac-
of γ-diversity (i.e.the diversity in a region) which is not part of cord with a certain value of a biodiversity index when all species
α-diversity (i.e. the diversity of a certain habitat) are distributed equally (i.e. when all species are equally abun-
γ-diversity: regional diversity; diversity of a landscape dant)
See also: Biodiversity indices: 3.1.4

Basics: cataloguing biodiversity 169
α-diversity describes biodiversity within a habitat. The most common index for
α-diversity is the Shannon index, which incorporates the species richness and evenness
of distribution of species. The α-diversity of this and other habitats represented here
is the same (three species in an abundance ratio of 3:2:1). For each of the habitats the
Shannon index is therefore 1.0 whereas the Gini-Simpson index is 0.61
Different indices are in use to compare the diversity between two habitats. The most
habitat 1
commonly used indices relate species richness of discrete habitats (in this case, 3) to
species common to both habitats (in this case, magpies and pheasants), and to species
only occurring in one habitat (here bee-eaters in habitat 1 and jays in habitat 2).
The Sørensen index (QS) is calculated as QS = 2C/(A+B), where A represents the number
of species in Habitat 1, B the number of species in Habitat 2, and C the number of species
common to both habitats. In this example, QS = 2×2/(3+3) = 4/6 = 0.66. Similarly, the
Jaccard index (J) is calculated as J = C/(A+B–C). Here, J = 2/(3+3–2) = 2/4 = 0.5.
Both indices only reflect presence-absence data, whereby the Sørensen index gives
weight to species common to both habitats more heavily than does the Jaccard index.
The Renkonen index, on the other hand, refers to species dominance between samples.
For both samples, it adds together the lowest relative frequency value for all species. In
this example, the Renkonen index can be calculated as Re = 0.33 (at least 33 % magpies
habitat 2
in both habitats) + 0.33 (at least 33 % pheasants in both habitats) + 0 (bee-eaters in only
one habitat) + 0 (nutcrackers in only one habitat) = 0.66.
Both of these measurements are taken into account by the Wainstein index (Kw), which
measures the product of the Jaccard and Renkonen indices: Kw = 0.5 × 0.66 = 0.33
habitat 3
β-diversity describes biodiversity between habitats. When habitats share a low number
of species, β-diversity is high. In its original sense, β-diversity describes the ratio of spe-
cies in a habitat (in this case, 3) to the total number of species across all habitats (here,
6). According to this definition, β-diversity is calculated as (6/3=2) and represents the
theoretical measure for how many habitats, with a mean species richness and without
overlapping species, are needed in order to reach the total number of species across
a landscape. In this example, two habitats each with three species were sufficient to
uncover the total species richness of the landscape, i.e. pheasant, magpie, bee-eaters
(corresponding to habitat 1) and hoopoe, oriole, and jay (corresponding to habitat 6).
If one calculates the β-diversity as the difference between γ-diversity a α-diversity, the
result for the Shannon index is a β-diversity of 0.6 (Hβ= Hγ–Hα, therefore Hβ =1.6–1.0 =
0.6; equivalent to 37 % of the γ-diversity) and for the Gini-Simpson index a β-diversity of
habitat 4
0.03 (Dβ= Dγ–Dα, therefore Dβ=0.78–0.61 = 0.17; equivalent to 21 % of the γ-diversity). In
both cases, the β-diversity indices calculated here are a distorted measure of diversity.
In contrast, if one calculates the β-diversity from true diversities (in other words, from
the respective indices according to the corresponding number of uniformly distributed
taxa), a different picture emerges: The true diversity is calculated for the Shannon in-
dex (H) as eH, for the Gini-Simpson index (D) as 1/(1–D). Based on the Shannon index,
the β-diversity is therefore (eHγ–eHα)/eHγ = (5–2.7)/5 = 0.45 (corresponding to 45 % of
the γ-diversity). Based on the Gini-Simpson index, β-diversity is [1/(1–Dγ)– 1/(1–Dα)]/[1/
(1–Dγ)] = (4.6–2.6)/4.6 = 0.44 (corresponding to 44 % of γ-diversity). The results based
on true diversity offer more realistic estimates of shifts in diversity compared to the
respective underlying indices
habitat 5
The γ-diversity describes diversity within a landscape, integrating the α-diversities of

the landscape’s individual habitats. The spatial scale of relevant landscapes remains
undefined and therefore a comparison of γ-diversities is often difficult. In general, the
total species count (in this case, 6) serves as a basis, with common and rare species
weighted differently depending on the approach. For the γ-diversity, the Shannon index
habitat 6 is 1.6 and the Gini Simpson index is 0.78
Landscape with six habitats
3.1.6
Species concept limitations: viruses

Viruses are organic structures existing on the fringes of single-stranded DNA (ss-DNA) bacteriophages. RNA phag-
what constitutes life. They are non-cellular particles that es are among the smallest known bacteriophages, measuring
multiply by infecting a host cell. Although viruses contain only around 25 nm in size and usually consisting of a protein
all of the necessary genetic information to code for their coat containing single-stranded RNA.
structure, they do not have their own metabolism and are Around 3,000 types of viruses have been described so far,
unable to replicate independently without the metabolism of and likely several millions have yet to be discovered. It is as-
the host cell. sumed that each eukaryotic organism carries one or several
In their free form, viruses exist as virions after being dis- host-specific viruses. The diversity of viruses and their eco-
charged by host cells and spread into the environment. The logical significance is potentially enormous. Aquatic habitats
envelope (capsid) of virions is mostly made of proteins or, as contain 10–100 times more viruses than they do bacteria, i.e.
is the case with the influenza virus, of ribonucleic proteins. more than 100 million virions per ml. In sediment, the viral
Capsids contain either RNA or DNA. Upon infection, viri- load can even be one or two orders of magnitude higher. A
ons either completely enter or release their nucleic acids into significant portion of the primary production in the sea is
the host cell. The infected cell usually dies as soon as newly- directly converted to viral biomass through viral infections
formed virions are released. of phytoplankton, or set free through cell lysis as dissolved
Viruses infecting bacteria or archaea are known as bac- carbon and then subsequently fed through the microbial food
teriophages. Double-stranded DNA (DS-DNA) bacterio- web.
phages are usually larger than the mostly small and spherical
Viruses are the smallest known reproductive units, rang- ‘quasi-species’ is often used for describing phylogenetically
ing from between 15 and several hundred nanometres in related virus populations.
size. Although they display several characteristics of life, Infectious genomes without capsids are called viroids.
they are usually not considered to be alive including within They often consist of an autocatalytic single-stranded RNA
NASA’s official definition. Although viruses themselves do molecule (ribozyme). Unlike viruses, viroids, which exist
not metabolise, they are subjected to Darwinian evolution. predominantly in land plants such as potato, tomato, grapes,
Therefore, they share evolutionary properties with other and citrus crops, have no additional proteins or lipids within
forms of life, including splitting into independent phyloge- the capsid.
netic lineages, and can be classified in the same way species The biology of infectious proteins, known as prions, re-
can, though not in the traditional biological sense. The term mains virtually unknown, though these are important trig-
gers of certain illnesses, such as Creutzfeld-Jacob disease.
quasispecies (viral): a group of virus genotypes which have

resulted from the same viral genome in a host
See also: Archaea: 4.1.2.2; Bacteria: 4.1.2.1; Definition of life: 1.3; DNA, RNA: 2.2.1.2
Basics: species concept limitations 171
capsid
head
collar
core
contractile
tail protein sheath
tail fibres
baseplate
Bacteriophages: diagram and electron micrograph of different phages
lipid envelope
capsid
neuraminidase
(sialidase)
hemagglutinin
nucleoprotein
(RNA)
Viruses: diagram and electron micrograph of the mumps virus (bottom-left), coronavirus (bottom-middle), and HIV (right)
3.1.7
Species concept limitations: lichen

Lichens are the product of a symbiosis between myco- relationship, the mycobiont-photobiont interaction is often
bionts (fungi) and a photobiont. The fungal component is known as ‘controlled parasitism’.
usually a member of the Basidiomycota or sometimes of the Basic properties of lichens, such as growth patterns and
Ascomycota. The photobiont is either a green algae (Chlo- the formation of characteristic acids, differ so widely from
rophyta), referred to as a phytobiont, or a cyanobacterium, those of their constituent partners that they appear as dis-
known as a cyanobiont. There are around 25,000 known li- tinctive organisms. Lichens are distinguished from each oth-
chen species. er according to their shape and surface patterns: fruticose,
Although lichens are comprised of one fungal species, foliose, crustose, leprose and gelatinose. This subdivision
they can be made up of several phytobionts or cyanobionts, does not correspond, to phylogenetic relations.
though these rarely co-occur within the same lichen. Algae Crustose lichens are firmly anchored to the substrate by
may be grouped either in one layer (heteromeric) or may be their underside. Fruticose lichens have narrow ramifications
evenly distributed (homomeric). and specific stabilising elements. Gelatinous lichens swell
Lichens are named according to the mycobiont they con- when they absorb water and shrink together when under
tain. The mycobiont is often reliant on the symbiosis for dry circumstances. The lichen leaf or leaves are often only
life, whereas phytobionts or cyanobionts are typically able loosely attached to the base of the organism, or with adhe-
to sustain themselves outside the partnership. Carbohydrates sive organs (rhizines). Their thallus is lobed and erect.
and other nutrients supplied from the photobiont power the Lichens colonise different locations and materials, includ-
mycobiont. The symbiotic advantage for algae is less clear, ing tree bark, soil, and the surface of rocks. Since they are
however, though as a result of the mycobionts, the algae are highly tolerant to cold, heat, and desiccation, they are also
protected from UV-radiation and desiccation. In any case, found in extreme environments, including in Antarctica.
as the mycobionts seem to gain more from the symbiotic
Lichens face an exceptional reproductive challenge, since Soredia are small structures consisting of one to several
both symbiotic partners must be simultaneously distributed photobionts, closely surrounded by hyphae. They are formed
into the environment. For the most part, propagation is in soralia and are actively emitted by the thallus and spread
vegetative, in other words, a sexual and with only one plant by wind.
involved and the offspring resulting from just one parent. Within the lichen, only the mycobiont can reproduce
Either the fragments of the thallus or special structures, the independently by forming characteristic fruiting bodies
isidiae or soredies, are distributed. (apothecia) containing sporangia. The sporangia release
Isidia are growths emanating from the thallus (often the meiospores on their upper surface or on the edge of the
as needles or scales) that break off and then are passively thallus. Conidia, which are non-motile spores, make lichens
disseminated. Within the isidia are photobionts surrounded capable of asexual reproduction. However, new lichens
by a shell of hyphae. can only arise when new hyphae are combined with the
appropriate photobionts, a process known as lichenification.
thallus: multicellular undifferentiated vegetative tissue in plants,

algae and fungi without the organisation of a cormus (sections
incl. stem, root, and leaf)
See also: Ascomycota: 4.2.2.4; Basidiomycota: 4.2.2.5; Chlorophyta: 4.4.3; Cyanobacteria: 4.1.2.1
Basics: species concept limitations 173
Rocella fuciformis is a fruticose lichen with a shrubby thallus. It grows from Rhizocarpon geographicum is a crustose lichen. Its thallus grows close to
the tips of individual branches. Rocella is the source of the blue-violet dye the ground, or it can grow through the ground. This type of lichen can live
litmus to over 1,000 years of age, and can therefore be used for dating the retreat
of the ice cover (glaciers)
Through cracks in the surface (sorale),

the soredies – hyphen connected to al-
gae – can pass and thereby disperse the
photo- and mycobiont together
Upper cortex: thick hyphae
Algal layer
Photobionts reproduce only asexually by division,

while mycobionts can also reproduce sexually,
Core layer (medulla): loose thread-like forming apothecia or perithecia where fungal
hyphae without algae spores form (apothecia of Cladonia sp., top). Dur-
ing the germination of the spores, the fungi again
form a symbiosis with a suitable photobiont (phy-
Lower cortex: thick hyphae with fungus-
tobiont or cyanobiont)
like hyphae (rhizines) attached to the
substrate
Structure of a foliose lichen
Collema nigrescens is a gelatinous lichen, and the photobiont of gelatinous Xanthoria ectaneoides is a foliose lichen with flat leaves that lies along the
lichens are cyanobacteria. Upon humidification, the lichens swell, like gela- substrate. The sheet-like shape of the leaves optimises photosynthesis of
tine. They are usually blackish or dark olive green the photobiont
174 Distribution of present-day biodiversity
3.2
Biodiversity distribution
Life is unevenly distributed, primarily as a result of cli- regions. Various phylogenetic groups are generally limited to
mate as well as Earth history, specifically plate tectonics. particular ranges of distribution, determined by recent and
Biodiversity generally increases nearer the tropics, since historical barriers.
temperature and precipitation play key roles. The distribu- These patterns are particularly striking in land plants and
tion of the predominant life forms is particularly apparent animals; their applicability to other organisms, especially mi-
when one compares different biogeographical, or ecological croorganisms, remains unclear.
The historical drivers of present-day biodiversity relate Precipitation is a central factor in determining species dis-
primarily to the physical connections between continents. tributions in temperate areas as well, for example in inland
These explain distribution patterns mostly at the level of areas or in the wind shadow zones of mountains. In cooler
phylogenetic groups (genera, families, orders). regions, temperature is also an important climatic factor de-
Climatic factors, on the other hand, explain current dis- termining the distribution of species. For example, water is
tribution patterns and the dominant life forms within a re- unavailable during periods of frost, even when precipitation
gion. For example, the availability of water allows for the is high.
development of rich vegetation: Forests dominate in areas Similarity, deserts prevail in areas of even lower water
of normal-to-high precipitation in both tropical (tropical rain availability, leaving them with little or no vegetation cover.
forests) and temperate (deciduous and boreal coniferous for- Climatic conditions and their effect on vegetation are
ests) climatic zones, whereas grasslands dominate regions of also of central importance to the distribution of animals.
lower water availability. For example, large migratory herds of herbivores and small
In subtropical and tropical regions, water availability is ground-dwellers tend to dominate seasonally dry grasslands.
linked to overall precipitation and to seasonal fluctuations. The former migrate large distances to avoid adverse climac-
Savannas are found in the transition zones between the hu- tic conditions, whereas the latter have either seasonal resting
mid tropics and arid, subtropical deserts. phases and/or stockpile food, in response to these seasons.
biodiversity: (definition given by the UN Convention on Bio- munities, and environmental conditions’ (WWF definition); the
logical Diversity) the variability among living organisms from all term ‘ecoregion’ was originally used in the context of geographi-
sources including, inter alia, terrestrial, marine and other aquatic cal scholarship (meaning a ‘recurring pattern of ecosystems as-
ecosystems and the ecological complexes of which they are a sociated with characteristic combinations of soil and landform
part; this includes diversity within species (genetic diversity), be- that characterize that region’)
tween species (diversity of species) and of ecosystems (and the life form: integrates organisms with a similar morphological
interactions contained within them) structure and way of life; term most frequently used in botany
ecoregion: a relatively large area of the earth’s surface ‘contain-
ing a geographically distinct assemblage of species, natural com-
See also: Island biogeography: 3.2.1.4; Plate tectonics: 2.1.1.2

Biodiversity distribution 175
Taiga
Mediterranean biome
Desert
Savannah
Rainforest and mangrove

3.2.1
Patterns and mechanisms

Two million different species have been described so far, around 85 % of vertebrates, 65 % of land plants and 25 % of
of which roughly 80 % are terrestrial and the remaining 20 % invertebrates have been described. Moreover, under 10 % of
are aquatic. planet’s microorganism groups are thought to have been de-
There are approximately 61,000 described vertebrates (of scribed.
which half are fish), 1,260,000 invertebrates and 290,000 Based on what is known so far, the estimated number of
land plants. Far fewer fungal (72,000), protist (78,000), and total species on Earth is thus around 71,000 vertebrates, 5.5
prokaryotic (8,000) species have been described. million invertebrates, 440,000 land plants, 1.5 million fungi,
The vast majority of Earth’s species are thought to be still 800,000 protists, and over a million prokaryotes.
unknown or uncharacterised. To that end, it is assumed that
Estimates for global biodiversity range from around 3.5 ber of newly described species, the total number of species
million to more than 100 million species. These predictions could be estimated.
are based on extrapolations of known biodiversity, making The number of higher eukaryotes in the wild is probably
use of a number of different calculations. 5–10 million, although this estimate could double if it in-
For example, based on the number of extant insect species cluded parasites which remain under-studied. Similarly, it is
found on any given host plant, the total number of insects not possible to make a plausible estimate of the total diver-
can be estimated based on the number of known plant spe- sity of eukaryotic and prokaryotic microorganisms.
cies. However, such estimates rely on a profound knowledge For a number of reasons, even the total number of de-
of host specificity; since knowledge in this field is not precise, scribed species can only be estimated: firstly, many species
strongly diverging estimates can be found. have been described multiple times, leading to the simulta-
Other approaches estimate global biodiversity on the ba- neous usage of synonymous names until taxonomic revi-
sis of regional diversity in well-studied regions; for example, sions eliminate all but one of them. Secondly, many species
can be estimated a global number of fungal species based on descriptions are taxonomically invalid. Thirdly, particularly
the relatively well-known number of fungal species found on older descriptions were based on poor methodology in com-
the British Isles. parison to modern techniques; it is often difficult to clarify
Other approaches are founded on the assumption that the to which type species these descriptions refer. Furthermore,
ratio of species richness between different groups of organ- some ‘species’ are in fact species complexes rather than indi-
isms is similar across different geographic regions. Based on viduals, comprising morphologically similar but inaccurately
this assumption, the global biodiversity of various groups of delineated species.
organisms can be extrapolated from the relative diversity of Finally, the uncertainty behind the estimation of the
these organisms at one location. Total diversity can be esti- number of known species stems from differences in rules for
mated starting from a well-studied region and at thus one species description between relevant disciplines (zoology,
globally studied organismal group. botany, microbiology, etc.). For example, several protist spe-
A very different approach attempts to estimate total species have been independently characterized both using the
cies diversity using the rate at which new species are de- zoological and botanical codes. The variety of species con-
scribed. Decreasing numbers of new taxa discoveries, for cepts existing between disciplines results in widely different
example, would indicate that most of these groups of organ- species definitions and, ultimately, in a variety of often con-
isms have already been described. By extrapolating the num- flicting species descriptions.
extrapolation: process of estimating variables outside a given

interval based on the known variables inside the interval
See also: Development of biodiversity: 2.3.1

Biodiversity distribution: pattern and mechanisms 177
Taxon Described Estimated number

species of total species
vertebrates 60,979 71,000 The diversity of vertebrates is well known. To date, over
mammals 5,416 5,500 85 % of species are estimated to have been described
birds 9,917 10,000
reptiles 8,300 10,000
amphibians 5,743 7,500
fish 28,900 35,000
invertebrates 1,263,700 5,500,000 The number of existing invertebrate species, especially

insects 950,000 4,000,000 insects, is very high. Although more species of insects have
other arthropods 150,000 635,000 been described than of any other group of organisms,
molluscs 70,000 120,000 only about a quarter of insects are thought to have been
nematodes 25,000 500,000 recorded thus far
platyhelminths 20,000 80,000
land plants 289,000 444,000 The diversity of land plants is well known. An estimated
bryophytes 16,600 22,000 two-thirds of land plant species have been described thus
ferns and club mosses 12,838 15,000 far
gymnosperms 930 1,000
angiosperms 258,650 320,000
lichen 17,000 25,000 Fungi, protists (including algae), prokaryotes and viruses
fungi 72,000 1,500,000 are relatively poorly understood. Only a few percent of
protists 77,540 800,000 estimated totals have been described, and the current
prokaryotes 7,793 1,000,000 estimated number of microorganism species many even
viruses 2,000 400,000 be too low by several orders of magnitude. Analyses of
molecular diversity, based on high-throughput sequences
of environmental samples, indicate a potentially enormous
diversity of these organisms
Described species: Proportion of estimated undescribed species:

The vast majority of described species are insects, fol- Only a fraction of species have been described so far
lowed by Magnoliophyta. Whereas the total number of (colours) whereas the majority of species remains
vertebrate species is relatively low, the lack of described undescribed (white). The largest proportion of unde-
diversity for other organismal groups largely stems from scribed species is made up of microorganisms, espe-
a lack of targeted work cially protists, fungi and nematodes. Since it is precisely
the protists for which the species concept is currently in
transition, the actual proportion unknown organisms is
probably much higher in these groups than shown here
vertebrates
insects
other arthropods
Mollusca
Nematoda
other Metazoa
Magnoliophyta
other land plants
fungi (including lichen)
protists (including algae)
Prokaryotes are not shown, as the species concept differs markedly when applied to prokaryotes compared to eukaryotes. Although species number
estimates are therefore hardly comparable, the number of prokaryotic species is likely to exceed that of eukaryotes
3.2.1.1
Biodiversity hotspots
Biodiversity on Earth is unevenly distributed: Some areas and coldspots are not necessarily the same across organismal
are particularly species-rich (‘hotspots’) whereas other areas groups: for example, the southern tip of Africa, rich in plant
are populated by relatively few species (‘coldspots’). diversity, does not contain particularly many vertebrate spe-
The estimate of biodiversity in a region usually hinges on cies.
one or a few organismal groups, often land plants or verte- Most organisms are not included when hotspots are be-
brates. Plants and vertebrates often have a higher biodiversity ing considered; it is thus unknown whether or not the areas
in tropical or subtropical regions. For plants, the southern which have been determined to be plant or vertebrate hot-
tip of Africa is particularly rich in endemic species, anchor- spots are also particularly rich in fungal, protist, or prokary-
ing the biodiversity of the wider region. Biodiversity hotspots otic diversity.
According to the original definition, biodiversity hotspots biodiversity hotspots are not just areas of high biodiversity,
are regions in which large numbers of endemic plant species but are also home to particularly endangered organisms. The
can be found and whose habitats are particularly vulnerable. idea behind this definition had to do with species conserva-
Specifically, a hotspot was defined as an area where at least tion, i.e. the aim of protecting as many organisms as possible
1,500 endemic vascular plant species (i.e. at least 0.5 % of at the lowest possible cost.
total described species) could be found and where a loss of at This approach is controversial for a number of reasons,
least 70 % of the primary vegetation is known to have taken not least that it presents a biodiversity analysis with the (po-
place. Most regions that meet these criteria are tropical or litical) goal of cost-effective species protection rather than
subtropical habitats, together comprising less than 2.5 % of strategic conservation of the most ecologically important
the total land area on Earth yet accommodating over half of species. In addition, it also defines target regions for protec-
all known vascular plant species. tion based only on a few organismal groups, thought to be
It is notable that, in this definition of the term, the level indicators of general biodiversity health.
of threat to organisms plays a central role; in other words,
endemic: occurrence of organisms within a defined restricted floristic kingdom: biogeographical region that differs mark-
geographical area edly from other regions due to its endemic floristic taxa
See also: Mediterranean biome: 3.2.2.8; Rainforest: 3.2.2.11

species count
vascular plants
low
high
The Cape flora is isolated from the rest of the African continent by dry
areas (Kalahari and Namib deserts) and has many endemic species
Tropical rainforests, especially the Amazon basin, are characterised by

a high diversity and an abundance of endemic animal and plant species
A high fish diversity developed in Lake Malawi (top) and in the other Rift
Valley lakes of East Africa
species count
vertebrates
low
high
3.2.1.2
Ecological niches
The coexistence of multiple species – the basis of biodi- the realised compared with the fundamental niche. Mutual-
versity – raises many questions. Different species often re- istic relationships, however, can lead to an increase in niche
quire the same resources and compete for them, raising the size.
fundamental question of how coexistence is even possible. Species coexistence is possible when species use resources
Why does the ability of one species to efficiently use a dis- differentially well, and when each species is better able to
tinct resource not lead to the extinction of other species? The cope with a particular set of environmental conditions than
principle of competitive exclusion is founded on the argu- the other species. Spatial ecological niches and temporal
ment that two species with the same ecological requirements factors such as seasonality also enable coexistence between
(i.e. identical ecological niches) cannot coexist in the same species with similar ecological requirements in the same
environment, eventually leading to the extinction of one of habitat. In general, species are only well adapted to certain
these species. combinations of environmental factors; biotic interactions
The ‘fundamental niche’ of a species is a theoretical niche further modify these interactions. Predation pressure can
based on the genetic variability and norm of reaction of that sometimes alter the basic dynamics of an ecosystem. For ex-
species, i.e. the range of abiotic and biotic environmental ample, relatively weaker prey species populations may ben-
conditions under which the species could in theory survive efit from increased predation pressure on otherwise stronger
(including in the laboratory). In contrast, the ‘realised niche’ prey species. Predation can also reduce the abundance of
refers to the part of the fundamental niche that is actually prey organisms to the extent that competition between prey
used. Competition with other species leads to a reduction of species disappears.
The apparent coexistence of many species in structurally have a relatively high diversity of species: some species are
poor habitats, such as the many species of phytoplankton in adapted to stable conditions but can also survive at levels of
a lake, appears to contradict the fundamental premises of medium environmental disturbance, whilst others, adapted
the niche concept. This contradiction was formulated as the to more frequent disturbance or to primary succession, will
‘paradox of the plankton’: how can coexistence occur when also survive. A moderate frequency of disturbance thus cre-
so many different planktonic species depend on the same re- ates a dynamic temporal habitat, which promotes each spe-
sources and light? There are various possible explanations cies at a different time. The conditions in such habitats do
for this paradox. For one, based on the niche concept, one not last for long, so species which are not well adapted to a
could argue that there are simply not enough factors includ- particular change do not die out completely.
ed in an analysis of any given habitat, and that each habitat The ‘neutral theory’ is an alternative, more controversial
is actually comprised of many more niches than was previ- explanation for coexistence. According to the neutral theo-
ously thought. Alternatively, it is conceivable that simply the ry, species may coexist even in entirely overlapping niches;
presence of new species creates new niches. Finally, it is also niche differentiation and competition play no role in coex-
conceivable that several species occupy the same niche and istence. According to this, abundance curves are stochasti-
can coexist within that niche. cally explained: speciation and extinction are based solely on
The ‘intermediate disturbance hypothesis’ postulates that random processes. On the basis of such simple assumptions,
coexistence is possible at a medium frequency of disturbance abundance curves typical for many habitats (i.e. with few
in the habitat. According to this hypothesis, undisturbed hab- common and many rare species) can be modelled. Which
itats are dominated by a specialist species and are relatively species end up being common is purely coincidental. The
species-poor. Conversely, in highly disturbed habitats, i.e. fact that certain species occur and dominate in different
those altered regularly by climate change or human activity, habitats contradicts this theory. Although the neutral theory
only species that are adapted to frequent change can survive; therefore cannot explain observed distribution patterns, it
therefore these habitats also have relatively few species. In contributes to the debate by recognising of stochastic ele-
contrast, habitats with a medium level of habitat disturbance ments into niche theory.
norm of reaction: width of phenotypic variation which can de- primary succession: plant life occurring on substrate devoid of
velop from a distinct genotype vegetation or on newly formed substrate
See also: Species concept: 3.1.2

tolerance The fundamental niche of a species is defined as the range of

intolerance intolerance
an environmental gradient in which it could live. To that end
optimum
the niche space refers to the area in which a species could live
across multiple environmental gradients
environmental gradient
fundamental niche The realised niche is the portion of the fundamental niche
realised niche within a particular ecosystem that is occupied by the species
in question. By overlapping the fundamental niches of a num-
ber of species you shrink their realised niches. Mutualistic re-
lationships, however, may extend the realised niche area
Competition with other species, or even competition between
isolated populations of the same spaces, leads to niche dif-
ferentiation. If certain areas of the fundamental niche are not
used due to competitive relationships, that fundamental niche
may shift and species may lose the ability to live under those
conditions. At the same time, the fundamental niche may ex-
pand in other directions
Two different species sharing ecological niches compete with

each other, which may lead to the extinction of one species
through competitive exclusion, particularly if that species can-
not occupy a different niche (competitive exclusion)
Species that are less tolerant to environmental Species belonging to climax communities domi-
change tend to dominate the latter phases of nate after long periods of stability. Under these
succession conditions, competition between species is of
particular importance for the reduction of di-
Pioneer species dominate a habitat immediately versity
following a disturbance. The greater and more
frequent the disturbance, the lower the number
of species able to tolerate the conditions
species diversity
time after disturbance

The greatest level of biodiversity is achieved at a medium disturbance frequency: the effect of disturbance is small enough that even species adapted to
stable conditions can establish themselves. In addition, competition is low enough that other different pioneer species are still able to survive
3.2.1.3
Speciation mechanisms
Speciation, i.e. the differentiation of one species into two ductively isolated. Ecological niche separation may, also
new ones, is preceded by separating gen pools of two sub- eventually lead to reproductive isolation.
populations of the parent species. In principle, at least for The isolation of two populations of the same species can
biological species and for species that reproduce sexually, occur as a result of geographic barriers, such as oceans or
genetic material is exchanged and recombined between indi- mountains, but also as a result of climatic or geological fac-
viduals of a population. The gene frequencies within a gene tors, or by human intervention. These mechanisms of spe-
pool can shift within a population, but they stay homoge- cies differentiation by geographic isolation are referred to as
nously mixed between individuals. allopatric speciation.
Speciation involves the divergence of the gene pool into Speciation can also occur without spatial isolation. This
two sub-populations of the ancestral species. Speciation type of speciation is referred to as sympatric speciation.
occurs as a result of an increasing divergence between the However, certain mechanisms of selection must take effect
gene pools of separate populations of a species. When the in order for the gene pool to diverge without spatial separa-
exchange of genetic material between separate populations tion. For example, this can occur as a result of disruptive
slows or is interrupted completely, these populations diverge selection, or diversifying selection, when extreme values for
further from each other with each generation. Random mu- a trait are favored over intermediate values so that the vari-
tations and sometimes also adaptive mutations decrease fur- ance of the trait increases and the population is divided into
ther the genetic similarity between populations. The popu- two distinct groups. Assortative mating, i.e. mating between
lations also increasingly differ phenotypically (i.e. in their individuals which are particularly similar in certain traits, is
appearance and metabolism). Finally, individuals from the an example of disruptive selection. Parapatric speciation re-
diverging populations develop incompatible reproductive or- fers to a situation in which populations are either temporar-
gans or incompatible genetic mechanisms of reproduction ily separated or live in separate but slightly overlapping areas.
(number of chromosomes, meiosis) and thus become repro-
Reproductive isolation is achieved via several different Post-zygotic isolation mechanisms refer to those that oc-
mechanisms apart in addition to sexual incompatibility. cur after the formation of a hybrid zygote, which however,
These can be understood as either pre-zygotic or post-zygotic is usually either not viable or is sterile. When such hybrids
mechanisms. are viable and fertile, they become reproductively isolated
Pre-zygotic isolation mechanisms occur before fertilisa- because they may have a lower ecological fitness.
tion and thus prevent the formation of a zygote. One such Sudden isolation mechanisms, occurring within a single
mechanism is gamete incompatibility, where copulation (or generation, are also known to exist. In plants, polyploidisa-
pollination in plants) occurs, but not fertilization. For exam- tion, or the multiplication of chromosome sets per cell, can
ple, either the pollen tubes are incompatible (plants) or sperm cause immediate reproductive isolation. Similarly, a com-
are wrongly adapted (animals). Other examples of pre-zygot- plete reproductive isolation condition also occurs in insects,
ic isolation mechanisms are sexual selection and spatial or for example, through infection by incompatible, endosymbi-
temporal niche differentiation. otic bacteria (especially of the genus Wolbachia).
adaptive mutation: mutation resulting in improved adapta- fertility: the ability to produce offspring
tion hybrid: (Lat.: hybrid = mixture) offspring resulting from cross
ecological fitness: adaptation of an individual to its environ- breeding by parents of different species
ment infertility: the inability to produce offspring
endosymbiotic bacteria: symbiotic bacteria living in other or-
ganisms
See also: Plate tectonics: 2.1.1.2

The collision of North and South America and the raising of the Panama land bridge ap-
proximately 3.5 million years ago interrupted the connection between the Pacific and
Atlantic oceans. The populations of different marine species were thus reproductively
isolated and subsequently developed separately. This formation of new species by geo-
graphic separation is called allopatric speciation
Atlantic: Anisotremus virginicus (Virginia porkfish)

Pacific: Anisotremus taeniatus (Panama porkfish)
Metriaclima spp. grazes food at the nursery with its terminal mouth
Metriaclima sp. Metriaclima callainos
Pseudotropheus spp. picks algae with its downwards-facing mouth
Pseudotropheus demasoni Pseudotropheus sp.
Labeotropheus spp. scrapes algae at the nursery with its inferior positioned mouth
Labeotropheus trewavasae Labeotropheus fuelleborni
The diversity of cichlids in Lake Malawi has emerged through successive radiations. Those found in rock biotopes (Mbuna) are characterized by a
mode of nutrition suitable to that way of life, including a different mouth position. Subsequently within each genus different colorations have evolved
and radiated. Sympatric speciation occurred by assortative mating (i.e. sexual selection); in other words, through speciation without the geographical
separation of populations
3.2.1.4
Island biogeography
Island biogeography theory is concerned with the rela- are better able to reach individual islands than are mammals
tionship between species extinction and range extension or reptiles.
for the creation of stable species richness. It is therefore not A fundamental principle of island biogeography is that
necessarily restricted to islands, although these are the natu- larger islands are inhabited by a greater number of species
ral testing grounds for the theory as they present clearly dis- than are smaller ones. Similarly, islands lying close to other
tinguishable habitat partitions placed at definable intervals. landmasses are richer in species number than more isolated
Thus, the significance of the geographic barriers can easily islands. These principles of island biogeography therefore
be characterised. Island biogeography theories generally fo- suggest that a strong network of adjacent habitats allows
cus on the importance of geographical barriers, including for higher levels of biodiversity, an insight that has particu-
isolated marine and freshwater habitats, forests, mountain lar importance for species and habitat conservation. Smaller
ranges, or valleys. According to these theories, ‘islands’ are populations are more endangered in small national parks or
any habitat surrounded by other types of habitats. This gen- biotopes than are more stable populations in larger areas.
eral definition makes it easy to understand that the degree of The size of a particular protected habitat and the number of
isolation of any particular habitat, caused by a geographical neighboring habitats are thus extremely important factors for
barrier, is not the same for different groups of organisms. the conservation of biodiversity.
This is of course also true for real islands: for example, birds
The species richness of islands is determined by the im- these rates are reversed, diversity decreases. Over time, biodi-
migration of new species, the extinction of existing species, versity reaches equilibrium. For the reasons given above, this
and by the speciation processes. Species immigration rates equilibrium is higher for larger islands and for islands close
depend on the accessibility of the isolated habitat (‘island’) to other inhabited land masses. The comparatively small
from other populations: Factors which affect these rates are populations on islands may also develop separately and in-
thus abiotic factors such as the distance between the habi- dependently from the founder population. The best-known
tats, the wind direction and the strength of ocean currents. example of such island speciation is finch populations ob-
The extinction rates of species living on an island depend on served by Charles Darwin on the Galapagos Islands.
the size of the habitat: the larger the island, the larger each These principles of island biogeography also played a role
distinct habitat can be and, therefore, the greater the habi- in the radiation of early reptiles in the Upper Carboniferous:
tat heterogeneity. Greater habitat heterogeneity allows more forest habitats were isolated as ‘islands’ when forest cover
species, with a broader range of ecological requirements, to diminished during this period. At the same time, amphib-
survive, and the larger habitat area permits larger and thus ians began to play a less prominent role in the increasingly
more stable populations. When species immigration rates dry ecosystems, whereas reptiles, better adapted to drier cli-
are higher than extinction rates, biodiversity increases. When mates, diversified as a response to environmental change.
extinction rate: number of species that become extinct in a habitat: area inhabited by a particular species
given time period (year, decade…) radiation: rapid diversification of a taxon giving rise to an array
founder population: usually just a few individuals of a species of new forms
which become established in a new area and form the basis of a
new, larger population
See also: Carbon: 2.3.3.8

plant species
Galapagos islands
reptile species
island area (km2)

Caribbean islands
The amount of biodiversity on an island generally increases with the island’s area. Top: Plant diversity on the Galapagos Islands. Bottom: Amphibian
and reptile diversity on the Caribbean islands. Both figures are double logarithms (modified from MacArthur and Wilson 1967)
immigration and extinction rates
The immigration rate decreases

with increasing species richness
The extinction rate in-

species richness
creases with increasing
equilibrium
species richness
species richness on the island
The larger the island or the closer it is to other

landmasses, the higher the immigration rate
and the lower the extinction rate
immigration and extinction rates
Island biogeography relates not only to islands but also to all kinds of
isolated habitat types, including lakes, mountain ranges, and isolated
patches of forest. Higher levels of species richness on an ‘island’ lead to
increasing extinction rates and decreasing immigration rates (top-right).
As the size of the ‘island’ increases and the distance to similar habitats
decreases, the point of equilibrium between immigration and extinction
shifts towards a higher species richness (bottom-right) species richness is
higher at equilibrium
species richness on the island

3.2.1.5
Global biodiversity gradients

One of the most striking patterns of global biodiversity in the tropics, but so far a balance in species richness has yet
distribution is the decrease in the number of species with in- to be reached. These theories can thus be termed ‘imbalance
creasing latitude. In the low latitudes (tropics) the number theories’, and they rely heavily on climate history and par-
of species is very high, whereas the opposite is true for the ticularly on the effects of glaciation in the Quaternary as well
higher latitudes (temperate and polar zones). This does not as the effect of warmer climates over long periods of time on
seem surprising at first from an anthropogenic point of view; the evolution and diversification of extant organisms.
however, a number of species are adapted to cold climates Another set of theories explains latitudinal biodiversity by
and would not be able to survive in the warmer temperatures assuming that the temperate and polar climates have already
of the subtropics and tropics, which seem so comfortable to reached a balance of species richness, but that the upper lim-
humans. It is in fact not easy to explain the increase in spe- its for the number of species they can hold is lower than in
cies diversity in warmer climate zones, and many hypotheses the tropics for a number of reasons. These explanations are
which attempt to explain this distribution pattern have been known as ‘equilibrium theories’ and are based on the larger
postulated. These explanations are difficult to test because of land and water bodies found in the tropics than in temperate
the lack of independent systems of comparison – we do not and polar regions, as well as on the higher levels of available
know of any other Earth-like planets capable of maintaining energy (higher levels of solar radiation and the associated
life. higher level of primary production) in the tropics. Also im-
Existing hypotheses for the latitudinal distribution of bio- portant in equilibrium theories is the importance of various
diversity can be divided into two groups. In some theories climatic conditions on the stability of habitats and their food
the assumption is made that the number of species in the webs.
temperate and polar regions can ultimately be the same as
Imbalance theories are based on the assumption of a slow tats in the northern hemisphere also occupy large areas of
colonisation (or re-colonisation) of climate zones; in other land, but this fact is not reflected in high species richness.
words, the adaptation and dissemination of organisms in A second explanation based on equilibrium theory suggests
more recent geological periods have impacted their current that survival is simply ‘easier’ in the tropics, as it requires
distribution. To that end, the colonisation of cooler climate fewer special adaptations. Life in colder climates requires
areas remains ongoing, as most taxa originated and diver- more specialised adaptions for survival during long periods
sified under warmer conditions. Geologically, we now live of frost. In the tropics, the necessity for certain combinations
in a relatively cold period after a long, considerably warmer of traits is far less restrictive and the probability of survival
period of time. Higher species richness in the tropics, there- for newly evolved species with new combinations of traits
fore, may simply represent a ‘head start’ in the adaptation should be higher. Therefore, more species adapted to warm
of species to these climatic conditions. Ice ages have also climates should evolve over time than species adapted to
contributed to current conditions, as they were responsible colder climates. A third equilibrium-based theory is based
for higher extinction rates of species living in temperate and on solar energy, postulating that the tropics receive a higher
polar regions. The low number of species in cooler climates amount of solar radiation, and thus more energy is at the
could therefore also be explained as an incomplete post-gla- disposal of primary producers. The resulting higher primary
cial recolonisation of this habitat. production allows for a stronger niche differentiation (for
Equilibrium theories can be explained by distinct hypoth- certain foods) at the highest trophic levels, thereby allowing
eses, three of which are outlined here: Firstly, tropical and for more coexisting species. However, the higher specializa-
subtropical habitats occupy a greater area due to the spheri- tion of herbivores causes a correspondingly higher rate of
cal shape of the planet. These habitats potentially offer more specialization in plants. In contrast, fewer species are able
space for organisms and more room for the differentiation to coexist in cooler locations where there is lower primary
of taxa. However, the higher biodiversity levels in the tropics production and higher seasonality.
cannot be entirely explained by area alone: Temperate habi-
latitudinal: distance north or south of the equator measured

along a meridian
See also: Ice age: 2.3.5.6; Climate: 3.2.2.1, 3.2.2.2; Plate tectonics: 2.1.1.2
Equilibrium theories, which explain the distribution of species, often relate to species-area relationships and solar radiation:
The tropical and subtropical habitats occupy a greater land Tropical species do not require adaptations to cold and
area and can therefore also offer more space and niches for drought, since the tropics are frost-free and endure low lev-
more species. However, the large areas of land in temperate els of variation in temperature and precipitation. The proba-
climate zones of the northern hemisphere have compara- bility of survival of (randomly) evolved species in tropical ar-
tively few species and therefore do not match the postula- eas is therefore higher than in temperate and polar regions
tions of this model
The tropics are exposed to considerably greater levels of

solar radiation than the temperate and polar climes, lead-
ing to higher primary production rates. The correspondingly
large supply of food in the tropics can therefore be a cause
of greater niche differentiation
90
60
30
30
60
90
0 5 10
relative proportion of solar radiation latitude division of land masses relative species
landmass (kWh/m2/day) distribution
Disequilibrium theories, which explain the distribution of species, often relate to climatic conditions in the younger and older geologic history:
Glacial periods during the Cenozoic ice age led to (at least
regional) extinctions of species in temperate and polar re-
gions
Angiosperms as well as the extant vertebrate groups (espe-

cially birds and mammals) diversified during the upper Mes-
ozoic (Cretaceous) and the lower Cenozoic (Paleogene) eras
25 °C
average global temperature during the Cenozoic (red)

compared to present-day temperatures (dashed)
5 °C
Paleozoic Mesozoic Cenozoic

3.2.1.6
Biogeography of microorganisms
The distribution of prokaryotic and eukaryotic micro- distribution were based on microscopic (and hence morpho-
organisms is poorly studied. It remains unclear whether logical) observations. In this original work, morphologically
dissemination and biogeographic theories established for similar species were often grouped together; as a result, pro-
higher-level organisms also apply to microbes. Various hy- liferation analyses often refer to morphological species com-
potheses have been postulated. On the one hand, the ‘every- plexes and not the distribution of individual species. With
thing is everywhere, but the environment selects’ hypothesis, this in mind, it is probable that many of the individual spe-
established over a century ago, postulates that microbial species within such species complexes may have geographically
cies have a worldwide distribution but that the habitat char- restricted distribution areas. Furthermore, for several groups
acteristics affect the occurrence of taxa. In contrast, other of microorganisms morphological traits are generally of lim-
theories, in line with observations of higher-level eukaryotes, ited value for species delimitations. Molecular analyses have
propose that microorganisms have endemic distribution pat- supplemented or even replaced conventional morphological
terns. studies of microbial distribution, as they often allow for a
Globally, the number of known species of higher animals higher phylogenetic resolution. However, increasing the level
and plants increases with decreasing body size. However, of phylogenetic resolution does not adequately answer the
there are only relatively few types of described microorgan- question for the level of phylogenetic resolution required for
isms. This trend suggests that microbes may be fundamen- separating species and for the species concept to be applied.
tally more widespread than larger organisms but may also The debate about microbial distribution patterns is still
just reflect the poor knowledge on microorganisms. based on too small a number of dissemination studies. Reli-
The taxonomic basis for biogeographic analysis of micro- able molecular and morphological data exist only for a lim-
organisms is controversial. Originally, studies of microbial ited number of taxa.
Historically, the discussion of microbial distribution is able habitats, and dissemination theories were not necessary,
based on a combination of morphologically similar species since de novo organisms could occur anywhere. The refuting
found in geographically distant areas and on misconceptions of abiogenesis by Pasteur required an alternative explanation
about the evolution and distribution of these organisms. Be- for the assumed distribution patterns of microorganisms, i.e.
fore experiments by Louis Pasteur (1822–1895) disproved a worldwide distribution across large geographical distances
theories of spontaneous generation of life from mud and and barriers. The high density of microbial populations, cou-
contaminated water, it was assumed that lower forms of life pled with their microscopic dimensions, serves as an argu-
could emerge anywhere and at any time wherever suitable ment for easy dispersal of species; it is probable that micro-
living conditions prevailed. This spontaneous emergence of organisms are easily distributed far and wide by such vectors
life was known as abiogenesis. It was a logical consequence as water, wind or via other life forms.
of this view to expect microorganisms everywhere in suit-
endemic: occurrence of organisms within a defined restricted phylogenetics: the study of the evolutionary relationships be-
geographical area tween organisms and the evolution of species during the history
morphology: form or shape of organisms; related to external of the Earth
appearance/shape taxonomy: (Grk.: taxis = order, nomos = law, ordinance) (usu-
ally hierarchical) classification of organisms
ubiquitous: broadly distributed, to be found everywhere
See also: Species concept: 3.1.2; Eukaryotes: 4.1.2.3; Prokaryotes: 4.1.2.1

silicate scales
The flagellates of the genus Paraphysomonas (Chrysophyceae) have been used as evidence for the world-
wide distribution of protists (top-left: Paraphysomonas sp.; top-right: distribution of this species). These
flagellates possess silicate scales that can be used to differentiate species. The fact that these scales are
found globally wherever similar physical and chemical environmental conditions are found has been used
as evidence for the global spread of protists, and of microorganisms in general. However, recent studies
question whether or not the subjects of these studies are really different species or, rather larger groups of
morphologically similar (or cryptic) species. For example, the organisms formerly assigned to the type spe-
cies Paraphysomonas vestita have now been assigned to many different species. They differ from each other
in terms of the structure of their scales (three selected examples are shown to the left, enlarged to the same
scale) and in their molecular characteristics. The geographical spread of these now more narrowly defined
species is, however, unclear, and can currently not be used as evidence for or against a worldwide distribu-
tion. Similarly, the suitability of molecular markers (‘barcodes’) for the analysis of distribution patterns in
microorganisms remains controversial; again, it is unclear to what extent the markers actually necessitate
the reclassification of various known species
distribution patterns largely unknown distribution patterns largely known

Microorganisms
Estimates of the number of species are often
based on superficial morphological criteria.
Many species considered ubiquitous
Macroorganisms
Estimates of the number of species often
based on high-resolution morphological cri-
species diversity
teria and molecular markers. Many species

endemic
species delineation largely unknown species delineation largely known
size of organisms
The assessment of total biodiversity at the global level makes an important contribution to the debate about protist distribution patterns. The number
of known species of macroorganisms increases as body size decreases. Morphological analyses demonstrate a reversal of this trend for organisms of less
than a millimeter in size. Possible reasons for this trend include the wider geographical distribution of these species due to their high population densi-
ties and high rates of dispersal. According to this view, few species occupy physically and chemically similar niches across the planet. However, estimates
of diversity as a function of body size go hand in hand with increasing uncertainty surrounding species delimitation for smaller organisms
3.2.1.7
Alien and invasive species

Alien species are taxa that have established themselves in In order to survive, alien species must be competitive in
an area where they did not exist before. As this has been the their new habitat. They are therefore often characterised
case for many species throughout Earth’s history, this defini- by high reproductive rates, rapid growth, and high levels of
tion is commonly applied only to species that have migrated adaptability. Alien species are thus often r-strategists and gen-
in the recent past. Although not universally accepted, an eralists. Alien species are also often associated with humans,
important year of reference for the delimitation of modern- colonising anthropogenically altered landscapes quickly.
day alien species is 1492, the year in which Christopher Co- They often fundamentally change the composition of the lo-
lumbus reached the New World and the exchange of species cal biocenosis, for example through predation or as a result
between the Americas and Europe intensified. Humans are of competition pressure. Along with habitat fragmentation,
among the most important means (vectors) of transport for invasive species represent one of the most important factors
alien species. This is particularly true for travel by ship, as contributing to the extinction rate of current species.
the ballast water of boats plays a major role in facilitating the
spread of aquatic organisms.
The propensity for existing biodiversity to be threatened ien species. Disturbed ecosystems are also susceptible to the
by alien species is complex. In terms of individual habitats, establishment of new species, since disturbance events tend
areas of high biodiversity seem less prone to the establish- to lower competitive pressures in an area. This phenomenon
ment of invasive species. In such habitats, competition for re- explains why alien species so easily invade anthropogenically
sources is generally high and the immigration of new species influenced habitats.
may therefore be difficult to establish. On the other hand, the Some of the most important alien species cannot be re-
opposite has been shown to be true for larger ecosystems: the garded as invasive, despite their continuous dissemination
number of invasive species appears to increase with the num- and detrimental economic impact. For example, grape phyl-
ber of species present. Larger ecosystems may be more prone loxera, a pest of commercial grapevines worldwide, spread
to species invasions because of an increased availability of slowly and its negative impact is only observed in plant
resources or because of a high internal heterogeneity of the (grape) species monocultures and almost not at all on the
ecosystem itself. Both factors favour the establishment of al- wider biodiversity of newly invaded habitats.
anthropogenic: (Grk.: anthropos = man, gen = cause) caused, habitat fragmentation: process by which habitat loss results
influenced, brought about by human beings in the division of large habitats into a greater number of smaller
generalists: organisms able to survive under a variety of condi- patches
tions r-strategists: species which focus on producing a high quantity
habitat: area inhabited by a particular species (r) of offspring
sailing ballast: water used by ships (voyaging without cargo)
to keep the vessel upright
See also: Distribution of biodiversity: 3.2.1.5

Wine regions (red) and the spread of phylloxera (shaded)

Phylloxera (Viteus vitifoliae) is a serious viticultural pest. In a complex generational alteration, it infests the roots and leaves of grapes (Vitis vinifera). It
originated in the 1860s in the northeastern United States and spread to European wine regions before dispersing worldwide to grape-growing areas.
Since it spreads slowly and only affects monocultures within the plant cultivation area, phylloxera is not referred to as an invasive species
origin of the
Colorado potato
beetle
Origin (red) and spread (shaded) of the potato

Blight spread worldwide within the cultivation of potatoes (left: potato leaves infected by Phytophthora infestans). The Colorado beetle (middle:
Leptinotarsa decemlineata, the Colorado potato beetle) originates in the southwestern United States whereas Phytophthora infestans has an unclear
background, though its first documented outbreak was in 1843 in the eastern US. The transmission of infected potatoes to Europe triggered the great
Irish famine of 1845–1953
19th and 20th centuries

1990
1995
natural
2010 1986 distribution
Zebra mussel (Dreissena polymorpha))

The zebra mussel (Dreissena polymorpha) originates near the Black Sea
and spread across Europe in the 19th and 20th centuries. In 1986, it was
first detected in North America (Lake St Clair) and reached the Great
Lakes in 1990 and central to western US by 1995
Zebra mussel distribution

The spread of zebra mussels fundamentally altered limnic ecosystems and the organisms they housed. A notorious example of the wider impact of zebra
mussel introduction is on bitterlings, which lay their eggs using an ovipositor into the gill chamber of large freshwater mussels, such as the painter’s
mussel. The young fish subsequently develops there before leaving the shell a few weeks later. However, zebra mussels colonise the shells of these
mussels, so bitterling eggs no longer can reach the gill cavity, putting their reproductive success at risk
Painter’s mussel (Unio pictorum)) European bitterling (Rhodeus amarus)

3.2.1.8
Cenozoic mass extinction

Many species have gone extinct in Earth’s history, not modern humans across the planet, although the extent of the
only during the prehistoric mass extinctions but also during effect of early humans on extinction rates remains unknown.
relatively recent history, including during the upper Cenozoic Climatic fluctuations and associated habitat shifts are also
Era. These relatively recent extinctions are partly a result of thought to have affected megafaunal extinction patterns.
changes in climatic conditions but are mainly due to human The effect of human activity on extinction patterns is
activities. Climatic fluctuations during the Quaternary (the clearer in the more recent past. Some species were even de-
most recent of the three periods of the Cenozoic), especially liberately eliminated, such as the thylacine (also known as
fluctuations between glacial and interglacial periods, closely the Tasmanian tiger). Other species went extinct when alien
coincide with the extinction of many organisms. Extinction species were introduced, the best known example being the
rates of many larger mammals (megafauna) reached their dodo (Raphus cucullatus). This large, flightless bird, endemic
peak near the end of the last glaciation, roughly 11,000 years to the island of Mauritius, was wiped out when its nest sites
ago. This particular extinction included many large mam- were destroyed by rats and feral livestock introduced by hu-
mals of the colder periods, including the mammoth (Mam- mans. Many species are currently threatened with extinc-
muthus primigenius) and the woolly rhinoceros (Coelodonta an- tion, and it is likely that many of these will in fact go extinct
tiquitatis), as well as those adapted to warmer periods, such in the coming decades. The extinction of some of these spe-
as the forest elephant (Elephas antiquus) and the forest rhi- cies, for example the Sumatran rhinoceros, can be delayed by
noceros (Dicerorhinus kirchbergensis). Many predators also dis- national and international protective measures, although to
appeared at the same time, including the saber-toothed cats what extent these measures will be able to sustainably protect
(Homotherium spp., Smilodon spp.). The time of these extinc- endangered wildlife remains unclear.
tions roughly correlates with the appearance and spread of
Extant biodiversity is only a small fraction of the planet’s due to the alternation of glacial and interglacial periods. Due
total diversity over time. Over 99 % of the 4 billion species to current factors including increases in atmospheric carbon
estimated to have lived throughout Earth’s history are ex- dioxide concentrations, habitat fragmentation, increases in
tinct. Extinctions are normal when considered in geological the dispersal of alien species and ever-increasing concentra-
time scales; mass extinctions, however, were relatively rare. tions of pollutants, stress levels on existing species are cur-
Only a small number of total extinctions have thus occurred rently much higher than they have been in the past. These
during mass extinction events. In the paleontological sense, factors and many others are likely to pave the way towards
mass extinctions are periods in time when extinctions out- the next period of mass extinctions.
weigh speciation so that there is a loss of more than 75 % of Species known to be endangered or extinct are increasing-
species diversity within a geologically short period of time ly well documented. Although the number of such species is
(less than around 2 million years). In that sense, two of the increasing rapidly, it is still almost certainly a considerable
great mass extinctions, known as the Big Five, are not strictly underestimation of the actual number, as many species have
mass extinctions (the Devonian and Triassic) but rather only not yet been formally described. It is clear, however, that cur-
massive biodiversity depletions. During these two events, rent extinction rates are already higher than during some of
the extinction rate remained relatively normal but speciation the other major geological periods of heavy extinction. On
rates were considerably lower than usual. the other hand, the total number of species which have gone
Major geological mass extinction events usually appeared extinct during the Quaternary is so far not as high as during
alongside major climatic, atmospheric, and ecological up- the known periods of mass extinction. However, if one in-
heavals. The combination of different stress factors was cludes endangered species, i.e. those at risk of extinction, it is
likely related to the strength of the impact of each event. likely that within a few hundred years the number of extinct
Accordingly, in the current Cenozoic Ice Age (Quaternary), species will have reached the dramatic levels which existed
ecosystems have been exposed to increased climatic stress during the mass extinction events.
Cenozoic Era: most recent era in Earth’s history (covering the megafauna: large or giant species of animals from the Neogene
last 66 million years) and the early Quaternary
glacial: (Lat.: glacies = ice) interval of time marked by cold tem- palaeontology: (Grk.: palaios = old, logos = discourse) the sci-
peratures entific study of life before the Holocene
habitat fragmentation: process by which habitat loss results Quarternary: the most recent period in the Cenozoic Era span-
in the division of large habitats into a greater number of smaller ning the last 2.588 million years and including the present
patches recent: (Lat.: recens = fresh, new) having happened not long
interglacial: interglacial period; warm period between two gla- ago
cial periods
See also: Ice age: 2.3.1.1, 2.3.5.6; Cenozoic: 2.3.5; Mass extinction: 2.3.1; Alien and invasive species: 3.2.1.7; Quaternary: 2.3.5.5
Fraction of extinct species (blue) based on extinct mam- At least 75 % of species went
mals (M), birds (B), reptiles (R), and amphibians (A) dur- extinct during the largest mass
ing the past 500 years: 1–2 % extinctions
Fraction of extinct species including threatened

species (yellow): 2–10 %
[extinct species per 1,000 species in 1,000 years]
Fraction of extinct species including endan-

gered species (red): 10–30 %
extinction rate (speed of extinction)
1000 The extinction rate of the largest Phanerozoic mass

A extinction (Permian-Triassic extinction event) was
B M
A between one and ten extinctions per 1,000 species
R within 1,000 years
100 M
B
R The ‘normal’ background rats of extinctions is be-
M tween 0.1 and 1.5 extinctions per 1,000 species
10
B over a time of 1,000 years
1.0
0.1
0 25 50 75 100
extent of extinction during the mass extinction [ % of species]
The current rate of species extinction (blue dots) is significantly higher than the average background level during Earth’s history (yellowish area). Even
the extinction rates during the largest mass extinction of the Phanerozoic (Permian-Triassic, orange area) were well below those witnessed today.
Although the proportion of species which have gone extinct within the last 500 years is still quite low (blue dots), if you add the potential extinction of
threatened (yellow dots) and endangered (red dots) species in the calculation, nearly 30 % of species are likely to go extinct in the near future
Climate change and habitat loss contribute to the acceleration of the current species extinction rate. For example, the consequences of a changing cli-
mate has led to the bleaching of corals (left) and the retreat of glaciers (e.g. Briksdalen glacier, Norway, 2003 (middle) and 2008 (right))
Saber-toothed cats (left: Smilodon sp.), along with many other large mammals, went extinct at the end of the last glacial period. The thylacine (middle:
Thylacinus cynocephalus) was once widespread in Tasmania, but was heavily hunted and eventually eradicated by 1930 after the introduction of sheep
farming. The last individual thylacine died in a Tasmanian zoo on 7 September 1936. The Sumatran rhino (Dicerorhinus sumatrensis, right) is classified as
critically endangered, with just under 300 heavily protected individuals thought to inhabit different national parks across Sumatra and Malaysia
3.2.2
Biogeographic regions
Biogeography is the study of the current distribution of from the deserts of Central America occupy a similar niche
organisms and the historical development of this distribu- as euphorbias (the spurge family) from the Namib desert in
tion. Likewise, phytogeography and zoogeography are terms southern Africa.
referring to the biogeography of plants and animals respec- Floral and faunal composition changes strongly near the
tively. boundaries between different biogeographic areas due to
Biomes are regions where similar life forms occur; the the long periods of geological time during which lineages
plants and animals which occur there have similar adapta- evolved independently, i.e. in spatial isolation from each
tions to the environmental (climatic) conditions of that habi- other. Floral and faunal borders are mostly natural distribu-
tat. Floral and faunal kingdoms are, on the other hand, those tion barriers, like oceans, mountains or deserts; the degree
with systematically or taxonomically similar communities of of difference in flora and fauna across a particular border
species. These characteristics reflect the relative position of depends on how long the barrier has existed. Biogeographic
land masses to each other over the course of Earth’s history. separation at such borders therefore includes differences in
Life forms in different biogeographic provinces are of- higher-level taxa (families and genera) as well. The charac-
ten made up of different plant and animal families, despite teristic flora and fauna for each biogeographic province is
potentially similar ecological functions. For instance, cacti known as its floral or faunal element.
The borders of phytogeographic and zoogeographic biogeographic isolation of southern Africa is therefore far
provinces often run alongside each other, but they are not less pronounced.
exactly the same. This is particularly obvious in southern Noticeable differences between zoogeography and phyto-
Africa, which has its own phytogeographic kingdom – the geography are also found on the border of the Indo-Malayan
Cape Floristic Region – which is phytogeographically but (Orientalis) and Australasian regions. The zoogeographical
not zoogeographically separate from the Paleotropical King- border at that location is marked by the Wallace line (be-
dom (Paleotropis), which includes the rest of Africa. On the tween Bali and Lombok in the south and between Borneo
other hand, subdividing the Holarctic into the Palearctic and and Sulawesi in the north). The area between the Wallace-
the Nearctic as well the Paleotropis into the Afrotropic and line and the Australian shelf edge is also referred to as Walla-
the Indo-Malayan (Orientalis) is more common in zoogeog- cea and is partially separated from the large faunal kingdoms.
raphy than phytogeography. Present-day species distribution patterns here correlate with
The Cape Floral Region is the smallest of the six floral the presence of land bridges during the last ice age: Sumatra,
kingdoms on the continents, and includes the winter rain Java, Bali, and Borneo were connected to the Asian main-
area on the southwestern tip of Africa. The dispersal of land via land bridges, and islands on the Sunda shelf were
plants to and from other floral kingdoms is greatly hampered connected to Australia in the same way. In contrast, the is-
by adjacent deserts and semi-deserts (the Namib, Koo, Kala- lands of Wallacea were not linked to the mainland through
hari). Consequently, many of the species found within the land bridges during the last ice age, and therefore deviate
Cape Floral Region are endemic; this region is also the most zoogeographically from the Indo-malayan or Australasian
species-rich floral kingdom in relation to surface area. For regions. The phytogeographical boundary in the region runs
the (mobile) fauna, the geographical barrier into the Cape along the Australian mainland. Only a few islands harbour
Floral Region is considerably easier to overcome; the zoo- Australasian flora, whereas the Pacific island arc falls within
the Paleotropical Kingdom.
endemic: occurrence of organisms within a defined restricted

geographical area
See also: Plate tectonics: 2.1.1.2, 2.3.1.1

Biodiversity distribution: biomes 195
The Palearctic and Nearctic were connected to each other for a long period Terrestrial habitats are divided into eight biogeographic regions (also
of time. These regions were united within the continent of Laurasia after the known as ecoregions or ecozones) closely corresponding to the areas
breakup of Pangaea, and were separated around 150 mya by the development of distribution of many animal and plant families. Their distribution
of the Atlantic. North America and Asia were also connected via the Bering patterns can be explained by the historical positions of the continents.
Strait as a result of the low sea levels during Cenozoic glacial periods. Their his- Land masses which were previously connected by land bridges exhibit
tory of connectedness is reflected in their similar flora and fauna. The Nearctic many common plant and animal families today. The significance of
and Palearctic are therefore known together as the Holarctic. In contrast, the each region and its borders are differently interpreted in phytogeog-
present-day connection between North and South America via the Isthmus of raphy and zoogeography: although the World Wide Fund for Nature
Panama is relatively new; these areas were joined only 3 million years ago after (WWF) attempts to combine the two systems, a slightly stronger use
a long time of separation of zoogeographic than phytogeographic information can be noticed
in the divisions
The Palearctic includes Europe,

The Nearctic comprises North Ameri- northern Africa and northern Asia Oceania comprises many small islands in the Pacific. The
ca, including the highlands of Mexico, to the northern edge of the Hima- boundaries of the biogeographic region deviate from the cul-
northern Florida and Greenland layas tural-economic demarcation of Oceania in that the latter also
includes Australia and New Zealand
Nearctic Palearctic
Oceania
Neotropic Indomalaya
Afrotropic
Oceania Australasia
The Neotropic includes South and Central America, Australasia includes the areas that were connected
Mexico, and the south of Florida. From a botanical to Australia via a land bridge during the last ice age
perspective, the southern tip of South America is ex- (Australia, New Guinea and Tasmania) as well as New
cluded from this region and instead part of the Ant- Zealand and parts of Indonesia
arctic floral kingdom
The Afrotropic includes Africa south of the Sahara. From a phyto- The Indomalaya or Oriental Region covers Asia south of the Hima-
geographic perspective, most of Sahara and the Arabian Peninsula layas and some areas to the east
belong to this region, whereas the southern tip, known as the Cape
Floristic Region, is excluded
The Indomalaya and Afrotropic are combined (as the Paleotropic) as they share many plant and animal species. India was linked to southern Africa
for a long time until the Indian plate broke up during the Jurassic and drifted northward during the Cretaceous. The Himalayans served as a dispersal
barrier after the collision of the Indian plate with the Eurasian plate in the Tertiary, limiting the exchange of species between the Indomalaya and the
Palearctic
The classification presented here divides the planet into 14 major tropical and subtropical moist deciduous forest temperate grassland
habitat types, following the suggestion presented by the WWF. For
tropical and subtropical arid deciduous forest montane grass- and bushland
example, similar to the Anglo-American biome delineation, temperate
tropical and subtropical coniferous forest flooded grassland
and hot deserts are placed together, whereas these are considered to
be separate in other systems. The relationship between rainfall and temperate deciduous and mixed forest tundra
evaporation rates plays a central role in this delineation of biomes. temperate coniferous forest Mediterranean forest and bushland
Other systems, such as the one widely used in Germany, take the boreal forest / taiga desert and arid bushland
seasonality of temperature and precipitation into consideration as well tropical and subtropical grasslands and bushland mangrove
rock and ice sheets
3.2.2.1
Global precipitation and temperature distribution

Climate zones of the world and thus also the ecoregions The time when precipitation occurs also affects this clas-
are largely defined by the availability of sunlight and the re- sification, i.e. conditions are assessed according to whether
sulting temperature and precipitation conditions. Seasonal rainfall occurs predominantly in winter or in summer. If
changes in precipitation and temperature conditions are usu- rainfall is measured in mm and temperatures in degrees Cel-
ally presented in climate diagrams, including the frequently sius (ºC), the winter rainfall areas of deserts receive annual
used Walter and Lieth climograph, in which the amount of rainfall values below that of their annual mean tempera-
precipitation and the temperature have been scaled so that ture, whereas precipitation values in winter rainfall areas in
humid conditions (when the precipitation line is above the steppes are maximally twice as high as their mean tempera-
temperature line) and arid conditions (when the precipita- tures. Precipitation in summer rainfall areas of dry climates
tion line is below the temperature line) can both be directly are generally somewhat higher.
read. Warmer-temperate rain climates have a higher total pre-
Global temperature and precipitation patterns result in a cipitation than dry climates. In general, the coldest month in
formation of a basic pattern of climatic zones, and with that the temperate climates has a mean temperature of between
of biomes, with increasing distance from the equator. The –3 and 18 ºC and the warmest month over 10 ºC.
distribution of land masses and high mountains also affect Boreal climates are characterised by average monthly
regional climatic conditions. The Köppen-Geiger classifica- temperatures of below –3 ºC in the coldest months and over
tion zones are distinguished as follows: tropical rain climates 10 ºC in the warmest months.
are characterised by high rainfall and a monthly average Snowy climates are characterised by an average tempera-
temperature of at least 18 ºC during all months of the year, ture in the warmest month of below 10 ºC (tundra), or of
whereas drier climates are characterised by low rainfall and below 0 ºC (permafrost).
are divided further into desert and steppe climates.
The location of land masses affects climatic patterns; in ing air currents and, importantly, by forcing air to rise and
general, precipitation decreases with increasing distance cool (forced convection) causing moisture in the air to con-
from coastal regions, e.g. precipitation is considerably lower dense, forming clouds and eventually rain. On the leeward
in the interior of Asia or North America compared with their (downwind) side of the mountain, air masses sink again and
coastal areas. Furthermore, the distribution of precipitation increase in temperature, decreasing relative humidity and re-
is affected by wind patterns: The westerlies of Central Africa sulting in low levels of precipitation. For example, the west
(from the Atlantic Ocean to the east) lead to high rainfall coast of North America receives relatively high levels of rain-
in the western and central areas, whereas eastern regions fall, whereas land east of the Rocky Mountains is far drier.
are drier. Mountains also impact climatic patterns by caus-
arid: dry sociated with characteristic combinations of soil and landform

ecoregion: a relatively large area of the earth’s surface ‘contain- that characterize that region’)
ing a geographically distinct assemblage of species, natural com- humid: relatively high level of water vapour in the atmosphere
munities, and environmental conditions’ (WWF definition); the Intertropical Convergence Zone (ITCZ): low-pressure trough
term ‘ecoregion’ was originally used in the context of geographi- near the equator measuring only a few hundred kilometres
cal scholarship (meaning a ‘recurring pattern of ecosystems as- across; it appears as a band of thick cloud and is an area of high
precipitation
See also: Climate evolution: 2.3.1.1; Global wind systems and climate zones: 3.2.2.2
Annual precipitation [mm]

20 50 100 150 200 250 300 350 400 450 500 600 700 800 900 1,000 1,200 1,400 1,600 1,800 2,000 2,500 3,000 3,500 4,000
Precipitation is generally higher near coastlines than in inland are-

as. Precipitation intensity is also influenced by the direction of wind
and the location of mountains
Precipitation is higher
on the windward side of
mountains than in the lee-
ward areas
Precipitation is generally high in the Inter-

tropical Convergence Zone, and low in sub-
tropical areas
Westerly winds prevail in Equatorial Africa,
leading to significantly higher levels of rain-
fall in the west compared to the east
Climate diagrams show temperature and precipitation patterns. Climate diagrams in the style of Walter and Lieth show monthly average temperatures
(red line) on the left ordinate (y-axis) alongside rates of monthly average rainfall (blue line) on the right ordinate. A precipitation of over 100 mm is
shown five-fold compressed. The graphs are scaled so that 10 °C corresponds to 20 mm of rainfall
[°C] [mm]
In this type of diagram (i.e. temperature difference of 10 °C is scaled to Allahabad, India
correspond to a precipitation difference of 20 mm), when the tempera- 300
ture curve is below the precipitation curve, the conditions are humid. 200
The area between curves is shaded, but in the case of negative tem-
peratures only down to 0 °C, as precipitation cannot be negative. Above 50 100
100 mm of rainfall the (compressed) area is fully colored 40 80
30 60
20 40
In this type of diagram (temperature difference of 10 °C scaled to a pre-
cipitation difference of 20 mm), when the temperature is shown above 20
precipitation, evaporation prevails and, conditions are arid. The area be- 0 0
tween the two lines is dotted
J F M A M J J A S O N D
Temperature is highest around

the equator, dropping towards
the poles
Temperature decreases with altitude: in moun-
tains and other high altitude areas, tempera-
tures are low despite high levels of sunlight
–39 –36 –33 –30 –27 –24 –21 –18 –15 –12 –9 –6 –3 0 3 6 9 12 15 18 21 24 27 30 33 36 39
Annual average temperature [ °C]
3.2.2.2
Global wind systems and climate zones

Climate zones are regions of similar climatic conditions, criteria. Precipitation and temperature distribution patterns
which usually span east-west around the earth. Astronomi- are particularly important for the classification of climates.
cally, the tropics (between the northern and the southern The term ‘biome’ refers to major habitat types includ-
Tropical Circles), the mid-latitudinal zone (between the ing the animals and plants (biotic communities) potentially
Tropical and Polar circles) and the polar zone (between each living in this habitat type, as well as the abiotic factors oc-
Polar Circle and its pole) are separated based on insolation. curring there. According to the current way of thinking, the
As the actual climatic conditions follow only loosely these term is therefore an ecological one. The definition of a bi-
borders, the effects of climate such as vegetation patterns are ome is based on the occurrence of distinct (ecological) life
increasingly included within the classification system in ad- forms and on particular adaptations of the organisms, not
dition to the actual climatic elements. Therefore the zones on taxonomy or systematics. As the distribution of life forms
used in the climate classification largely correspond to major is largely driven by climatic factors, climate (particularly pre-
habitat types or biomes established according to ecological cipitation and temperature distribution) is the major factor
behind the definition of biomes.
The sun is at its highest point around the equator; conse- Walter classification features nine distinct biomes which take
quently, equatorial territories experience the highest levels of established patterns of seasonality in precipitation and tem-
solar radiation and temperatures on Earth. Solar radiation perature distribution into account. It distinguishes between
levels and average temperature drop with increasing distance Zonobiomes, Orobiomes and Pedobiomes. Zonobiomes
from the Equator. comprise landscapes similar with respect to climate, vegeta-
The high levels of sunlight around the Equator cause tion, fauna and soil types; they run circularly around Earth
warm and moist air to rise. Consequently, the rising air cools in a similar manner to the climatic patterns. Orobiomes form
off and the saturation vapour pressure sinks, causing water a narrow girdle around the altitudes of mountain ranges, and
vapour to condense and form rain. The tropics are therefore Pedobiomes cover special sites characterised by distinct soils
consistently warm and humid. The rising air flows into high- such as sand, rocks and saline soils.
er altitudes and disperses toward the poles; an atmospheric The English-speaking world often uses the Whittaker
circulation known as the Hadley cell. classification of biomes in which 25 biome types are char-
These air masses sink again in the subtropics. As the air acterised mainly according to mean annual precipitation and
masses warm as they descend, the saturation vapour pressure evaporation. The discrepancy between this system and the
increases (the air can take up more moisture, meaning that German one is mainly based on varying methodologies of
the relative humidity sinks). As a result, the subtropical lati- grouping ecosystems with similar climatic conditions, and
tudes are drier. The descending air masses split, either head- on the difference in emphasis on the seasonality of precipita-
ing back to the Equator or towards the poles. tion and temperature.
In temperate zones, the air tends to rise again (Ferrel cell), Another current biome classification system was designed
again causing higher levels of precipitation. At the perma- by the World Wide Fund for Nature (WWF) and features
nently cold poles, the air current finally sinks again (Polar 14 major habitat types (biomes). This system is based on the
cell). result of various international case studies and conservation
Various authors present differing classification schemes assessments.
for biomes. In the German-speaking world, the Breckle and
evaporation: vaporisation of moisture from unvegetated land between the solar climate zones are the tropics and the polar
or the surface of a body of water circles
solar climatic zones: classification of climate zones based ex-
clusively on the intensity of solar radiation; the lines of division
See also: Global precipitation and temperature distribution: 3.2.2.1

Atmospheric circulation patterns are driven by the differing intensities These climate diagrams display:
Danmarkshavn
of sunlight at the equator and around the poles. Warm air rises at the Temperature (red): –30 °C to +30 °C
equator; colder air descends around the poles. This circulation results in Precipitation (blue): 0–300 mm/month
three circulation streams: the Hadley, Ferrel, and Polar cells (Diagrams not according to Walter and
Lieth)
Polar cell Essen
Ferell cell
Kufra
Malakal
Hadley cell
Makokou
Livingstone
Alexander Bay
Invercargill
Novolazarevskaja
tropical and subtropical moist deciduous forest tropical and subtropical grasslands and bushland desert and arid bushland
tropical and subtropical arid deciduous forest temperate grassland mangrove
tropical and subtropical coniferous forest montane grass- and bushland rock and ice sheets
temperate deciduous and mixed forest flooded grassland JFMAMJJASOND
temperate coniferous forest tundra
month
boreal forest / taiga Mediterranean forest and bushland
3.2.2.3
Tundra
The tundra biome begins just north of the 10 ºC July iso- into the ground. However, rates of evaporation are also low,
therm and extends to the polar deserts. Tundras are mainly as a result of the low temperatures and because permafrost
found in the northern hemisphere, comprising about 7.6 % prevents the seepage of water into the soil. Tundra habitats
of the earth’s total land area. are therefore very moist despite the low levels of precipita-
The climate within the tundra is polar, with very short tion.
summers and low temperatures throughout the year (under The growth period for plants is relatively short (6–16
10 ºC on average for each month of the year); even in the weeks). However, in the summer months this may include 24
summer the average temperature is around 0 °C. During the hours of sunlight per day, giving plants a long assimilation
coldest months, the average temperature may drop to be- time despite the short growing season. Subarctic and arctic
tween –15 ºC and –40 ºC. Only in areas strongly influenced tundras feature treeless vegetation, dominated by mosses, li-
by the ocean may winter temperatures hover around freez- chens, grasses and microbial mats, along with isolated herbs
ing. and dwarf plants. Due to the short growing season, most
Precipitation in the tundra is low, usually only 50–100 mm tundra plant species have the capacity to reproduce vegeta-
per year, although in some areas of the Arctic it can reach tively. Plant biodiversity is relatively low, with only about
700 mm per year. Most precipitation falls as snow; as a result, 1,000 angiosperm species known mostly from drier sites,
tundra habitats are usually snow covered for more than eight such as on hillsides. Most tundra species belong to the Eri-
months per year. Snow cover is usually thin due to the low caceae, Cyperaceae, and Salicaceae families.
amount of precipitation; consequently, frost penetrates deep
As in the taiga, soils in the tundra are waterlogged and hill soil slippage (solifluction) is common even at gentle hill
are also characterised by low rates of organic decomposi- slopes due to water saturation.
tion. They are humus-rich permafrost (Gelisols), experienc- On the basis of the vegetation type, one can differentiate
ing strong mixing by repeated freezing and thawing of upper the upper polar lichen and moss tundra from the lower po-
soil layers (cryoturbation). Microbial degradation plays a mi- lar dwarf shrub and meadow tundra. In addition to conifers,
nor role due to the low temperatures. The soils are only of woody plants found in the tundra are various deciduous trees
slight thickness, and are acidic and boggy. Soils in the area of such as birch and willows; the latter, however, are mostly
tundra bogs are rich in organic material (Histosols). Down- dwarf shrubs and rarely proper trees. The impact of frost in
the winter is slightly lessened due to snow coverage.
assimilation: conversion of matter from the environment into isotherm: (Grk.: isos = same, therme = heat) line on a map
the body’s own materials indicating the same temperature
euthermic: maintaining an optimal temperature torpor: decreased physiological activity with reduced metabolic
rate
See also: Lichen: 3.1.7; Bryophytes: 4.4.3.2

[°C] Danmarkshavn, Greenland [mm]
10 20
0 0
Tropic
Equator –10
Tropic
–20
The tundra extends from the polar ice deserts to the boreal forest and is primarily limited to the northern hemisphere. Its climate is characterised by
severe frosts, with a short growing season and low precipitation
cryoturbation
Soils in the tundra are usually thin and nutrient poor. Soils on permafrost often thaw in the summer, leaving a wet and boggy habitat. Microbial activ-
ity, which is important for pedogenesis (soil formation), is low. Repeated thawing and freezing of the Gelisol leads to cryoturbation (left). The vegeta-
tion of tundra is dominated by mosses, lichens, grasses, microbial mats and a few dwarf shrubs. Tall trees are completely absent. Animals avoid the
seasonal food shortage either through migratory behavior, as is the case for large herbivores such as reindeer, by storing fat reserves (e.g. musk oxen,
right), or through periods of hibernation in or on the ground (e.g. many small mammals)
Survival during winter months can be achieved by reducing activity and energy consumption levels. This hibernation strategy is common in a variety of
organisms. It is not even restricted to cold biomes; similar strategies are also common in other climates for survival in extremely dry and hot conditions
40 °C Energy consumption in the cold season can be decreased by lowering

body temperature. During hibernation, the European ground squirrel
drastically reduces its body temperature in a state of torpor. Its body
temperature (upper curve) approaches that of the surrounding soil
(lower curve). If the soil temperature drops considerably under 0 °C,
muscle contractions raise the squirrel’s core temperature to keep it at
0 °C –2 to –3 °C. Body fluids will not freeze at this temperature. Torpor is
regularly interrupted by short euthermic breaks
–15 °C
In plants, seed dormancy (a period of general inactivity) is a common
strategy during persistent cold seasons. During this time, water con-
tent (blue curve) within the seed is drastically reduced, whereas nutri-
ent content (red curve) increases considerably. The further develop-
ment of the embryo comes to a near halt during this phase. The seed
takes on more water at the end of the dormancy period, so that the
embryo begins to develop again and eventually germinates
Some organisms, including lichens and cyanobacterial mats, survive

complete dehydration or freezing without damage. During such peri-
ods they exhibit no sign of life at all (both pictures: the reindeer lichen
Cladonia rangiferina)
3.2.2.4
Taiga
The boreal forest (taiga) biome is located between the 50º temperatures do not exceed 10 ºC for more than 120 days
latitude and the Arctic Circle in the northern hemisphere per year. At the taiga’s northern boundary, only around 30
and covers around 7.8 % of total land area. days per year have an average temperature of 10 ºC or higher.
The taiga is characterized by long winters with tempera- Annual precipitation in the taiga is 250–500 mm, with the
tures dropping as low as to –70 ºC; temperatures rise above colder temperatures contributing to the low transpiration
an average of 10 ºC only in the three summer months. The rates that keep the water balance positive.
vegetation period in the taiga is short, spanning 80–150 Often just one or two tree species dominate boreal for-
days. The longest periods of growth can be found in areas ests, commonly firs, spruces, larches and pines. Blueberry,
that are close to the ocean, for example in Scandinavia. The cranberry and mosses are common smaller plants of the
shortest growing season, on the other hand, can be found shrub and herb layer. The foliage of conifers is xeromorphic,
in the taiga’s northern continental areas bordering the tun- adapted to cold and desiccation; larches dominate in the par-
dra. The southern border of the boreal coniferous forest is ticularly cold winters of eastern Siberia because they are able
located where conditions are too unfavorable for the growth to drop their needles in winter and are thus better adapted to
of deciduous forest; in other words, roughly when average survive severe frosts.
Soils of the taiga are typically podzols. Conifer needles to further leaching of iron and aluminum compounds and of
are difficult to decompose, causing thick layers of litter to humic substances from the topsoil. These substances perme-
accumulate on the ground. Many nutrients therefore re- ate the subsoil, where they precipitate and accumulate.
main bound in the litter layer and trickle only slowly into In many areas of the boreal forest, the permafrost only
the ground, resulting in a dearth of nutrients in the soil for thaws in the upper 50–100 cm of the soil in summer. As a
plant growth. The lack of replacement of (alkaline) nutrient result, and despite the low rates of precipitation, taiga areas
ions acidifies the topsoil, with the resulting low pH leading are prone to flooding and commonly feature boggy areas.
air embolism: embolism (blockage in a vessel) caused by an air humin: high-molecular weight substances in humus soil types,
bubble in the vascular system including humins (insoluble), fulvic acids (soluble in alkali, acid
and water) and humic acids (soluble in alkali)
xeromorph: plant which has adapted to arid habitats
See also: Ferns: 4.4.3.4; Gymnosperms: 4.4.3.5; Bryophytes: 4.4.3.2

[°C] Novosibirsk, Russian Federation [mm]
30 60
20 40
Tropic
10 20
Equator 0 0
Tropic –10
–20
The taiga is the largest forest biome, extending as a belt of coniferous forests around the northern hemisphere. The climate is mostly continental with
long, cold winters, and short, warm summers. Precipitation is relatively low (200–700 mm)
acidified soil
surface
leached, bleached
soil horizon
precipitation horizon
Taiga soils have a slight thickness and are nutrient poor. Decomposing needles from conifers release organic acids, acidifying the topsoil and by that
increasing further leaching from the underlying soil through organic acids. Taiga flora is dominated by conifers; its fauna dominantly comprises large,
migratory herbivores and hibernating animals
Animals in the taiga are adapted to extreme cold conditions, for example
through a compact body. Within a given animal taxon, the size of body ap-
pendages become smaller from species living in warm biomes to cold bi-
omes (above, from left to right: the ears of the fennec fox, red fox, and arctic
fox). While the big ears of the fennec fox help the animal with thermoregula- xeromorphic needle-leaf
tion in subtropical deserts, the ears of the arctic fox are relatively smaller, an
adaptation developed to prevent heat loss and freezing
Plants have also developed adaptations to the cold and heavy frosts. Dur-
ing the long winters, plants cannot take in water through their roots and
are therefore adapted to survive drought conditions. The leaves (needles) of
xerophytes, for example, reduce evaporation by their sunken stomata and by
wax deposits on the surface. Xerophytes also keep their needles throughout
the winter, a more efficient strategy to avoid growing them anew for each
short summer season. The narrow lumen of tracheids of conifers also render
them less vulnerable to collapse due to an air embolism caused by frost-
induced dryness, as compared to the wide lumen trachea of deciduous trees
coniferous wood
3.2.2.5
Temperate forests
Temperate broadleaf and mixed forests are found primar- The four seasons are pronounced, with precipitation
ily in the northern hemisphere on the east coast of North peaking during the summer. Total annual rainfall in temper-
America and in Asia and Central Europe. In the southern ate forest regions lies between 500–1,000 mm, and droughts
hemisphere, temperate forests can only be found on moun- rarely ever happen.
tain slopes in the Andes and New Zealand. In total, temper- Deciduous trees with greater frost resistance dominate
ate broadleaf and mixed forests occupy 9 % and 2.8 % of the temperate regions. The greatest diversity of species can be
planet’s total land area respectively. found within the temperate forests of North America and
The temperate forest climate is moderate with distinct East Asia, while the forests of Central Europe comprise
seasons and short periods of cold in winter. The average tem- comparatively fewer species. Oak, beech, maple, and birch
perature exceeds 10 ºC for four to eight months, and even in typically dominate the tree diversity in temperate forests,
the coldest months the average temperature is around 0 ºC in though in Asia these are occupied primarily by bamboo. Co-
the oceanic areas but below 0 °C in more continental areas. nifers also make up part of the forest biodiversity, including
However, during longer winter cold spells, temperatures may pine, fir, and spruce.
fall well below the freezing mark.
Temperate forests generally grow on Cambisols (brown transpiration during periods of frost would therefore damage
soils), layered with an upper soil horizon containing accu- the plants by frost drought. Budding on trees is prepared in
mulated humus on top, above a horizon characterized by the autumn and opens in spring. Leaf development and the
iron oxidation and new mineral formation. Brunification ripening of fruit require a growing season of at least four
and loamification are characteristic processes of pedogen- months. Dropping of foliage is not an appropriate strategy
esis. for shortened vegetation seasons; in such conditions adapta-
Deciduous forest dominates in areas where the mean tem- tions of the leaves to tolerating frost are needed. Conifers
perature is over 10 ºC for over 120 days per year, as opposed therefore dominate in areas with short summers and long,
to coniferous forests which require only 10–120 such days. cold winters.
As a result, coniferous forests are more common at higher The relatively low species diversity of forests in Cen-
altitude. tral Europe is a consequence of the repeated displacement
The dropping of foliage is a vital adaptation to the winter of species during the ice advances of the Cenozoic ice age
cold, reducing transpiration and protecting trees from freez- and the comparatively limited recolonisation events due to
ing. Transpiration is a particularly important problem, since the Mediterranean and European mountain ranges, which
frozen soils contain very little water for use by plants. High blocked colonisation to the south.
browning: process of soil formation in which iron compounds hibernation: active/passive strategy for surviving winter in se-
form, thus influencing the colour of the soil lected mammals
clayification: process of soil formation yielding smaller clasts as humus: the totality of dead organic matter in soil
the result of silicate weathering and the new formation of clay nemoral: deciduous
minerals obligatory: necessary, essential
frost dessication: dessication (of plants) due to a lack of wa- soil horizon: a layer of soil with common physical characteris-
ter as the result of frost, and simultaneous loss of water due to tics differing from the horizons above and below it
transpiration
See also: Half-evergreens: 3.2.2.11

[°C] Dresden, Germany [mm]
30 60
Tropic
20 40
Equator
10 20
Tropic
0 0
Temperate forests are usually characterised by an oceanic climate. Temperate deciduous forests (light blue) mainly live on the Asian and North Ameri-
can east coasts as well as in Europe. Western North America (dark blue) is populated mainly by temperate coniferous forests
Luvisols and Cambisols are typical soils of temperate forests. Cambisols (left soil profile) mostly occupy a brownish, weathering horizon between the
humic topsoil and bedrock. Luvisols (right soil profile) have an upper horizon characterised by low clay and a lower clay accumulation horizon. Trees
are favoured due to a lack of pronounced dry seasons. Typical vegetation is deciduous. Big game is active all year round, while many of the smaller
animals avoid winter, as in the taiga, by migration or hibernation
The biome of temperate forests is characterised by warm summers and a veg-

etation period of at least four months. During winter, periods of strong frost
are common. Many animals avoid the cold season by migration to warmer
climates or by hibernation.
The regular frost periods require adaptations of plants such as frost resist-
ance of leaves and wood. Given the long vegetation period (as compared to
the taiga) the formation of annual soft but not frost-resistant leaves is usu-
ally more efficient than the formation of xeromorphic perennial leaves. The
coarse-grained wood of broadleaf trees with trachea allows for an efficient
water transport during spring. Sensitivity to frost drought is low due to the
temporary frost periods
seasonal migration by birds
deciduous tree in summer deciduous tree in winter deciduous tree wood

3.2.2.6
Temperate grasslands
Temperate grasslands and steppes are found predominant- average temperature of the coldest month is below –10 ºC
ly between 40° and 50° latitude. They include the steppes of with long periods of heavy frost. In the summer, the average
Russia and Central Asia, the North American prairies, and temperature for at least four months is above 10 ºC.
the pampas of South America, covering around 9.7 % of the Rainfall in temperate grasslands is lower than evaporation
planet’s land area. With increasing aridity, temperate (cold) rates, with annual precipitation between 100 and 400 mm.
deserts replace the temperate grasslands. Depending on the Because of the low precipitation during the warm season,
definition of the biome in question, the temperate deserts tree growth is hardly possible. Instead, temperate grasslands
are either combined with temperate grasslands or with hot are dominated by steppe and desert vegetation, with adapta-
deserts. tions to resist frost conditions.
Temperate grasslands experience a continental arid cli-
mate, with long, cold winters and short, warm summers. The
Temperate grasslands are dominated by soils rich in ac- conditions. Leaching is hardly present at all in these soils,
cumulated humus, particularly Chernozems (black soils) though rising groundwaters can cause these soils to become
and kastanozems (brown soils). Chernozems, named after more carbonate-rich.
the black colour from the humus-rich topsoil, are character- Grazing is of central importance to grasslands, preventing
istic of the humid tallgrass steppes, whereas Kastanozems, the emergence of hemicryptophytes and a build-up of litter.
named after their maroon colouration, are often found in As a rule, underground biomass is greater than that found
more arid, shortgrass plains. These soils are formed from above ground. Wetter areas are more likely to contain tall
calcareous materials subsequently mixed intensively by grasses, whereas shorter grass grows best in drier regions.
soil-dwelling animals through the process of bioturbation. Herbivores make use of two strategies to deal with
Climatic fluctuations, especially phases of drought or frost, drought conditions. Large herbivorous species, such as buf-
reduce the degradation of organic matter, leading to the ac- falo, may migrate great distances in order to find a seasonal
cumulation of humus and the creation of a humus-rich top- food supply. Smaller herbivores, on the other hand, such as
soil. Kastanozems are formed under similar conditions com- prairie dogs, tend to rest under the earth during unfavourable
pared with the Chernozem soils, though in slightly more arid seasons.
arid: dry plant litter: dead organic material on the top layer of soil
hemicryptophytes: plants with a growth-point (bud) near the shortgrass prairie: prairie dominated by short grasses
soil surface tallgrass prairie: prairie dominated by tall grasses, such as that
humid: relatively high level of water vapour in the atmosphere native to central North America
See also: Savannah: 3.2.2.10

[°C] Taras, Kazakhstan [mm]
20 40
Tropic
10 20
Equator
0 0
Tropic
–10
Temperate grasslands are located in the temperate latitudes, in intracontinental locations or in the lee of mountain ranges. The climate is characterised
by a pronounced dry period, usually in the summer
Deep, humus-rich soils are typical of temperate grasslands. The soils of humid grasslands are particularly deep and rich in humus, visible by their black
colour (Chernozems, left profile). The soils of the drier, shortgrass plains are usually slightly more shallow and not as rich in humus, and therefore more
brown-coloured (Kastanozems, right profile). Grasslands dominate this biome because the shortened growing season, which is usually shortened by a
summer dry period, makes it more difficult for trees to grow. Large herbivores manage to live through periods of drought by migrating
Shortgrass steppes dominate precipitation-poorer regions (left), comprising mainly annual grasses, which rarely grow taller than half a metre. The
grass seeds enable the species to survive dry periods. Tallgrass steppes (middle) are characteristic of wetter regions, where grasses, like the pampas
grass (right), can grow to over two metres in height. These grasses are usually horst grasses and perennial
Several species rest during dry periods: grasses form renewal buds and spurs close to the ground (left and middle) and many animals – especially
smaller ones that cannot avoid drought by migration – spend most of their time underground (right: prairie dog)
3.2.2.7
Montane and flooded grasslands

Montane grass and bushlands are found in tropi- Flooded grasslands are found on several different conti-
cal, subtropical, and temperate climates in the montane nents, mainly in subtropical or tropical climates. Some of the
and alpine altitudes. They are particularly common in most well-known such areas are the Everglades, the Pantanal
the South American puna and paramo, as well as in the and the Niger, as well as the Okavango Delta. Flooded grass-
steppe areas of Tibet. Montane grass and bushlands ac- lands make up only around 0.7 % of the planet’s total land area.
count for around 4 % of the planet’s total land area. Flooded grasslands are usually formed around tropi-
As is common at altitude, climatic conditions in these ar- cal or subtropical rivers in lowland areas of river deltas.
eas are usually cool and moist, with high levels of sunlight. They form a network of flooded grasslands, often just a
Montane grassland plants exhibit typical adaptations, in- few centimetres deep but with a width of up to several
cluding rosette growth forms, hair, and wax deposits on the hundred kilometres, of deeper water basins and islands.
surface. Species are often endemic, especially in grass and Temperatures are often tropical to subtropical, and the
bushlands in isolated small mountain areas, such as at Kili- precipitation has very little impact on the formation of
manjaro or Mount Kenya. Horst grasses are also typical. The vegetation, since the floodplains are fed by larger rivers.
grass and bushlands of humid (tropical) regions are often re- Grasses grow in the low water level areas of flooded grass-
ferred to as paramo, whereas the drier (subtropical) regions lands, though trees are known to grow at higher ground levels.
are known as puna. These terms are derived from the re- The fauna is dominated by amphibious animals and birds.
gional designations of the grass and bushlands of the Andes.
Montane and flooded grasslands are special locations, slope. In addition, soils usually succumb to high erosion
where climatic conditions differ greatly from zonal ones. rates and do not store much water.
Temperatures decrease with altitude by around 0.6 ºC Soils in flooded grasslands, on the other hand, are largely
per 100 m, though at the same time solar radiation increases cut off from atmospheric oxygen supplies and are therefore
with height and the colour spectrum of the available sunlight anaerobic. Above-ground organs supply the rest of the plant,
shifts towards a higher ultraviolet (UV) component. including the roots, with oxygen.
Despite higher rates of rainfall, montane sites are often Since flooded grasslands predominantly occur in low
relatively dry since precipitation flows quickly through the altitudes, their climatic conditions correspond to the zonal
climate conditions.
endemic: occurrence of organisms within a defined restricted tussock grasses: grasses which grow close together in tufts or
geographical area clumps
See also: UV protection: 4.2.1.7

[°C] Qamdo, Tibet [mm]
40 80
30 60
Tropic
20 40
Equator
10 20
Tropic
0 0
Montane grasslands occur as a result of mountain ranges and not because of particular zonal climates. Flooded grasslands, too, are formed as a result
of geomorphological factors rather than climate
Montane locations are unique, with tempera-

tures decreasing as altitude increases whereas
irradiation corresponds to the zonal conditions,
i.e. the latitude. However, the relative contri-
bution of UV increases with height. As a result
of high levels of rainfall, erosion is strong and
consequently soil formation is generally weak.
Vegetation is dominated by herbaceous plants
(left: Gentiana) and cushion plants. Animals mi-
grate seasonally (above: ibex) or hibernate
Flooded grasslands are found in lowlands and

often at the mouth of larger rivers, character-
ised by large areas of shallow water with just
a few centimetres water level. Water in these
streams flows extremely slowly.
Left: the Nile Delta; Top centre and top right:
Everglades; Bottom centre: papyrus forest
3.2.2.8
Mediterranean biome
The Mediterranean biome is found mainly between 30° in winter to over 40 ºC in the summer, and rainfall intensities
and 40° latitude on the western edge of continents, cover- also vary greatly. Monthly mean precipitation levels may be
ing around 3 % of Earth’s total land area. Most of it can be reached within a single or few heavy precipitation events.
found on the coasts of California and Chile, as well as the Mediterranean vegetation ranges from forest areas to
south-western tips of Africa and Australia. steppes. It must withstand long periods of drought and short
The Mediterranean climate regions lie between the sub- frosts. As a result, many Mediterranean plant species have
tropical desert areas and temperate regions, and are charac- thick, hard leaves (sclerophytes) with a thickened epidermis
terised by winter rainfall and summer drought. In contrast and a pronounced cuticle layer. Areas of winter rain com-
with tropical regions, the Mediterranean biome experiences prise, along with the humid tropics, some of the most bio-
rare instances of frost. Annual precipitation is around 500– diverse regions on Earth. To that end, the Mediterranean
1,000 mm, with for the most part around five humid months vegetation of southern Africa (‘fynbos’) is its own floral king-
per year. The Mediterranean vegetation period lasts for five to dom, known as the capensis.
nine months. Temperatures are highly variable, from freezing
During summer periods, Mediterranean biome regions aridity; the typical shrub- and tree-shaped xerophyte vegeta-
experience subtropical anticyclones, with correspondingly tion is strongly influenced by humans in many areas.
low rainfall. In winter, in contrast, they experience low pres- Laurel forests dominate warm-temperate, perhumid ar-
sure levels and high rates of precipitation. Litter composition eas. In some classification schemes they are classified as a
rates are relatively high as a result of the mostly high tem- separate biome, in other schemes as a part of the subtropical
peratures during the winter rainy season. Loamification is evergreen forest (WWF classification) or of the Mediterrane-
common, limestone and salts are often accumulated in soils. an biome. The temperature fluctuations in the laurel forests
The most commonly found Mediterranean soils are calcium- are lower than in the Mediterranean biome. Conditions are
rich, such as the Calcisols, cobbly soils of slight thickness humid and mostly frost-free throughout the year; long peri-
(Leptosols) as well as soils with lessivation characterised by ods of drought are uncommon. Laurel forests are evergreen
horizons of low and high clay, respectively (Luvisols). and therefore contrast greatly with deciduous forests. They
Fire plays a major role in the Mediterranean biome and its also differ from tropical rainforests since they tend to have
incidence has risen sharply in recent decades due to anthro- less complex layers of vegetation and generally less dense
pogenic influences. vegetation. They can be found on the east coasts of conti-
Highlands are dominated by forests, which, with increas- nents around 25° to 35° latitude, in particular in California,
ing altitude, shift from evergreen forest at low altitude to southern China, south-eastern Brazil, as well as in the south-
deciduous forests, eventually being replaced by coniferous east of Africa and Australia.
forests at high altitude. Xerophyte abundance increases with
Calcisol: soil that possess a strong secondary calcic horizon perhumid: extremely wet climate, including ten to twelve hu-
heavy rain: intensive precipitation over a certain time span; mid months
over 10 mm precipitation per hour plant litter decomposition: breaking down and mineralisa-
hematite: Fe2O3, a common iron oxide tion of organic substances by decomposers
humid: relatively high level of water vapour in the atmosphere sclerophytes: evergreen arboraceous plants in the tropics and
subtropics which have adapted to periods of drought
See also: Capensis: 3.2.2

[°C] Cordoba, Spain [mm]
40 80
30 60
Tropic
20 40
Equator
10 20
Tropic
0 0
Mediterranean forests and bushlands are found on the western edge of continents between 30° and 40° latitude. They are characterized by a longer,
marked dry season in the summer. In winter, temperatures are generally above freezing with occasional periods of frost
clay-depleted horizon
clay accumulation
horizon
Übersicht
clay horizon extending
into conglomerate
rock
In the wet winter months, the upper horizon of Mediterranean soils decalcifies as a result of carbonate solution. As a result, clay is relatively enriched
(residual clay) in the upper horizon of these soils (Cambisols). During moist periods of winter precipitation, clay minerals eluviate from the upper soil
horizon to deeper layers. These soils are called Luvisols (referring to the displacement of clay). They are often deep red as a result of the weathering of
silicates and recrystallisation of the released iron oxides. Local flora and fauna show adaptations to the dry, hot summer conditions
Succulence is a common adaptation of crops to the summer dry season (left: Aeo-
nium sp.). Cold-blooded animals are typical in the frost-free climates (right: green
lizards)
The bushland of the South African Cape region is known as the Laurel forests are the typical vegetation of the warm temperate perhumid area.
fynbos (‘thin bush’). The Cape area is one of the most species- They are considered as independent vegetation zones in some classification
rich floral regions in the world schemes
3.2.2.9
Hot and temperate deserts

Hot and temperate deserts occupy around 13 % and 10 % The flora and fauna of deserts is sparse. The few plants
of the planet’s surface area respectively. Depending on the and animals that can live in desert conditions are specially
exact definition, they are grouped as single or separate bi- adapted to the long-lasting arid conditions. For example,
omes, characterized by their low rates of precipitation. plants are adapted to store water (succulence), reduce evapo-
Hot deserts extend approximately between 20° and 25° ration (wax deposits, thick cuticle, C4-photosynthesis, reduc-
latitude to the north and the equator to the south. Their aver- tion of leaves), and develop annual strategies. Animals also
age temperature is over 10 ºC for eight months per year. The have a set of specific adaptations to desert conditions; for
largest hot deserts on Earth are the Sahara in North Africa, example, by reducing the amount of water they excrete (for
the Namib in South Africa, and the Great Indian Desert in example, desert mice have an extended loop of Henle in the
Pakistan. kidneys) or through behavioural strategies that minimise
In temperate deserts the average temperature is above their activity during the hottest times and seasons.
10 ºC for four to eight months, with little or no rain through- Many desert plants and animals, especially those inhab-
out the year. Temperate deserts often lie in the lee of large iting coastal areas, which regularly experience periods of
mountains or at the interior of large continents; for example, morning fog, have developed ways of extracting moisture
the Gobi Desert in Asia or the Great Basin Desert in the US. from the air.
Deserts result from conditions of low moisture and rain- ter loss. As water will become more available to some plants
fall. A warming of the climate, as is currently taking place, inhabiting regions that border desert areas, they will in future
will, however, not lead to desertification, but rather to the be able to expand further into desert habitats.
creation of more grasslands: global warming leads to in- Chemical weathering processes are stronger than micro-
creased evaporation rates and therefore to increases in pre- bial degradation, which is heavily restricted by the arid con-
cipitation. In desert areas, precipitation rates are higher than ditions in deserts. Desert soil, furthermore, is poorly differ-
evaporation. entiated and in early developmental phases. Nutrient-poor
Climate change, which includes increases in atmospher- regosols are widespread in the desert aridity, highly suscep-
ic carbon dioxide concentrations, will allow plants to open tible to erosion. Saline soils (Calcicol, Solonchak, Gypsisol)
their stomata for a shorter period of time to carry out photo- and soils with secondary silicate enrichment (Durisols) are
synthetic functions, thus enabling them to greatly reduce wa- also widespread.
chemical weathering: processes leading to the chemical al- stomata: pore in a plant which serves to regulate gas exchange
teration or dissolution of minerals with the environment; the resultant transpiration cools the tissue
undifferentiated soils: soils are not or only weakly differenti-
ated into horizons
See also: C4-photosynthsis: 2.3.5.3, 2.3.5.4; Carbon dioxide and climate: 2.2.2.1, 2.3.5.3
Kufra, Libya
30 60
Tropic 20 40
Equator
10 20
Tropic
0 0
Deserts extend along the subtropical climate zone and in the rain shadow of large mountain ranges. The desert climate is characterised by arid condi-
tions throughout the year. Subtropical (hot) and temperate (cool) deserts are considered to be independent biomes in other schemes
Desert soil formation is driven by drought conditions. Salt accumulations are common in topsoil, including enrichment of carbonates (left soil profile:
Calcisol), gypsum (Gypsisol) or mixtures of chloride, sulfate, carbonate and nitrate (Solonchak). Silicate-rich soils are known as Durisols (right soil
profile). The dry conditions do not allow most vegetation to occur. The lack of vegetation, erosion, and wind displacement of particles causes the
formation of dunes. Most animals are adapted to nighttime activity, in order to avoid the hottest periods of the day
Adaptations to the dry and often hot desert climate relate primarily to the regulation of water supply. This includes the formation of deep roots (mid-
dle: Welwitschia) and succulence, which helps improve storage rates of water within plant tissues and which is often associated with adaptations to
reduce evaporation (left: living stones). In animals, examples are behavioural and physiological strategies, such as highly concentrated urine in order
to minimize the excretion of water (right: gerbil)
Succulent growth forms, an adaptation to the desert climate, have evolved in various plant families. Left: the euphorbia Euphorbia canariensis and
Euphorbia horrida; right: the cactii Pachycereus weberi and Echinocactus grusonii
3.2.2.10
Subtropical and tropical grasslands

Tropical and subtropical grasslands occupy around 14.3 % pecially in areas of xeric shrubland, the opposite is true. The
of Earth’s terrestrial landscape, lying mainly between 5° and dry season lasts between three months near tropical areas
20° (north and south) latitude. Their precise boundaries are and 10 months in regions bordering desert.
difficult to determine, as transition into drier forest areas is Tropical and subtropical grasslands include a range of
smooth. habitat transitions, from acacia-dominated areas, drylands,
Tropical and subtropical grasslands experience semi-hu- treelined savanna, as well as xeric shrublands. However, of
mid to semi-arid conditions during the summer rainy sea- these, the most common are probably the treelined savannas,
son and a cooler winter dry season. Average temperatures comprising grasslands and scattered trees. The herbivores
are over 10 ºC for at least eight months per year. Summers present in such habitats are usually large, migratory herd
are hot and humid. Precipitation rates are between 600 and animals, including antelopes, giraffes, and elephants. The
1,500 mm, though as low as 200 mm in border desert areas. proportion of small rodents, which generally inhabit the soil,
During the dry season, evaporation rates are, in general, is lower compared with in temperate grasslands.
higher than precipitation, though for the most part, and es-
The savannas border areas and the drier forest habitats adapted to heavy drought conditions, including succulents,
experience a summer rainy season and winter drought. In geophytes, and ephemerals. Fungi are far less common than
winter, savanna areas fall under the influence of subtropical in the humid tropics. Termites play an important role within
high pressure areas, leading to a pronounced drought. In the such arid ecosystems, building effectively using plant bio-
summer, however, the same regions are influenced by the in- mass; as a result, savannas are characterised by a high meta-
tertropical convergence zones, leading to heavy and regular bolic rate, despite their aridity.
rainfall. Savanna soils are characterised by high clay content (verti-
Humid savanna experiences a relatively high 1,000– sols) and have high proportions of iron minerals and a strong
1,500 mm of rainfall, with a drying time of only three to five reddish or yellow-brown pigment. The clay minerals in the
months. As a result, the vegetation is comprised mainly of soil regularly contract and expand as a result of the fluctua-
tall grasses, for example elephant grass, which grows to a tion between dry and wet periods: during the dry season,
height of 6 m, as well as sparsely distributed trees (and open cracks and crevices up to half a metre deep may be visible.
to partly closed forests). These are subsequently filled again when the next rain causes
In drier savanna areas precipitation is between 500– the soil to swell. This pedoturbation prevents the creation of
1,000 mm, with a drying time of five to seven months. The an even vertical soil profile. Apart from vertisols, the savanna
vegetation is characterised by medium-height grasses and contains soils that display relatively strong clay leaching: as
many plants display adaptations to the drought conditions. a result of the degradation of organic matter by termites and
In xeric shrublands precipitation can be as low as 250– the sparse vegetation cover, coupled with the availability of
500 mm, with drought periods of up to 10 months per year. cations, clay particles are suspended and stored in deeper
Grasses remain short (under 30 cm) and cover only partial soil layers at the onset of the rainy season. The resulting soil
areas. The climate is usually too dry for trees; thorny bushes profile features an upper horizon poor in clay above a lower
dominate the landscape and are mixed with other plants clay-rich horizon characterized by Acrisols or Luvisols.
Acrisol: extensively eroded, red-coloured acid soil with accu- Luvisols: soil with eluvial horizons which are not as leached or
mulated subsurface layers of clay, this soil group is produced by acidic as acrisol
extensive leaching pedoturbation: soil perturbation not caused by illuviation (the
ephemeral: (Grk.: ephemeros = for one day) having a short life re-distribution of water)
span semi arid: mostly arid climate; evaporation is greater than pre-
geophyte: plant with concealed storage organs cipitation over six to nine months
Intertropical Convergence Zone (ITCZ): low-pressure trough semi humid: mostly humid climate; precipitation is greater than
near the equator where the northeast and southeast trade winds evaporation over six to nine months
converge
See also: C4-photosynthsis: 2.3.5.3, 2.3.5.4; Quaternary climate change: 2.3.5.3; Temperate grasslands: 3.2.2.6; Hominisation: 2.3.5.7
[°C] Malakal, South Sudan [mm]
50 100
40 80
Tropic
30 60
Equator 20 40
Tropic 10 20
0 0
Tropical grasslands are widespread on both sides of the equator between 5° and 20° latitude. Their transition to bordering dry forests is fluid. Seasonal
variations are low, with a climate characterised by fluctuations between a summer rainy season and a dry season in winter
The periodic wetting of the soil in high temperature causes a strong chemical weathering. The soil which is relatively humus-poor as a result of termite
activity. In dry savanna and treelined savanna areas, heavily weathered, humus- and clay-poor surface layers sit atop clay-rich layers (left soil profile:
Lixisols). During the dry season, cracks form within the clay-rich soils found on plateaus and at the foot of slopes (right soil profile: Vertisols). Macro-
fauna is dominated by large herbivores that migrate as a result of seasonal rainfall and the need to find food
Grasslands are regularly exposed to wildfires. The fires encroach on

bushlands and threaten trees, engulfing large amounts of biomass each
year. Microbial degradation is relatively low in grasslands, since biomass
is mainly obtained at the beginning of the dry season and microbial deg-
radation is less efficient in arid habitats. Termites are responsible for
much of the degradation of plant biomass in tropical grasslands (top-left:
termite mounds; bottom-left: termites). Termites are also able to build
from the resulting biomass during the dry season. Cellulose is broken
down by anaerobic bacteria and protists (for example, Metamonadida)
living within the termite gut. Methane is also produced by the anaerobic
activity within the termite gut; as a result, termites account for a signifi-
cant proportion of methane-based greenhouse gases. Whereas termite
activity on the one hand lowers the humus content of the soil, it contrib-
utes to bioturbation, or mixing of soil layers
3.2.2.11
Subtropical and tropical arid (xerophytic) forests

The arid forests found on the northern and southern bor- Some areas, which experience a shorter dry season of three
ders of rainforests are found between 5° and 15° latitude. to five months, are characterised by the growth of decidu-
The transition of older, drier forest areas to savannas is fluid ous forest. Rainfall decreases and the length of dry seasons
and may in itself be defined differently depending on vary- increases with distance to savanna areas.
ing biome definitions. Particularly in Africa, anthropogenic During the dry season, trees lose their leaves in order to
activities are increasingly turning dry forests into savanna. reduce evaporation rates. Their roots are also relatively deep,
Tropical and subtropical arid broadleaf forests make up relying on groundwater during the dry season. As a result of
around 2.1 % of Earth’s land area, whereas the subtropical the loss of leaves, sunlight reaches the ground in the dry sea-
and tropical coniferous forests occupy 1.1 %. son, allowing for a relatively dense undergrowth compared
Their climate is subtropical or tropical, with average tem- with evergreen rainforests.
peratures reaching above 10 ºC for at least eight months per The total species diversity is lower than in evergreen rain-
year. Annual precipitation is between 1,000 and 2,000 mm, forests, however, though still relatively high.
with a pronounced dry season of several months in winter.
The shift between dry and rainy seasons is related to sun- Soil fluctuates from permanently humid in summer to
light patterns: during the northern summer, the sun rises per- arid in winter. It is dominated by highly weathered Acrisols,
pendicularly along the Tropic of Cancer and not the equator. Alisols, and Ferralsols; in other words, highly iron- and al-
As a result, ascending, evaporating air masses at the Inter- uminium-rich soils. Since leaves fall at the beginning of the
tropical Convergence Zone migrate towards the north and dry season, their accumulated organic matter is barely bro-
rainfall is therefore very high there in the summer. In the ken down by microbes. Instead, the nutrient cycle at the soil
northern winter, the sun rises fully along the Tropic of Cap- litter level is driven by remineralisation by fire and dispersal
ricorn, thus causing lower precipitation patterns in the north by termites.
and higher rainfall south of the equator.
Acrisol: extensively eroded, red-coloured acid soil with accu- Intertropical Convergence Zone (ITCZ): low-pressure trough
mulated subsurface layers of clay, this soil group is produced by near the equator where the northeast and southeast trade winds
extensive leaching converge
Alisol: acidic soil caused by leaching with accumulated subsur- undergrowth: vegetation in a forest growing underneath the
face layers of clay, less eroded than Acrisols canopy
See also: Temperate forests: 3.2.2.5

Allahabad, India
70 300
60 200
50 100
Tropic
40 80
Equator 30 60
20 40
Tropic
10 20
0 0
Arid forests form at the transition between tropical grasslands and rainforests. Due to human activities, such as deforestation and planned fires, dry
forests are increasingly rare. Their climate is similar to that found in savannas, but slightly more humid
eluvial horizon (clay

leaching horizon)
clay enriched
horizon
The predominantly humid conditions cause clay to leach from upper layers of the soil and to accumulate deeper down. Typical soils include Acrisols,
poor in humus and acidity. Arid forest tree species drop their leaves seasonally as a result of water availability and not, as is the case in temperate
deciduous forests, because of temperature variations
A number of species are adapted to the transition between savanna and Human activity, such as artificial fire and deforestation for the production
rainforest: top: half-evergreens in Australia; bottom: monsoon forest in of firewood, causes half-evergeen forest to turn into savanna (bottom-left)
India and semi-arid (bottom-right) regions
3.2.2.12
Tropical rainforest
Tropical rainforests comprise about 15.3 % of the planet’s 3000 mm. Although precipitation intensity fluctuates season-
land area and stretch around the equator and 5–10° latitude ally, there is no pronounced dry season, with shorter dry pe-
in each direction. The major areas of rainforest occur along riods lasting a few days to a few weeks. Evaporation rates are
the Amazon Basin in South America, the Congo Basin in low, due to the high humidity, and as a result plants do not
Africa, and the Malay Archipelago and Pacific Islands. experience water stress.
The rainforest climate is formed by westerly wind zones Tropical rainforest vegetation is dominated by tall trees
in continental equatorial regions. As the clouds rain down which, as a result of the lack of seasons, have no annual
on the westerly side of continents, precipitation rates lower rings. In surface-weathered soils the trees are often shallow-
in eastern areas. As a result, rainforests are rare near the east rooted, stabilized by the formation of buttress roots. Moving
coast of South America and Africa. up from the surface, three layers of rainforest trees are com-
Tropical rainforests do not experience frost at any time of monly formed: a 20–30 m lower tree layer, a 30–40 m main
the year. Average monthly temperatures near the ocean are crown layer, and the 50–70 m high giant trees. A roughly 15 m
above 18 ºC and within lowland rainforests range between shrub layer grows among these layers. There is no herb layer
24 and 30 ºC. In general, seasonal temperature variations are in tropical rainforests, as no light (<1 % of total) penetrates
low: the annual amplitude, the difference in average temper- to the forest floor. Mangroves dominate tropical rainforests
atures between the coldest and warmest months, is often a at coastal areas, where high salinity levels and water level
maximum of 5 ºC. fluctuations make it more difficult for normal trees to grow.
Precipitation rates are high in tropical rainforests, ranging
between 1,000 and 15,000 mm with an average of roughly
The humid daytime air of tropical rainforests results from The high humidity combined with high temperatures
the year-round nearly vertical sun. The climate is largely di- favours microbial conversion processes in the soil. Leaf lit-
urnal, meaning that the temperature fluctuations between ter and other biomass are therefore degraded quickly and,
day and night are higher than seasonal variations at the same as a result, the humus and litter layer of the soil tend to be
location. relatively shallow. The soil is acidified to pH values of 4–4.5
Evaporation is high as a result of the strong sunlight. The as a result of chemical weathering and leaching. Iron and
rising warm air cools with increasing height, forming clouds aluminium oxides are created. The main minerals found in
and subsequently rain. Especially in areas that are further tropical rainforests are goethite in the topsoil and hematite
away from the equator, the intensity of precipitation changes in subsoils. Silica-depleted kaolinite forms by argillacious
seasonally as the sun’s position shifts. alteration of silicates, further desilication results in the for-
The diversity of trees in tropical rainforests is very high, mation of aluminium oxides – this process of desilication
with over 300 different species able to grow in a single acre. is known as loamification. The combined enrichment of
However, many of these species are commonly represented iron and aluminium (ferralitisation) and depletion of sili-
by just one individual. Important plant families include cium (desilication) is known as lateritisation. The soils in
the Arecaceae (palms), Moraceae (including the figs), and tropical rainforests are therefore usually Ferralsols (German
Piperaceae (pepper family). In the neotropics Bromeliaceae classification=laterites; US classification=oxisols).
(bromeliads) also dominate, as the Pandanaceae do in the
paleotropics.
buttress root: large, rib-like roots arranged in a star formation mangrove: ecosystem in tropical mangroves; saline-tolerant
around a tree to increase stability trees and shrubs in a mangrove
desilification: part of the process of silicate leaching which pro- perhumid: extremely wet climate, including ten to twelve hu-
duces orthosilicic acid mid months
leaf litter: mostly undecayed dead plant material on the ground
See also: Global wind systems: 3.2.2.2

Manaus, Brazil
70 300
60 200
50 100
Tropic
40 80
Equator 30 60
20 40
Tropic
10 20
0 0
Tropical rainforests are found on either side of the equator on the side of continents with the highest precipitation rate. The climate is warm and humid
throughout the year. Daily fluctuations in temperature are greater than those between seasons (diurnal climate)
the process of
ferralisation leads to
a reddish to yellowish
‘ferralic’ horizon
The permanently humid warmer climate favours deep chemical weathering of the soil, often down to 50 m in depth. The weathering of silicates leads
to the accumulation of iron oxides. Typical soils are mostly red or yellow Ferralsols (left). The forest is organised in layers, comprising giant trees, the
main canopy, a lower tree layer, and a shrub layer. Little light penetrates all the way to the ground; as a result, grass is unable to grow. Animal life is
adapted to the trees
In contrast to the sparse layer of grass, epiphytes are common across tropical rainforests. Despite the humid climate, epiphytes tend to grow in dry and
nutrient-poor conditions; they therefore have a number of adaptations to help them survive (left: carnivorous pitcher plant; middle-left: water collec-
tion in bromeliad rosettes; middle-right: leafcutter ant. The virtual absence of climatic selection factors reinforce the importance of biotic interactions.
Many plants therefore have developed high toxicity defences (right: poison dart frog)
Due to the strong competition for light, trees grow tall. Buttress roots (left) are crucial for rainforest trees to maintain stability. Other species, such as
epiphytes, use other trees as a climbing aid. Salt-tolerant mangroves grow in coastal rainforest areas
3.2.2.13
Lakes
The basic distinction between two different types of gradient. In wetlands, swamps and bogs blur the boundary
aquatic biomes is whether they are marine or freshwater. between terrestrial and aquatic habitats.
Only 2.6 % of Earth’s water is fresh water, the bulk of it Trophy is commonly used to assess ecological water qual-
bound within ice and snow in the polar ice caps and glaciers. ity in standing water, whereas flowing water waterbodies are
Only 0.3 % of the Earth’s water runs within lakes and rivers. often defined by their level of saproby. Trophy refers to the
Fresh water is characterised by the very low salinity of intensity of photoautotrophic primary production. Since it is
the water, running between groundwater or underground only possible to measure primary production indirectly in the
(closed) waters and the open waters at the surface. Surface field, trophy is commonly measured by the concentration of
waters are further distinguished into standing waterbodies nutrients (usually of phosphates, since phosphate is the limit-
and watercourses. The physical and chemical conditions of ing nutrient in many freshwater bodies) or of chlorophyll (as
inland waters can be very different depending on regional an indirect measure of algal biomass and therefore of pho-
conditions. They can vary in acidity from pH 2–12 and in toautotrophic organisms). In contrast, saproby denotes the
salinity from salt-poor to brackish to the hypersaline lakes intensity of the oxygen-consuming process. It is possible to
of the Dead Sea. Fresh waters can also vary in their trophic estimate the biological or chemical demand for oxygen. Thus
character, from ultra-oligotrophic to hypertrophic. In estuar- systems exist for measuring organismal communities by both
ies, fresh water is mixed with marine water along a salinity their trophic and saprobic characteristics.
Most lakes undergo at least a sporadic mixing of water the surface temperature rises to 4 ºC in the summer months
layers. This circulation is normally driven by the wind. How- and allows for circulation, or in warm temperate to subtropi-
ever, full circulation is prevented by the stable stratification cal areas, where the surface water cools down to 4 ºC during
of water layers according to their density. These density dif- the winter months.
ferences stem from variations in temperature or salinity be- Dimictic lakes circulate twice per year, usually in spring
tween layers. Since water at 4 ºC has the highest density, deep and autumn, and experience warmer surface temperatures in
water layers usually have temperatures around 4 °C, at least summer and colder temperatures in winter.
in temperate zone lakes. Circulation starts taking place when Oligomictic, characterised by a few irregular circulations,
surface waters reach this temperature and, thus, the same and polymictic conditions, with many irregular circulations,
density as deeper waters. are found mainly in large, shallow, and wind-exposed lakes.
No circulation takes place in amictic lakes, for example in In these lakes, high wind conditions may interrupt what is
Antarctic lakes covered by permanent ice sheets, or in stably otherwise a more stable stratification.
stratified, salt-rich deep-water lakes. In meromictic lakes, only the upper layers of the water-
Monomictic lakes are characterised by seasonal circula- body circulate, whereas lower levels, which are dense and
tion periods and can be found either in subpolar areas, where mostly anoxic, remain at the bottom.
decomposers: organisms that live on dead or decaying organ- phytoplakton: (Grk.: phyton = plant, planktos = drifting) pho-
isms and which are involved in the process of decomposition totrophic organisms which float in water (plankton)
See also: Photo pigments and vertical ecological niches: 4.4.2

Lake Superior
(386,400 km2)
Big Bear Lake
Great Slave Lake
(31,153 km²)
Lake Baikal (27,048 km²) Aral Sea Lake Victoria
(31,722 km²) (68,000 km²) (58,016 km²)
Lakes are still waters that are completely surrounded by land. Most lakes con-
tain fresh water, though some, such as the Caspian or the Dead Sea, are saline.
This figure shows the ten largest lakes in the world. The largest is the Caspian
Lake Huron Sea. Lake Baikal is the oldest, dating back roughly 25 million years. It is also the
(59,586 km²) deepest, measuring down to 1,642 m. As a result of water extraction and arti-
Lake Michigan
(58,016 km²) ficial irrigation, the Aral Sea has shrunk from 68,000 km² in 1960 to 13,900 km²
in 2010. Lake systems are divided into pelagic (open water zone) and benthic
Caspian Sea Lake Tanganyika (bottom zone) layers. The latter is subdivided by their distance to the shore
(386,400 km2) (32,893 km²) (littoral vs profundal)
litoral (riparian) zone pelagial (free water)
reed zone
epilimnion,
floating plant
(trophogenic zone)
zone
underwater
plant zone be
nt
hi metalimnion
Limnetic open water areas are stratified either by temperature, as the c (bo
epilimnion (surface water), metalimnion (thermocline), or hypolimnion tto (compensation zone)
m)
(deep waters) or according to biological functionality: the photic, or zo
ne
trophogenic zone, where photosynthesis dominates and the tropholytic
zone where respiration dominates. In stratified lakes, stratification zones hypolimnion,
and functional layers more or less correspond to each other. The benthic (tropolytic zone)
zone of a water body, which includes the bottom sediment, is subdivided
according to its distance from the shoreline into the litoral or riparian
(close to the shore) and the profundal (far from the shore) or depth zones profundal (deep) zone
Still waters comprise puddles (short-term), basins (regularly desiccating water), and lakes (large permanent waters). In terms of ecological structure,
lakes can be distinguished between littoral (left: near the shore), pelagic (centre: open water), and benthic (right: near the bottom). In addition, a
distinction is made between the light-filled trophogenic zone, where photosynthesis and thus primary production takes place, and the low-light tro-
pholytic zone, where oxygen-consuming processes take place. The boundary between the trophogenic and tropholytic zones is known as the compen-
sation depth. Trophy is often used to ecologically classify lakes. It refers to the primary production potential of a lake. In oligotrophic lakes, primary
production potential is low, mostly because nutrient concentrations are low. In contrast, in eutrophic lakes, primary production is high, and these lakes
are therefore characterised by higher nutrient concentrations
3.2.2.14
Rivers
Watercourses can be divided, according to their size, into pends on the entry of organic material at its upper reaches,
creeks, small, and large rivers. Furthermore, watercourses creating a gradual series of changing interactions from the
can be divided into stream types, including by region-speci- source to the mouth of each river. This is known as the river
fic characteristics, such as ecoregion, altitude, and geology. continuum concept.
Longitudinally, watercourses can be divided by the upper, The saprobic quality is used to assess the ecological qual-
middle overflows, the underflow, and the estuary. The divi- ity of running waters. Saprobity describes the intensity of
sions have ecological importance, since upstream processes oxygen-consuming processes, which can be estimated based
affect downstream waters whereas the opposite cannot take on the chemical or the biological oxygen demand.
place. The food chain within a watercourse also strongly de-
Watercourses may represent a complex array of habitats, ten low in oxygen. Flow conditions are highly variable, but
including both the body of water itself and the riverbed, as on average, levels of erosion are stronger than sedimentation.
well as the terrestrial environment around the waterbody. The rhithron is characterised by higher flow rates than
This habitat is heavily influenced by the flow of water near- crenon and potamon zones. Erosion rates are therefore
by, in particular on floodplains, where still and flowing wa- high and the riverbed is commonly composed of gravel and
ters are separated from each other. stones. Due to the narrow width of rhithron waters, these are
There are many systems of classification of river zones strongly influenced by the surrounding vegetation and there-
based on their condition. For example, a system of zonation fore also usually heavily shaded; as a result, higher aquatic
used primarily in francophone and German communities di- plants and phytoplankton play a minimal role in the rhithral
vides rivers into three primary zones: the crenon, rhithron, ecosystem. Rhithron waters are often oxygen-rich as a result
and potamon. of lower temperatures due to shading and the strong mixing
The crenon is strongly influenced by groundwater and due to heavy flow.
therefore experiences only gradual temperature fluctuations. In the potamon, the water flow is low and waters are ex-
With the exception of source regions in heavily agricultural posed to higher levels of sunlight due to the generally wider
regions, where rates of nitrate are often high, nutrient con- waterbody. As a result of the increased light levels, aquatic
tent in the crenon is generally low. Also, as a result of the plants tend to populate potamal zones more densely, and
strong influence of groundwater, crenon zone waters are of- phytoplankton is more abundant. The potamon riverbed is
fine-grained due to the generally lower flow rates.
estuary: (Lat.: aestuarium = bay) broad body of water where a saproby: collective term given to all digestive processes of dead
river flows into the sea organic matter
See also: Erosion and sedimentation: 2.1.2.2

The five longest rivers in the world and their catchment areas:
Jenissei 1) The Nile is 6,852 km long and has a catchment area of 3,255,000
km2. The average water flow in the middle of the Nile reaches 2,770
m3/s at its peak and up to 1,250 m3/s at its mouth. Due to the ex-
Jangtsekiang traction of water for irrigation, the actual water flow at the mouth is
Mississippi-Missouri Nil reduced to 140 m3/s
2) The Amazon is 6,448 km long and has a catchment area of 5,956,000
km2, with an average flow of 206,000 m3/s. The Amazon is the most
water-rich river in the world
3) The Yangtze River is 6,380 km long with a catchment area of
Amazon 1,722,155 km2. Its average flow rate is 31,900 m3/s
4) The Mississippi River is 3,778 km long and has a catchment area of
2,981,076 km2 with an average flow rate of 18,400 m3/s. Its longest
tributary, the Missouri, is 4,130 km long and has a catchment area of
1,371,010 km2
5) The Yenisei River is 4,092 km long and has a catchment area of
2,580,000 km2, with an average flow rate of 18,395 m3/s
predators predators predators

shredders
grazers
collectors
shredders
grazers collectors
In limnology, rivers are classified as being either crenon (left: source region), rhithron (centre: creek region) or potamon (right: river region). The prop-
erties of flowing water, and in particular the availability and quality of organic matter, change as it moves from the source to the mouth of the river.
In the upper reaches of a river source (allochthonous), respiration rates are higher than production; these areas are dominated by organisms that are
able to shred the coarse plant material. In the middle reaches of a river, the supply of allochthonous materials decreases and, therefore, respiration
rates are lower than production rates. These habitats are dominated by grazers, feeding on algae, and the proportion of shredders decreases. In the
lower reaches of the river, the rate of suspended solids increases, limiting photosynthesis and increasing relative rates of respiration. Communities
near the mouth of rivers are dominated by collectors whereas the proportion of predators stays the same. These fluctuations along the watercourse
are known as the River Continuum Concept
3.2.2.15
Oceans and seas

Oceans cover around 71 % of the Earth’s surface, occu- tive composition of sea salt remains almost the same in all
pying a water volume of 1.34 billion km³. Only the upper saline waterbodies due to the high levels of mixing in the
euphotic zone of the ocean, down to around 200 m in depth, ocean. Sea salt is made up of 55 % chloride (1.9 g/L), 30.5 %
gets enough light for photosynthesis to occur, while deeper, sodium (1.07 g/L), 7.7 % sulfate (0.27 g/L), 3.7 % magne-
aphotic layers do not permit any photosynthesis. Coastal are- sium (0.13 g/L), 1.2 % calcium (0.04 g/L), 1.1 % potassium
as, which are up to 200 m in depth, in other words where pho- (0.04 g/L), and 0.8 % of other ions. Salt lakes, such as the
tosynthesis can occur throughout the waterbody, are known Dead and Caspian seas, in contrast, have widely different
as continental shelves. Continental shelves are linked to the salt compositions. As a result of the salt content, the freezing
deeper ocean by a sloping sea slope (continental slope) with point of seawater is –1.9 ºC.
depths down to 2,000–3,000 m, followed by the abyssal (up Despite their relatively low biomass, oceans are vital for
to around 6,000 m) and hadal zones (6,000 m and beyond). the global flow of nutrients because of their large surface
Seawater has a salinity of 3.5 %, though this may decrease area. About half of global primary production stems from
in some areas and regions. For example, the Mediterranean the ocean, mainly through diatoms (Bacillariophyta) and
has a salt concentration of 3.6–3.9 %, compared with the dinoflagellates.
Baltic Sea which ranges from 0.3–1.7 %. However, the rela-
Water depth is a vital factor in the distribution of life, in Large areas of the open ocean are ultraoligotrophic but
particular because of changes in carbonate solubility as a some areas have comparatively high concentrations of the
result of depth. In deeper water layers photosynthesis does main nutrients (phosphate, nitrate). However, algal growth
not take place due to the lack of light, whereas oxygen- in these areas remains low. The so-called HNLC (high-nutri-
consuming processes do, by way of through respiration of ent low-chlorophyll) regions are mainly upwelling areas with
heterotrophic organisms. In consequence, oxygen concentra- rising nutrient-rich deep waters, in particular at the circum-
tion decreases with depth whereas carbon dioxide concentra- polar oceans around Antarctica. Algal growth in these areas
tion increases. The forming of carbon dioxide and carbonic is limited as a result of low concentrations of micronutrients.
acid water leads to an increasing solution of carbonates. In the context of climate change, the nutrient-rich upwellings
For aragonite (calcium carbonate), the compensation depth of the Southern Ocean are of great interest to the scientific
is 3,000–5,000 m. For the most stable calcite (also calcium community, since they are vital for stimulating primary pro-
carbonate), it is 3,500–5,500 m. Below this depth, therefore, duction in the ocean and therefore enabling carbon fixation.
carbonates cannot be deposited. Deep-sea sediments consist
mostly of silicates.
aphotic zone: the deep water layers which sunlight fails to pen- circumpolar: surrounding one of the Earth’s poles
etrate euphotic zone: the uppermost layer of water, the sunlight zone
See also: Biomineralisation: 4.5.2, 4.5.2.1; Bacillariophyceae: 4.6.2.4; Dinophyta: 4.6.1.2; Light availability: 4.4.2; Carbonate balance 2.1.2.3
Oceans cover around 71 % of the Earth’s surface. The Arctic and Antarc-
tic are, depending on the point of view, considered as separate oceans
from the Pacific, Atlantic, and Indian oceans. Since photosynthesis only
takes place in the upper layers of the oceans, oxygen saturation de-
creases with depth
The Atlantic Ocean covers an area of around 80 million

km² and has a volume of 355 million km³. Its mean depth
is 3,293 m, with the deepest point being the Milwaukee
Deep (9,219 m)
The Pacific Ocean covers an area of 181 million km² and

The Indian Ocean covers an area of 75 million km² and has a has a volume of 714 million km³, containing over half of the
volume of 292 million km³. The mean depth is 3,936 m, with Earth’s water. Its mean depth is 3,940 m, the lowest point
its deepest point at Diamond Deep (8,047 m) being at the Witjas Deep within the Mariana Trench (11,034
m)
The organisms living in the surf zone endure high mechanical loads due The open ocean is ultraoligotrophic, extremely nutrient-poor. Currents
to wave action and sporadic periods of drought. Continental shelf areas are vital for the global flow of nutrients to the large area that they oc-
are generally richer in nutrients than the open ocean. In shallower sea cupy. Significant primary producers are diatoms and dinoflagellates
areas light can penetrate to the bottom
Photosynthesis is impossible below the photic zone, so food webs rely Coral reefs are extremely diverse marine ecosystems. The biominerali-
on the upper water layers (here: Bathypathes sp. – black coral with sation of reef-building organisms is geologically important for the rock-
deep-sea crabs) forming process
227
4. Megasystematics
The classification of eukaryotes has changed dramatically and defined by the particle’s sedimentation velocity, this
over the past two decades; the centuries-old divide of life into molecule is also known as the 18S rRNA (eukaryotes) or the
groups of animals or plants has been replaced by a system of 16S rRNA (prokaryotes and the mitochondria and plastids
several supergroups. In this new structure, animals in their of eukaryotes). Other genes followed the initial focus on
strictest sense (Metazoa) and plants in their strictest sense SSU rRNA and, with the introduction of high-throughput
(land plants) are just side branches in a far more complex sequencing techniques, the analysis of single genes and mo-
system of eukaryotes. lecular phylogenetics is increasingly replaced by sequencing
Since the introduction of PCR in the 1980s, molecular entire genomes and transcriptomes. To that end, the first
data have decrypted many formerly obscure relationships complete genome was sequenced in 1995 (Haemophilus in-
and have become increasingly important for the reconstruc- fluenzae). In addition to the sequence information itself, a
tion of phylogenetic relationships, where conventional mor- completely sequenced genome offered additional informa-
phological data were ambiguous. Molecular data thus have tion about the genome itself, including its size and structure.
reached or in many organismic groups even outpaced the The size of each genome and the correspondingly large
importance of morphological data for the reconstruction of amount of data featured within the analysis required elabo-
phylogenies. rate bioinformatics techniques. Whereas the procurement of
Initially, sequence data comprised single genes, often the data was previously the limiting step in morphological and
small subunit of the ribosomal RNA (SSU rRNA). Based molecular studies, the bottleneck of current large-scale se-
on its sedimentation coefficient, mesured in Svedberg units quencing is the curation and analysis of the data.
4.1 Basics of megasystematics

This introductory chapter provides an overview of the development of systems used to classify organisms
4.2 Unikonts
This chapter presents an overview of the unikonts, including the Apusozoa, which consolidated the Ophistokonta,
Holozoa, Holomycota, and Amoebozoa
4.3 Excavata
This chapter presents the Excavata, a large group comprising Metamonadida (Diplomonada, Retortamonadida,
Parabasalia, Oxymonadida), and the Discoba (Euglenozoa, Heterolobosea, Jakobida)
4.4 Archaeplastida
This chapter presents the Archaeplastida, the organisms with primary plastids, including Glaucocystophyta, Rhodo-
phyta, and the Viridiplantae (Chlorophyta and Streptophyta, including the land plants)
4.5 Rhizaria
The Rhizaria are related to the Chromalveolata and include many amoeboflagellates. They include Cercozoa (Filosa,
Endomyxa) and the Retaria (Polycystinea, Acantharia, Foraminifera)
4.6 Chromalveolata
This chapter presents Chromalveolata, comprising Alveolata (Ciliophora, Dinophyta, Chromerida, Apicomplexa)
and the stramenopiles (Bigyra, Pseudofungi, Ochrophyta)
4.7 Hacrobia
This chapter deals with Haptophyta and Cryptophyta. Their relationship is still not entirely resolved

228 Megasystematics
4.1
Basics of megasystematics
Organisms can be classified in many ways. Historically, tions based on human imagination differ widely from each
the focus of classification schemes has been on a search for a other.
'natural order', based on the assumption that life exists with- For example, among many schemes, organisms can be
in a predetermined order – and that the scientific challenge grouped according to their habitat, their morphological or ge-
would be to understand it. netic similarity, by their use or benefit to humans, or by their
With the development of a more progressive understand- feeding ecology. To that end, one could categorise species as
ing of evolution, the concept of a predetermined order for producers and consumers, as micro- and macro-organisms,
life was increasingly questioned. However, the demand for or by dividing life into aquatic and terrestrial groups. Clas-
a meaningful classification prevailed, changing according to sifications by other single criteria, such as colour, edibility, or
the nature of the underlying research question. Classifica- toxicity, have also been attempted.
The currently most favoured method for classifying living paraphyletic on the basis of more recent microscopic or mo-
organisms is based on phylogeny. On the one hand, this strat- lecular data.
egy reflects measurable phylogenetic relationshipswhilst also Prominent examples of this phenomenon are the assign-
creating a meaningful way of interpreting diversity across ment of crocodiles to reptiles, the classification of protists
disciplines. Since closely related organisms usually resemble into algae and Protozoa, or even divisions between animals
each other in many aspects, or at least are more similar to and plants. Crocodiles are phylogenetically closer to birds
each other than distantly related species, it is often possible than to other reptiles; nevertheless, they are grouped with
to generalise scientific findings within phylogenetically re- reptiles because of their lifestyle and many morphological
lated groups. and physiological similarities.
Other classification systems reflect different objectives Animals (Metazoa) and land plants are monophyletic kin-
and are often only useful within a single or few disciplines. ship groups. Colloquially and historically, however, the as-
Such frameworks are not problematic as long as they are signment of animal and plant status was achieved according
interpreted within their proper context, but they are prone to the mode of feeding – heterotrophic versus phototrophic.
to causing misunderstandings between disciplines when, for However, the grouping of cyanobacteria, the various groups
example, the same terms are applied to different organismal of primary producing algae and land plants, is quite useful,
groups and/or in a different context. The realm of misun- even according to today’s ecological knowledge, although it
derstanding is exacerbated by the fact that different classi- makes little sense in the context of phylogenetics or of other
fication systems and terminology originally appeared to be biological disciplines.
phylogenetically relevant, before being shown to be poly- or
algae: photoautotrophic, eukaryotic organisms not belonging primary producers: autotrophic organisms that synthesise
to land plants; ecology usually classifies cyanobacteria as algae complex organic molecules from inorganic compounds
consumers: (Lat.: consumere = to consume) heterotrophic or- protists: a large group of unrelated eukaryotic organisms with
ganisms which feed on other organisms no specialised tissue
phylogenetics: the study of the evolutionary relationships be-
tween organisms and the evolution of species during the history
of the Earth
See also: Golden algae: 4.6.2.3; Phylogenetic position of crocodiles: 4.2.1, 4.2.1.9; Polyphyly: 4.1.1.6, 4.2.2.3
Basics of megasystematics 229
Classification by phylogenetic and molecular criteria: the system shown here is the relationship between organisms. However, in part, this system con-
tradicts intuitive expectations: crocodiles group with birds and not with other reptiles; algae are not a homogenous group, here the green algae (far
right) do not group with the golden algae (middle-right). The relationship between photoautotrophic and mixotrophic golden algae (here: Dinobryon)
with heterotrophic golden algae (here: Spumella) is surprising
Classification by general abvious morphological criteria: crocodiles are grouped with the reptiles because of a similar appearance and lifestyle (scale-
bearing reptile-like animals with adaptations to an amphibian mode of life), even though they share a number of morphological characteristics with
birds
Classification by functional and ecological criteria: the term 'plant' is often colloquially used to summarise organisms that feed autotrophically through
photosynthesis. In the same way, 'animals' are described as being those organisms that absorb particulate food and move freely. In the example chosen
here, the 'algae' are grouped as primary producers, separately from the heterotrophs. The cold-blooded crocodiles are grouped with other reptiles
230 Megasystematics
4.1.1
Historical and philosophical basis of megasystematics

In historical classification systems, nature was divided to explain, since the natural sciences and science in general
into inanimate and animate nature. The latter, i.e. organisms, relied on literature nearly exclusively available in monastery
was divided into animals and plants; humans were usually libraries until the 19th century in Europe. As a result, the
given a special role within the classification. These histori- scientists with access to books also generally had theological
cal classifications were also the foundation for the traditional training. Even the increasingly important university libraries
division of natural sciences in universities into geosciences were theologically influenced, paving the way for theological
(inanimate), botany (plants), zoology (animals), and medi- and philosophical writings to affect the biological discourse
cine (humans). for a long period of time. In addition, Carl Linnaeus, the
The historical roots of this rough categorisation date back father of binary nomenclature, and Charles Darwin, who
to the philosophy of Ancient Greece (Aristotle and his dis- first described the theory of evolution by natural selection,
ciple Theophrastus) as well as to the creation stories of the both had at least rudimentary theological or philosophical
‘book religions’ (Christianity, Islam, and Judaism). training.
The origin of the different criteria for distinguishing be- In modern science, diet and mode of locomotion continue
tween animal and plant characteristics stems from these to be important differential criteria for separating plants and
sources: in general, animals were defined according to their animals. This historical perspective on classification corre-
mobility and their ability to perceive with their senses. sponds well with the overall life experience of younger hu-
In Genesis, animals that 'swarm', 'fly', and 'creep' were mans first getting to know their environment. When they
associated with each other and grouped as different from face more problematic organisms, from a classification point
plants. In practice, Aristotle’s philosophical foundations, of view – corals, sponges, carnivorous plants, parasitic het-
which were based on sensory perception, related directly to erotrophic plants, fungi, and protists – the concept has been
the intake of food as an easily detectable character, since the so deeply ingrained that the conflict between their conceptu-
senses are required for prey detection. The strong influence alisation and the natural diversity of ‘animals’ and ‘plants’ is
of philosophy and theology on writings in biology is easy not recognised, or is just accepted as a curiosity.
Microorganisms, comprising bacteria, Archaea, and pro- as complete miniaturised animals or plants – the internal
tists, are particularly problematic in the context of conven- structures were consequently interpreted as alimentary and
tional classification and megasystematics. regenerative organs, as in metazoa. An understanding of the
Recent efforts to classify these groups hinge on the de- cellular organisation of living things and of single-celled or-
velopment of microscopic and molecular methods. High- ganisms arose only after the mid-19th century, with the ad-
resolution light microscopy techniques, such as differen- vent of cell theory and its application to microorganisms.
tial interference contrast, and the development of electron As a result, microbes went from being regarded as basal
microscopy, allow for the detailed analysis of intracellular (simple) animals or plants to being systematically placed in
structures as well as for the analysis of microorganisms. their own respective realms. Since many microorganisms
However, the study of microbes dates back to the descrip- exhibit characteristics that could be considered typical for
tions of ‘little beasts’ (animalcules) by Antonie van Leeu- plants (plastids, pigmentation) or animals (free locomotion,
wenhoek which were, in fact, bacteria and protists. Van Lee- food intake), they were initially placed in both botanical and
wuenhoek classified them as small animals, based on their zoological classification systems. To date, this dual classifica-
free floating movement, and interpreted these organisms tion system remains unresolved, not without confusion.
differential interference contrast: technique used in optical electron microscopy: a form of microscopy which reveals the
microscopy in which differences in the optical path length are surface or the interior of an object using electrons instead of
changed into levels of enhanced illumination light; an electron microscope achieves a much higher resolution
than light microscopes
See also: The three domains: 4.1.2

Basics of megasystematics: historic and phylogenetic fundamentals 231
The basic classification of organisms stems from Greek philosophy, in particu-

lar from Aristotle (left) and his disciple Theophrastus, and from the creation
story of the ‘book religions’, Christianity, Islam, and Judaism. According to Ar-
istotle, all living things have the ability to nourish and reproduce (anima veg-
etativa). Only animals, including humans, have the ability to perceive (anima
sensitiva). The ability to think and to reason (intellect, anima rationalis) is
unique to human beings. Genesis emphasises free locomotion as a differential
criterion: "Then God said, Let the earth sprout vegetation: plants yielding seed,
and fruit trees on the earth bearing fruit after their kind with seed in them
(Gen 1:11) […] Let the waters teem with swarms of living creatures, and let
birds fly above the earth in the open expanse of the heavens (Gen 1:20) […]
Let the earth bring forth living creatures after their kind: cattle and creeping
things and beasts of the earth after their kind (Gen 1:24) […] Let Us make man
in Our image, according to Our likeness (Gen 1:26)"
Antonie van Leeuwenhoek (bottom-left) designed and built his own microscope (bottom-right) and drew early interpretations of Foraminifera (bottom-
middle-left: possibly Polystomella sp.) and a ciliate (bottom-middle-right: Coleps sp.)
232 Megasystematics
4.1.1.1
Carl Linnaeus and the fundamentals of modern systematics

In 1735, the Swedish naturalist Carl Linnaeus (born 23 aimed to, 'fathom the divine plan of Creation'. The lasting
May 1707 in Råshult, died 10 January 1778 near Uppsala) effect of Linnaeus is not seen in his extensive compilation
published the Systema Naturae, a comprehensive overview of of known organisms but, rather, in the introduction of
all known animal and plant species, describing around 7,700 binary nomenclature for the naming of species. Before
plant, 6,200 animal, and 500 mineral species. his work, species names were long descriptive phrases.
Linnaeus assumed that he had covered almost all of Linnaeus named each organism as a combination of genus
the existing biodiversity. However, his work represented name and species epitheton. By that, species names became
only 1–2 % of currently known living species. Although considerably shorter and, for the first time, a unified system
microorganisms were already known at that point, Linnaeus of nomenclature was established and applied to all life.
either did not incorporate them at all or merged them into Linnaeus’ system, known as binomial nomenclature,
collective species groups such as Chais infusorium. forms the underpinnings of current taxonomy. Of his many
Linnaeus was well aware of the importance of his work, works, the Systema Naturae and Species Plantarum remain
as expressed by his quote 'Deus creavit, Linnaeus disposuit' most influential to this day, as they provide the basis for the
(God created, Linnaeus organised). In addition, his words naming of animal and plant species, respectively.
illustrate the theological foundations of his work, which
Species Plantarum was published in 1753 and forms the In the tenth edition, Linnaeus also presents his view of
basis of botanical nomenclature. In the two–volume work, the classification of major organismal clades: stones, plants,
which features roughly 7,300 species, Linnaeus describes and animals:
every plant species known at that time systematically by • 'Lapides corpora congesta, nec viva, nec sentientia' (stones:
their genus and species epitheton, paving the way for the solid body, neither alive nor sentient)
acceptance of binary nomenclature in the field of botany. • 'Vegetabilia corpora organisata & viva, non sentientia'
Only later did Linnaeus apply the same nomenclatural (plants: organised body and alive, not sentient)
rules to animals in his comprehensive review of all known • 'Animalia corpora organisata, viva et sentientia' (animals:
biological diversity Systema Naturae. However, binary organised body, alive and sentient, spontaneously
nomenclature was only consequently applied to animals in moving)
the work’s tenth edition, which appeared in 1758, forming These definitions clearly reflect the historical roots of
the basis of zoological nomenclature as it appears today. the large-group classification in philosophy and theology.
The foundations of botany and zoology therefore In addition, Linnaeus, in contrast with his contemporaries,
emerged from two different works by Linnaeus, partly placed humans in the animal kingdom (for the first time since
explaining the differences in botanical and zoological rules Aristotle’s Historia animalium). He does, however, attribute
for nomenclature. This discrepancy is particularly influential the ability of self-knowledge ('Nosce te ipsum' – know thyself)
for organisms recognised by both systems, as is the case with as a feature unique to humans.
many protists. In such cases, descriptions may be considered
valid from the perspective of one field but invalid in the other.
binary (binomial) nomenclature: in taxonomy, the system of

giving species a name composed of two parts identifying both
the genus and the epithet
See also: Aristotle: 4.1.1

Carl Linnaeus (middle) and the title pages of his most influential work, the Systema Naturae (left) and the Species plantarum (right). The former was first
published in 1735 but it was not until 1758 and its tenth edition that Linnaeus presented the application of binomial nomenclature to animals
Lapides Plantae Animalia
In his work, Linnaeus differentiated between Lapides (stones), Plantae (plants), and Animalia (animals). In distinguishing between these three kingdoms,
he essentially followed the criteria known in Ancient Greece, where plants and animals were considered to inhabit inanimate nature. Animals differed
from plants, according to Linnaeus, because of their ability to feel. Aristotle differentiated animals by their anima sensitiva (ability to perceive). Contrary
to other classification systems of his time, Linnaeus included humans within animals. In this respect, the self-knowledge trait he describes follows
Aristotle’s philosophy of anima rationalis, or the ability to think and be logical
234 Megasystematics
4.1.1.2
Basics of modern phylogeny: Darwin and Pasteur

The concepts of evolution and the common ancestor of plained, because spontaneous creation remained an ongo-
all life have been discussed since at least the 6th century BC. ing, continuous process.
For example, the Greek philosopher Anaximander (approx. Based on Lamarck’s work, Alfred Russel Wallace and
610–547 BC) discussed how humans developed from other Charles Darwin presented new aspects of evolutionary the-
creatures. He also made two further assumptions, namely, ory in 1858, which formed the basis of our current under-
that life emerged spontaneously and that it originated in wa- standing of how life developed. Instead of the Lamarckian
ter. idea of increasing complexity towards perfection, Darwin
In the 19th century, the French biologist Jean-Baptiste de and Wallace presented natural selection as the driving force
Lamarck (born 1 August 1744 in Bazentin-le-Petit, France, of change. These considerations were brought together by
died 18 December 1820 in Paris, France) presented a theory Darwin’s comprehensive book On the Origin of Species, which
of evolution, which assumed that species change through the was published in 1859.
inheritance of acquired differences. The gradual variability Cell theory, which postulates that all living things are
of species (gradualism) was considered a fact; however, the composed of cells, had only just been presented at the time,
mechanisms behind these gradual changes remained unclear. supporting the evolutionary claim that animals and plants
Lamarck postulated that gradual changes in the environment are inherently similar and that evolutionary theory could be
caused the lifestyle of organisms to change which, in turn, applied to all living things.
caused the organisms themselves to change. The inheritance Almost simultaneously, Pasteur’s experiments disproved
of acquired characteristics remains a major topic within the theories of spontaneous generation, showing instead that life
field of epigenetics. begets life.
Moreover, Lamarck postulated an innate drive for change In the space of only a few years, these fundamental works
that caused organisms to become increasingly complex completely changed the central foundations of biology.
throughout evolution. Simple organisms still existed, he ex-
The mutability of species was already known in Darwin’s Much like Darwin’s findings for understanding evolution,
time and was a widely accepted fact. In particular, gradual Pasteur’s studies were vital for understanding the question
changes over time in fossil organisms, as had been set out of spontaneous generation, which stated that lower forms of
by Lyell’s Principles of Geology, influenced Darwin’s thinking. life could appear at any time from a suitable medium (for ex-
What was less obvious to Darwin and his contemporaries, ample: water, mud, or soil). Pasteur’s experiments provided
however, were the reasons behind organismal change. evidence that the spontaneous re-emergence of life was not
Darwin’s ideas on selection and fitness were strongly in- possible but, instead, that life can only arise from other life.
fluenced by Malthus’ An Essay on the Principle of Population. Previously alleged spontaneous creation was, he claimed, the
In this work, Malthus described that populations grow ex- result of environmental contamination with germs from the
ponentially in the absence of external controls whereas food air or from other sources. This led to the conclusion that the
production increases linearly. As a result, Malthus claimed theory of evolution could be applied to all life forms, and not
that exponential growth could only be maintained for a lim- only for more advanced species. These principles formed the
ited period of time before members of the population would foundations for proposing a unique origin of life and con-
start fighting each other for limited resources. This socially- sequently a phylogenetic relationship of all life with today’s
based outlook was a central starting point for Darwin’s the- biodiversity having evolved largely through mechanisms out-
ory. lined in Darwin’s Origin of Life.
gradualism: concept in evolutionary theory assuming that the spontaneous generation: spontaneous emergence of life
rate of evolutionary change is (roughly) constant, and that varia- from inanimate matter
tion takes place across several continuous processes rather than
in sudden leaps forward
See also: Origin of life: 2.2.1.1

Charles Darwin (born 12 February 1809 in Shrewsbury, UK; died 19 April 1882 in Downe,
UK) was a British naturalist known as the founder of the theory of evolution. The theories
of variability and evolution were not new at the time; however, Darwin was the first
to substantiate these considerations using a broad base of evidence from different
disciplines. In his notebook from 1837, Darwin produced the first sketch of the concept
of the tree of life
Louis Pasteur (born 27 December 1822 in Dole, France; died 28 September 1895 in Ville-
neuve-l’Elang, France) was a French chemist and microbiologist. His efforts contributed
significantly towards refutating of abiogenesis theory, which assumed that lower forms
of life can arise by spontaneous generation from inanimate water, mud, or soil. Before
Pasteur, this theory was applied not only to microorganisms (bottom-left: microbial mat),
but also to explain the appearance of maggots, worms, and other small Metazoa (top-left:
maggots on meat). Pasteur showed that no life could develop in sterile liquid but only after
the medium had been contaminated by non-sterile materials
236 Megasystematics
4.1.1.3
What is a plant?
'Plants are green, they photosynthesise, and are rooted synthetic free swimming Euglena (Euglena gracilis) animal or
into the ground.' This is a selection of traits intuitively as- plant? Or both? Or neither?
sociated with plants, although many plants do not fit within Taken together, these examples show that the term ‘plant’
such a framework. Parasitic plants, for example, are neither is defined in many different ways, and is futher complicated
green nor photosynthetic. Mosses are green and photosyn- by the term’s colloquial application, which combines defi-
thesise, yet they are not deeply-rooted in the ground. Also, nitions based on functional role, ecology, and morphology
what about carnivorous plants, such as the Venus flytrap? (photosynthetic, rooted) with attempts to find a systematic
And why are photosynthetic sea slugs, such as Elysia, not definition.
plants? In a phylogenetic context, the monophyletic land plants
Algae are often placed within the plants because they – mosses, ferns, club mosses, and seed plants – most closely
photosynthesise, yet they are morphologically dissimilar and fit within the ‘plant’ schema. Functional definitions tend to
most are only distantly related to land plants. Cyanobacteria include most photosynthetic organisms, thereby also includ-
are also often grouped as plants. In addition, is the photo- ing algae and, depending on the definition, cyanobacteria.
In Systema Naturae, Carl Linnaeus divided nature into Unlike the term ‘plant’, which (beside the ambivalent
three kingdoms: Lapides (minerals), Plantae (plants), and definitions above) is currently generally understood to define
Animalia (animals). Fungi, lichens, eukaryotic algae and a monophyletic group of higher plants, ‘algae’ is used pri-
cyanobacteria were historically ascribed to the plants, usu- marily in a functional context. In general definitions, algae
ally based on their phototrophy or, in the case of fungi, to are characterised as photosynthetically-capable organisms
the growth form of the macrofungus. Due to the presence that are not land plants. This very general definition would
of a cell wall, bacteria were also grouped with the plants as in principle include the cyanobacteria, although algae are
'Schizophyta'. usually understood to be as eukaryotic organisms. Here, too,
With the increasing clarification of phylogenetic relation- systematic, phylogenetic, and functional-ecological consid-
ships, the plants were defined as a monophyletic group, with erations play a role.
many groups within them placed in other categories: aside Despite their functional, photosynthesis-based definition,
from the ‘land plants’ discussed above, the monophyletic Vir- algae are in general placed within the eukaryotes. In ecologi-
idiplantae (land plats and green algae), or the Archaeplastida cal studies, on the other hand, phototrophic primary produc-
(organisms with primary plastids, including Viridiplantae, ers are grouped together; in this context, cyanobacteria and
Rhodophyta, Glaucophyta) were also considered 'plants'. algae are not separated.
carnivorous: (Lat.: carnivorus = meat eating) consuming meat motility: (Lat.: motio = movement) ability to move freely and
actively
See also: Land plants: 4.4.3.1 to 4.4.3.9; Stramenopiles: 4.6.2 to 4.6.2.4

Photosynthetic land plants are always categorised as ‘plants’. These organisms exhibit intuitive colloquial plant characteristics, including a lack of motil-
ity and photoautotrophy
Not all land plants show ‘typical’ plant features, however. Parasitic plants feed heterotrophically from their host plants (left: spruce asparagus Mono-
tropa hypopitys; middle-left: broomrape Orobanche haenseleri). Carnivorous plants obtain their nutrients through the digestion of animal prey (middle-
right: venus flytrap Dionaea muscipula). Duckweed (right: Lemna sp.) float freely on water
Algae and cyanobacteria are autotrophic. However, most taxa are not closely related to land plants. Brown algae (left: Fucus spiralis) and diatoms
(centre: Porosira glacialis) are among the Stramenopiles. Cyanobacteria (right: Anabaena sp.) are bacteria and are therefore not referred to as algae,
although they are often grouped with the eukaryotic algae in ecological studies
238 Megasystematics
4.1.1.4
What is an animal?
The term ‘animal’ seems intuitively clear, usually thought unicellular eukaryotes, such as Ciliophora (German: 'Wim-
to comprise vertebrates – mammals, birds, reptiles, amphib- perntierchen') or the Euglenozoa, with Euglena (German:
ians, and fish – as well as invertebrates, such as arthropods, 'Augentierchen'), with either plants or animals is problem-
molluscs, annelids, and others. atic. The original German names for these organisms point
This grouping is far less clear when applied to ‘lower’ ani- to this challenge.
mal phyla and microorganisms. The assignment of sponges, As with plants, categorising organisms as ‘animals’ is
corals, sea anemones, and other sessile organisms to animals complicated because of conflicting definitions between
is less intuitive. Historical taxonomic terms, such as 'flower colloquial and scientific terms, which include descriptions
animals' (Anthozoa), illustrate the confusion with assign- based on functional-ecological aspects (feeding, locomotion)
ing sessile organisms to animals. Similarly, the affiliation of as well as systematic and phylogenetic placement.
Coming up with criteria that clearly define 'animals' is the uptake of particulate food has been lost in some animals
even more difficult. Two commonly used criteria are free lo- and may be common in other groups, such as many algae.
comotion and the consumption of particulate food. Heterotrophy is also common in many (parasitic) plants.
These two criteria have historical roots going back to phil- When defining ‘animals’, it is therefore important to dis-
osophical and theological definitions, which differentiated tinguish between systematically- and phylogenetically-based
plants and animals by their freedom of movement and their groupings on the one hand and those based on ecology and
ability to perceive stimuli. Food intake subsequently replaced functional groups on the other. These aspects are muddled
the ability to perceive, since the former is easier to measure and not clearly differentiated in everyday colloquial lan-
and prove. guage. Whereas both aspects apply to most ‘higher’ animals,
This broad functional definition would also assign many definitions become particularly confusing when referring to
heterotrophic protists to 'animals'. In contrast, from a sys- the so-called ‘lower’ animals and protists.
tematics point of view the ‘Metazoa’ are closest to the term Clearly defining animals, therefore, can only be achieved
‘animals’ group. by the application of systematics- or ecology-based defini-
However, the two above criteria and combinations thereof tions: systematics would define animals, for instance as com-
are not enough to create a systematic (monophyletic) animal prising, all species within Metazoa, whereas ecology would
group, since not all Metazoa are motile in their adult stage: group together all heterotrophic or phagotrophic organisms
for example, corals, sponges, and many other organisms are as a functional unit. For higher-level organisms (higher
sessile. To complicate matters further, other organisms that plants, higher animals, and higher fungi), the systematic
are sessile in their adult stage are motile earlier on in their grouping largely parallels the ecological classification, so the
life cycle or at least during a reproductive stage. Similarly, two rarely come into conflict within their everyday use.
zoochlorellae: endosymbiontic green algae zooxanthellae: endosymbiontic dinophytes
See also: Amoebozoa: 4.2.3, 4.2.3.1; Holozoa, Metazoa: 4.2.1; Zooxanthelle: 4.6.1.2
The term ‘animal’ is colloquially used to refer to organisms that eat, taking in particulate food, and move around freely. This definition applies to most
metazoa. In particular, larger animals nearly always conform to this view
Many animals and heterotrophic protists may be able to obtain their energy using phototrophic symbionts (zooxanthellae or zoochlorellae) or using
plastids obtained within their food (left: anemone; top-middle: Paramecium bursaria; bottom-middle: Tridacna gigas; right: Elysia chlorotica)
Ciliates and amoebae are heterotrophs, eating bacteria, algae, and smaller protists, yet they are not closely related to metazoans. Ciliates (left: Para-
mecium sp.) are among the Alveolata. Amoebae are found in several different kinship groups (clades). The amoeba illustrated here (right: Saccamoeba
limax) belongs to the Amoebozoa
240 Megasystematics
4.1.1.5
What is a fungus?
As with animals and plants, fungi are also inaccurately taxonomic assignment. Systematically, the ‘true’ fungi are
categorised based on colloquialisms and the muddling of Holomycota, the sister group to Holozoa, characterised by
systematics or phylogenetics with functional or ecological cell walls containing chitin (chitinous fungi). Among others,
aspects. Due to their sessile lifestyle and the presence of cell the pillar-fungi including mushrooms and toadstools belong
walls, fungi were originally grouped with plants, but they to the true fungi (Dikarya: Basidiomycota and Ascomycota).
were subsequently grouped within their own kingdom based Functionally, other unrelated groups are also grouped with
on their unique form of feeding. the fungi as a result of their shared lifestyle. These include
Fungi are chemoorganotrophs (i.e. heterotrophic), mostly the slime moulds, the oomycetes, and the Actinomycetales.
living as saprophytes or parasites. This mode of nutrition is, Systematically, however, these groups do not belong to fungi.
especially colloquially, a key criterion for their conventional
Systematically, slime moulds are similar to Amoebozoa, important economic consequences by influencing agricul-
with a complex life cycle of unicellular free-living amoeboid tural stocks, for example, as potato blight and fish moulds.
phases and multi-nucleanated (plasmodial) or multicellular The ray fungi (Actinomycetales) are in fact actinobacteria,
stages that grow to form fruiting bodies. living aerobically and forming spores when exposed to rain-
The Peronosporomycetes (Oomycetes, or cellulose fungi), fall. They form filaments which grow to form braids, also
as with the true fungi, form hyphae. Their cell walls consist known as mycelia. They were originally assumed to be fungi
of cellulose, as well as glucans and hydroxyproline. They be- because of their branched networks of hyphae.
long to the stramenopiles. The zoospores of Peronosporomy- These groups were thus placed within fungi because of
cetes have flagella with tripartite hairs, typical of heterokont their similar lifestyle and superficial morphological traits.
stramenopiles. Many species live parasitically and may have This functional characterisation may remain meaningful in
a present-day environmental context.
chemoorganotroph: organisms that obtain their energy from phagotrophy: form of nutrition which involves consuming par-
oxidising organic electron donors ticulate matter
osmotrophy: the process of obtaining nutrition by taking in saprotrophic: feeding on dead organic matter and in doing so,
dissolved organic compounds; in contrast to phagotrophy breaking it down into its constituent parts
See also: Actinobacteria: 4.1.2.1; Holomycota: 4.2.2 to 4.2.2.5; Egg fungi: 4.6.2.1; Slime molds: 4.2.3, 4.2.3.1, 4.3.2
Fungi are osmotrophs. Presented here are examples of fungal species forming large fruiting bodies above the soil surface (left: chanterelle Cantharellus
cibarius; right: sulphur shelf Laetiporus sulphureus)
Slime moulds feed osmotrophically and saprotrophically, forming fruiting bodies (left) and multinucleate plasmodia (right). However, they are not fungi
but, rather, belong to Amoebozoa
Various phytopathogenic species belonging to the stramenopiles. Peronosporomycetes are summarised under the name ‘downy mildew’ (left: typical
mosaic pattern on the leaf of a cucumber). The ‘fish moulds’ also belong to this group (above-middle: Saprolegnia sp.). The Actinomycetes (bottom-
middle and -right: ‘ray fungi’) are actinobacteria
242 Megasystematics
4.1.1.6
Phylogenetic trees
Systematic relationships are often presented in the form of the target group can be traced back to the same ancestor, the
phylogenetic trees. Phylogenetic trees consider shared char- group is paraphyletic. Polyphyletic groups, on the other hand
acteristics, distinguishing between independently evolved have similar or identical properties but individual lineages do
features (homoplasia, convergence) and those that can be not have a common origin.
traced back to a single origin (homology). Whether a feature is considered to be a synapomorphy
Convergent characteristics have been independently or symplesiomorphy depends on the context of the groups
evolved (for example, succulence in cacti and euphorbias) under consideration. For example, mammary glands are a
and are therefore not relevant in the construction of relation- synapomorphy of mammals, though they are a symplesio-
ships between similar species. However, these are not always morphy if we consider relationships between various mam-
easy to identify and, importantly, to distinguish from homol- malian groups with each other.
ogous features. Phylogenetic trees are made nodes splitting into branches
Features that can be traced back to a common ancestor and twigs. When an outgroup has been defined, that is, one
can be distinguished as either being newly acquired (synapo- group of organisms that is closely related to the organisms in
morphies) or ancestral (symplesiomorphies). question but not part of the group itself, the family tree can
Symplesiomorphies are not relevant for phylogenetic re- be rooted, meaning it then has an orientation or direction.
constructions, and neither are newly acquired traits which Phylogenetic analyses result in many hierarchically or-
occur only in one taxon (autapomorphies). To that end, only dered parent groups. The traditional nomenclature, however,
synapomorphies, in other words a group of common, new- only presents a limited number of ranks. Phylogenetic clus-
ly-acquired (derived) features can be used for phylogenetic ters can therefore not easily be assigned to the nomenclatural
analyses. ranks. In addition, nomenclatural ranks in different groups of
Phylogenetic trees show the progressive splitting of clades organisms often correspond to different phylogenetic ranks.
over time. The individual clade’s sister groups are (ideally) The integration of phylogenetic insights into traditional no-
each characterised by the possession of specific synapomor- menclatural systems is therefore problematic and leads to in-
phies. consistencies in the naming of groups, in particular those at
A monophyletic group is one that can be traced back to higher taxonomic levels such as orders, classes, and families.
a single common ancestor. If additional clades not within
The ‘bootstrap method’ is used to analyse the reliability of An alternative to bootstrapping is 'jack-knifing', which
reconstructed phylogenetic trees. works by only partly removing features and not replacing
Bootstrapping occurs by replacing variables that are ran- them with others. The observed partial data sets are therefore
domly removed from the dataset with new ones, calculating smaller. Calculations necessary whilst performing the jack-
a new tree for each new dataset and then counting how often knife method are less computationally demanding compared
each group (in this case, assuming it is monophyletic) oc- with bootstrapping but they provide less accurate results; the
curs in the new trees. The frequency with which each clade method is therefore rarely used.
is considered a monophyletic group is given as the bootstrap
value (in percent).
apomorphy: a trait that is newly derived in the phylogenesis of plesiomorphy: ancestral trait which was already present before
taxa which was not present in their ancestors the formation of the ancestral line under consideration
autapomorphy: (Grk.: autos = self, trophe = nourishing) the symplesiomorphy: term given to homologous plesiomorphic
ability of organisms to produce and store organic nutrients exclu- characteristics exhibited by two or more taxa
sively from anorganic substances synapomorphy: an evolved characteristic common to a mono-
phyletic group
See also: Inconsistencies between phylogenetic and traditional nomenclatural systems: e. g. 4.1.1.1, 4.1.1.3, 4.1.1.4, 4.1.1.7
All organisms within a monophyletic group can be traced

back to a common ancestor; at the same time, all descend-
ants of that ancestor belong to this group. Examples of
Sister group taxa can be traced back to the same ancestor monophyletic groups are the angiosperms, land plants, and
as the target group and represent the closest relatives; in streptophytes
this tree, the gymnosperms are sister to the angiosperms
and Chlorophyta are sister to Streptophyta
Populus
Ricinus
Vis
Oryza angiosperms
Zea
Nuphar
Amborella
Gnetum
Welwitschia
All organisms in a paraphyletic group can be traced back Picea
to a common ancestor; however, not all descendants gymnosperms
Cryptomeria land
of this ancestor belong to the group. The streptophyte Cycas plants
algae are an example of such a group: their common an- Zamia Strep-
cestor has descendants that do not belong to this group: Ginkgo
tophyta
Ceratopteris
the land plants Adiantum
Huperzia
Selaginella
Physcomitrella
54
Tortula
Marchana
Spirogyra
90 Closterium strepto-
Coleochaete phyte
Chara algae
Klebsormidium
Mesosgma
Chlamydomonas
Polytomella
Dunaliella
100 Scenedesmus
Chlorella
Prototheca Chloro-
Coccomyxa phyta
Scherffelia
Micromonas
Ostreococcus
Pyramimonas
C. merolae
Galdieria sulphuraria Rhodo-
Gracilaria changii phyta
Porphyra yezoensis
The lineages chosen as outgroups (root) are related to the organisms in the target group but less closely than target group
members are to each other. In this example, the rhodophytes were chosen as the outgroup
taxon plants fungi animals

phylum -phyta -mycota inconsistent
subphylum -phytina -mycotina inconsistent
class -opsida -mycetes inconsistent
subclass -idae -mycetidae inconsistent
order -ales -ales inconsistent
suborder -ineae -ineae inconsistent
superfamily -acea -acea -oidea
family -aceae -aceae -idae
subfamily -oideae -oideae -inae
The conventional nomenclature dictates that only taxa corresponding to a rank can be formally designated. Especially for higher ranks, the formation
of taxa from different groups of organisms is inconsistent. A consequent application of traditional nomenclature on phylogenetic (cladistic) results is
therefore unfeasible: For instance, the traditional allocation of the ‘class’ rank to reptiles would require combining all birds, which are phylogenetically
only a subset of reptiles, within one genus. Another example of this phenomenon is found in the botanical nomenclature, where taxa from different
cladistic levels are assigned to the same level of nomenclatural clade or sub-clade. In zoology, unlike in botany and mycology, suffixes only relate up to
the rank of the superfamily
244 Megasystematics
4.1.1.7
Cladograms and phylograms

Reconstructing a phylogenetic tree requires data reflect- attribute, with the number of necessary character changes
ing the phylogenetic evolution of organisms. Earlier analy- (mutations) minimised during the calculation of the tree.
ses focused on morphological data for phylogenies but, with Resulting trees can be distinguished as being either clad-
the rise of molecular techniques such as PCR and sequenc- ograms or phylograms.
ing, these have largely been replaced by DNA and protein Cladograms emphasise the branching pattern (topology)
sequences. of relationships between taxa ignoring branch lengths. Clad-
In order to calculate a molecular phylogenetic tree, ho- ograms are thus used primarily for comparing the topology
mologous nucleotides or protein sequences are initially of different phylogenetic trees.
placed in a matrix, is commonly known as an alignment. A phylogram, on the other hand, also reflects molecular
A variety of standard strategies can then be applied to the distance between taxa, measured as substitutions and shown
alignment, grouped either as distance- or character-based in the length of individual branches. Phylograms (metric
methods. tree) and their branch length show a quantitative represen-
Distance-based methods determine distance between in- tation of taxonomic relationships, reflecting phylogenetic
dividual pairs of taxa. From these pairwise data, a tree is change over time. They are the most commonly used method
constructed with branching patterns corresponding to the of molecular sequence analysis.
observed distances. Phylogenetic trees are considered rooted (outgroup) or
Character-based methods incorporate the average dis- unrooted (no outgroup), depending on whether the analysis
tance between taxa as well as the distinct expression of each includes an outgroup or not.
Distance-based methods are carried out using a distance Character-based methods include maximum parsimony
matrix of sequences, where pairwise differences (distances) (MP) and maximum likelihood (ML). MP is based on the
between individual sequences are calculated. The two spe- principle of parsimony, which states that evolution is more
cies with the least number of differences form a subtree likely to take the shortest path, thus producing the most eco-
which is added to the analysis. The matrix (table) provides nomical tree. In practice, this method involves the calcula-
data both for the topology of the branches and their length. tion of multiple trees, with the tree featuring the minimum
Distance-based procedures include UPGMA (unweighted total length (sum of all evolutionary steps) serving as the
pair group method with arithmetic mean) and neighbour- selected final topology. ML trees, on the other hand, calcu-
joining methods. UPGMA clustering is a simple method, late the probability of determining each tree according to the
assuming that all species evolve at the same constant rate. observed data, selecting the tree with the highest probability
Neighbour-joining methods, on the other hand, are based on value according to the particular model of evolution.
the strategy of ‘minimum evolution’, and account for differ-
ences in the speed of evolutionary change.
Polymerase Chain Reaction (PCR): laboratory technique used

to make multiple copies of a segment of DNA
See also: DNA: 2.2.1.2; Phylogenetic trees: 4.1.1.6

Example illustration of the iterative inclusion of taxa, as observed in a neighbour-joining tree

Neighbour-joining is a distance-based method focusing on the mutual similarity of sequences (bottom-up approach). The two most closely related se-
quences within a distance matrix are first summarised as a branch on a tree. A new dataset is then calculated based on the initial comparison and the
process is subsequently repeated until all the sequences or taxa are included. The procedure is relatively rapid and is based on the assumption that no
unknown intermediate steps take place. In contrast, maximum parsimony methods compare a number of trees and select the one featuring the small-
est number of evolutionary steps as the most likely. Such trees are calculated according to the criterion of parsimony (frugality). Trees are calculated
in a similar way using maximum likelihood or Bayesian inference methods; these strategies, although commonly used, assign greater importance to
evolutionary assumptions
Unrooted trees are often presented as radial trees in or-

der to avoid the (wrong) impression that taxa placed at
the outside are outgroups. However, in principle, radial
trees provide the same information as the normal ‘rec-
tangular’ trees. Therefore, both cladograms and phylo-
grams can be displayed as radial trees
lla sp.
Selagine
Oryza sp. Col
eoc
hae
ta s
p.
p.
Zea sp. ella s
hyscomitr
P
Physcomitrella sp.
p . Zea sp.
ium s
Or
rmid
lebso
yza
Selaginella sp. K
sp.
Coleochaeta sp.
Klebsormidium sp.
Chlorella sp. .
sp
a
ell
yxa sp.
r
lo
Coccomyxa sp. Ch
Coccom
Nitrosococcus halophilus
Nit
Nitrosococcus halophilus
ros
oco
Nitrosococcus watsoni
ccu
sw
ats
on
i
Only the topology of the tree, its branching pattern, is

important on cladograms. Cladograms are often used
as intermediate steps in phylogenetic analyses, used to Branch length on phylograms indicates the strength of a
compare different variations of trees phylogenetic relationship
246 Megasystematics
4.1.1.8
Molecular diversity of the eukaryotic supergroups

The molecular diversity of eukaryotes is much greater tion each group has received rather than the number of spe-
than that suggested by the diversity of ‘higher-level’ organ- cies belonging to that group as it currently exists in nature.
isms. Estimates of biodiversity typically rely on the diversity The molecular diversity within each organismal group is
of animals (Metazoa) and terrestrial plants (Embryophyta), reflected by the branch length of lineages in a phylogram.
undoubtedly the most well-studied groups of organisms. The Within the Metazoa and Archaeplastida (land plants as
relative natural diversity of each organismal group is gener- well as the green algae, red algae, and Glaucocystophyta),
ally assumed by the number of known species. However, this this diversity is relatively low. The diversity of Amoebozoa,
methodology largely reflects the systematic-taxonomic atten- Rhizaria, Excavata, and the Chromalveolata is often consid-
erably higher.
The easiest way of estimating the degree of evolutionary fers in protein-coding regions: exchanges resulting in triplets
change between two species is to count the number of differ- coding for different amino acids are less likely.
ing nucleotides. However, it is possible that a single nucleo- Various substitution models were developed to take into
tide is polysubstituted; in other words, substituted multiple account the varying likelihood of exchange, thus modelling
times. Since simply counting a polysubstituted nucleotide as the course of DNA sequence evolution. Over time, with
just one substitution leads to an underestimation of distance, increasingly large data sets and more powerful computers,
estimates are derived for the probability of such substitutions these models became increasingly complex.
and included in the analysis. Among the best known and most frequently used mod-
A distinction is made between transitions and transver- els are the Junkes-Cantor (JC), the Kimura Two-Parameter
sions. A transition refers to the exchange of two nucleotides (K2P), and the General Time Reversible (GTR) models. JC
of the same basic chemical type (i.e. purine [A or G] or py- is the simplest model. It assumes that all substitutions are
rimidine [G or T] nucleotides). In contrast, transversions are equally likely and that the four bases have the same frequen-
the exchange of one nucleotide by a nucleotide of the other cy of occurrence. The K2P model distinguishes between
basic type (i.e. replacing a purine with a pyrimidine nucleo- transversions and transitions. The GTR model, finally, takes
tide, or vice versa). into account the relative probability of changes to each nu-
The likelihood of different transitions and transversions is cleotide.
different. In addition, the likelihood of such exchanges dif-
base triplet: a series of three bases (nucleotides) in DNA or RNA transition: point mutation in which a purine nucleotide is re-
which code for a specific, single amino acid placed by another purine, or a pyrimidine nucleotide is replaced
substitution: (Lat.: substituere = put in place of another) re- by another pyrimidine
placement, exchange transversion: point mutation in which a purine is substituted
for a pyrimidine or vice versa
See also: Phylograms: 4.1.1.7

Diversity within Metazoa: Diversity within Fungi: Diversity within Archaeplastida:
From left: Porifera, Plathelminthes, Asterozoa, From left: Nucleariidae, Zygomycota, Ascomy- From left: Glaucocystophyta, Rhodophyta, Chlo-
Mammalia cota, Basidiomycota rophyta, Streptophyta
Porifera Rhodophyta
Mammalia Nucleariidae Basidiomycota Streptophyta
Zygomycota Ascomycota Glaucocystophyta Chlorophyta

Asterozoa
Plathelminthes
Porifera: ATCGAGCCAGCGAGC Nucleariidae: ACGAAGTCAGCGAGT Glaucocystophyta: ACGAATTCAACGAGT

Plathelminthes: ACGGTATCAGCGAGT Zygomycota: ACGAAGTCAGCAAGT Rhodophyta: ATGCATTCAACGAGT
Asterozoa: AAGGGATCAGCGGGT Ascomycota: ACAGAGCCAACGAGT Chlorophyta: TTGCATTCAACGAGC
Mammalia: ACTGGCTCAGCGTGT Basidiomycota: ACAGAGCCAGCGAGT Streptophyta: ATGTATTCAACGAGT
The diversity among groups within the ‘visible biodiversity’ (top: Metazoa, Fungi, and Archaeplastida) is comparatively low compared to the diversity
observed in protist groups (bottom: Amoebozoa, Rhizaria, Excavata, Alveolata, Stramenopiles)
Diversity within Amoebozoa: Diversity within Rhizaria: Diversity within Excavata:
From left: Centramoebida, Flabellinia, Arcelli- From left: Cercomonadida, Vampyrellida, Fo- From left: Jakobida, Heterolobosea, Prokineto-
nida, Myxogastria raminifera, Acantharia plastida, Euglenida
Heterolobosea
Prokinetoplastina
Foraminifera
Flabellinia
Centramoebida
Vampyrellida
Myxogastria Arcellinida Cercomonadida Jakobida
Acantharia
Euglenida
Centramoebida: ATACGTTCAGCAAGT Cercomonadida: ATACGTTCATCGAGT Jakobida: GTGAGCTCAACGAGC

Flabellinia: TCTGGTGCAACGAGC Vampyrellida: ATGCAGTCAATAAGT Heterolobosea: ACGGTACCAGCGAGC
Arcellinida: ACGATTGCAACGAGT Foraminifera: GAACTCGCACCGAGT Prokinetoplastida: ACAAAGTGAATGAGT
Myxogastria: ATAAAGTCAACGAGT Acantharia: GTGTTTTCAACAAGC Euglenida: TCACAGTGAAGGTGT
Diversity within Alveolata: Diversity within Stramenopiles: Phylogenetic distance is a measure of the diver-
sity of organisms. Branch length is proportional
to the differences between species. The trees
shown are based on the sequences coding for
From left: Ciliophora, Dinoflagellata, Chromerida, From left: Bicosoecida, Phaeophyceae, Bacillari- the RNA of the small subunit of ribosomes (SSU
Apicomplexa ophyceae, Chrysophyceae rRNA). The size of each circle indicates the mo-
lecular diversity within each group.
Excerpts from the alignment (bottom of each
box) show differences at the individual nucleo-
tide level; identical bases in the sequences within
Chromerida each group of organisms are highlighted in blue
Dinoflagellata
Chrysophyceae Bicosoecida and the differences are shown in white
Ciliophora
Bacillariophyceae Phaeophyceae
Apicomplexa
Ciliophora: ACACGTTCAGCGAGT Bicosoecida: ACTGGTTCAACGAGT For the sake of clarity, illustrations show only
Dinoflagellata: ATACGTGCAACAAGT Phaeophyceae: ATGCATTCAACGAGT large taxonomic groups, although the analysis
Chromerida: ATGCAGTCAGCGAGT Bacillariophyceae: ATGCATTCAACGAGT was based on sequences from individual species
Apicomplexa: ATATGTATAACGAGT Chrysophyceae: ACATACGCAACGAGT
248 Megasystematics
4.1.2
The three domains

Living things can be classified in a number of ways. In However, the Achaea also have unique characteristics.
earlier work, life was divided into eukaryotes and prokary- For example, their membrane lipids are comprised of iso-
otes according to visible differences in the organisation of prenoids whereas those of the Bacteria and Eukaryota are
the cell. In the 1990s, Carl Woese proposed the domain mainly composed of ester-linked fatty acids.
model, dividing life into the domains Archaea, Bacteria, and Controversy still lingers regarding whether differences in
Eukarya. This classification is based on genetic differences, cell organisation between prokaryotes and eukaryotes are
especially within the ribosomal RNA region. more fundamental than gene sequence differences between
The Archaea share many properties with Bacteria: they the two. Perspectives differ as to: 1) the relative importance
both have a prokaryotic cell organisation, with 70S-ribo- of the evolution of sequences compared with that of the
somes and a circular chromosome (in most taxa, just one). cell’s internal organisation, and, 2) assumptions about the
In contrast, eukaryotes have a eukaryotic cell structure, with timing of sequence evolution in different groups of organ-
clearly visible internal compartmentalisation of organelles isms. Genome sequences of various organisms increasingly
and several linear chromosomes arranged within a mem- suggest that genes and genomes are able to transfer between
brane-bound nucleus. organisms – including between those belonging to different
The Archaea also share some characteristics with Eukar- domains. Such evidence indicates that, rather than being
yota, including the presence of introns within their genes. In split into domains, life may be linked within a larger web of
addition, archaean RNA polymerase and transcription fac- life, with strong links between very different groups. How-
tors are the same type as those of the Eukaryota and differ ever, the three-domain model remains the currently favoured
markedly from bacterial equivalents. viewpoint of the fundamental taxonomic relationships of
life.
The three-domain model is now widely accepted. Howev- example, requires proteins and genes that are able to tolerate
er, it remains controversial, especially regarding the relation- high temperatures. According to this view, therefore, the Ar-
ship between Bacteria and Archaea, specifically the origin of chaea may have developed as a rapidly evolving side-branch
Archaea, and the origin of eukaryotes. of the Actinobacteria. This argument, together with the sig-
Assuming a uniform speed of sequence evolution (muta- nificant differences in cell organisation between eukaryotes
tions over time), differences in gene sequences should indi- and prokaryotes, supports the basic classification of life into
cate phylogenetic distance; thus, a larger number of sequence prokaryotes and eukaryotes.
differences indicate an earlier divergence between lineages. A growing body of work supports an alternative hypoth-
This notion supports a relatively early separation of domains esies, starting that eukaryotes originated from Archaea (the
and the three-domain model. In contrast, some researchers Eocyte hypothesis). If confirmed, this viewpoint would con-
propose a theory of accelerated sequence evolution in the tradict the three-domain model, since following the Eocyte
ancestors of Archaea in the context of adaptation to extreme hypothesis Archaea and Eukarya would have a common
habitats. This assumption is not necessarily unlikely since origin.
the colonisation of extreme environments – hot springs, for
adaptation: the process of adapting ribosome: protein/rRNA complexes which enable protein syn-
compartmentalisation: (Lat.: compartere = to divide) division thesis
into separate, closed spaces RNA polymerase: enzyme which acts as a catalyst in the syn-
isoprenoids: natural compounds arising from isoprenes (2-me- thesis of RNA (ribonucleic acid)
thyl-1.3-butadiene)
See also: Origin of the eukaryotic cell: 2.2.2.5

Basics of megasystematics: the three domains 249
Electron microscope section of prokaryotic cells (Bacteria: Neisseria gon- Electron microscope section of a eukaryotic cell (Chlorophyta: Chla-
orrhoeae). An inner membrane system is absent; the cells are not com- mydomonas reinhardtii). The cell is compartmentalised by an inner mem-
partmentalised brane system
Archaea Eukarya Bacteria
The classic three-domain model showing the three sepa-

rate, early-diverging domains Archaea, Eukarya, and Bac-
teria
Archaea Eukarya Bacteria
The three-domain model taking into account of horizontal

gene transfer between domains
250 Megasystematics
4.1.2.1
Bacteria
The Bacteria are one of the three domains of life. They the Planctomycetes, Verrucomicrobia, Chlamydiae, and the
feature a typical prokaryotic cell organisation, with no endo- Lentisphaerae lack a cell wall or feature a greatly reduced
membrane system and usually just one circular chromosome structure. In contrast, the Firmicutes, Actinobacteria, and
freely arranged within the cell cytoplasm; genes usually con- representatives of the Deinococcus-Thermus group are char-
tain no introns and ribosomes are of the 70S type. acterised by a thick cell wall, making it easier to stain these
The diversity of metabolic pathways in bacteria is high taxa with a Gram stain. Two of these – the Firmicutes and
and many pathways are found in a number of different, often Actinobacteria – as well as Chloroflexi, are only surrounded
unrelated lineages. For example, oxygenic photosynthesis is by one membrane.
found only in the cyanobacteria whereas anoxygenic photo- Bacteria can be separated into two large kinship groups
synthesis is found in a number of loosely related lineages, (here referred to as the ‘Terrabacteria’ and ‘Hydrobacteria’),
such as within Chloroflexi, Firmicutes, the Proteobacteria, as well as a series of basal branching lines. The plastids found
and Chlorobi. in eukaryotes can be traced back to cyanobacteria and their
Bacterial cells are usually surrounded by two membranes, mitochondria can be traced back to α-proteobacteria related
separated by a cell wall made of peptidoglycans. In some lin- to Rickettsia.
eages, the cell wall is less prominent or absent; for example,
Most basal lineages within the Bacteria, collectively re- phytosynthesis. The closest living relatives of the eukaryotic
ferred to as the basal Thermophiles, are thermophilic and mitochondria are α-proteobacteria related to Rickettsia spp.
anaerobic. These possess a number of genes picked up from (causative agent of typhus (Rickettsia prowazekii) and Rocky
Archaea via horizontal gene transfer. Mountain spotted fever (Rickettsia rickettsii)). Planctomycet-
The ‘terrabacteria’ comprise the cyanobacteria (capable es, Verrucomicrobia, Chlamydiae, and Lentisphaerae also
of oxidative photosynthesis), the ‘Gram positive’ Firmicutes group together within hydrobacteria, a lineage characterised
and Actinobacteria (multi-layered peptidoglycan, which col- by intracellular compartmentalisation.
oured by the Gram stain), the Nitrospira, Chloroflexi, and The planctomycetes possess a nucleoid with a double
the heat- or radiation-tolerant Deinococcus-Thermus group. membrane, similar to the nuclear membrane found in Eu-
The ‘hydrobacteria’ comprise lineages from the large and karyota. Similarly, they also carry out endocytosis mecha-
diverse proteobacteria group, which are typical Gram-nega- nisms and have one protein-rich S-layer (surface layer) but no
tive bacteria. Their diversity is enormous, including anaero- peptidoglycan in their cell walls. The Chlamydia have little
bic and aerobic taxa, with some lineages capable of anoxic or no peptidoglycan in their cell walls.
aerobe: (Grk.: aer = air, bios = life) processes or organisms re- mesophilic: preferring moderate conditions (mostly in respect
quiring an oxygenated environment to temperature and humidity)
anaerobe: (Grk.: an = not, aer = air, bios = life) processes or obligatory: necessary, essential
organisms which can survive without molecular oxygen S-layer: layer of paracrystalline protein lining the cell wall in
anoxygenic: producing no molecular oxygen many prokaryotes
intron: uncoded genetic sequence lying between two encoded thermophile: preferring relatively warm temperatures, i.e. be-
genetic sequences (= exons) tween 45–80 °C; hyperthermophiles prefer temperatures over
80 °C
See also: Bacterial flagellum: 4.2; Holomycota: 4.2.2 and following; Peptidoglycan: 4.4.1
The Cyanobacteria (left: Gymnosphaeria sp.; right: Phormidium The proteobacteria are one of the largest bacterial groups. The genus Rick-
splendidum) are capable of oxygenic photosynthesis ettsia is particularly important for the understanding of eukaryotic evolution,
since it comprises the closest living relatives to mitochondria (left: R. rickettsii
The Chloroflexi (green non-sulphuric bacteria) are thermophil- in tissues; centre and right: R. parkeri in tissue, with the characteristic slime
ic. They only have one cell membrane, the photosystems are layer around the cell wall at the far right)
localised within the membrane-associated chlorosomes
The Actinobacteria and Firmicutes are gram-positive; The Chlorobi (green sulphur bacteria) include obligate an-
their cell walls are thicker than those of Gram-nega- aerobic phototrophic bacteria
tive bacteria. However, they are surrounded by just
one cell membrane
'Hydr
oba
cte
ria
'
'
ria
te
ac
Deferribacteres
Chrysiogenetes
mo g
no ram+
rab
In these groups, the

Fusobacteria
ia
acteria
de Pr
icrob
s
'Ter
rm ot cell wall is strongly

ete
mo gram eo
ba reduced or absent
cha
nod
Elusim
+
Acidob
cte
Ten
erm
Cy
ria
r
eri
mon
an
Sp i
oder α β
ob
cut ia
m Fir γ
ac
tes
es
Acti m
te
nob icute ide

δ
r
ro
act s cte
ε
Chlo er
rofl ia Ba orobi e
exi Chl sphaera
Nitrospira Lenti diae
Chlamy ia
gram+
Deinococcus Verrucomicrob
Planctomycetes
Thermus Gemmatimonadetes
Fibrobact
The Deinococcus-Thermus group includes thermophilic eres
Aquifi
bacteria (Thermus spp.) and the radiation-resistant Eukarya cae
Cald
Deinococci. The bacteria within this group possess a iser
Archaea Syn icia
thickened cell wall (similar to the Gram-positives) with erg
two cell membranes (similar to the Gram-negative bac- ist
Th cte
ete
er ria
teria). The Deinococci have a very efficient DNA repair s

ba
m
Th
od
system, which makes them resistant to ionising radia-

erm
es
tion. In phylogenetic trees based solely on 16S rRNA

ul
fo
oto
sequences, this group forms a deep-branching lineage

-
gae
earl
i er
bra
predominantly mesophilic taxa

n
predominantly thermophilic taxa

c hin
mesophilic and thermophilic taxa

lin g
predominantly aerobic taxa

ea
predominantly anaerobic taxa

ge
s
aerobic and anaerobic taxa

taxa able to carry out anoxygenic photosynthesis
taxa able to carry out oxygenic photosynthesis
252 Megasystematics
4.1.2.2
Archaea
Alongside the Eukarya and Bacteria, the Archaea are one S-layer can achieve a stability which is comparable in func-
of the three domains of life. Inhabiting all terrestrial and tion to a true cell wall. tRNA molecules of Archaea usually
aquatic habitats, the Archaea have a prokaryotic cell struc- have modified bases, especially archaeosine – a modification
ture, with an unbound circular chromosome located in the of guanosine – found in most archaeal species.
cytoplasm and 70S ribosomes. In contrast with bacteria, the Archaeal genomes are highly recombined by horizontal
Archaea do not contain any known pathogenetic taxa. gene transfer, an important factor in complicating phylo-
Cell membranes contain ether-bound isoprenoids. Ar- genetic reconstruction of this domain. In addition, the se-
chaeal cell walls do not contain peptidoglycan but, rather, are quences of basal archaeal groups differ so markedly from
made of pseudopeptidoglycan (Methanobacteriales, Metha- each other that standard molecular primers cannot be used
nopyrales) or the cell wall is entirely missing and replaced by to detect all Archaea; as a result, their molecular diversity is
one S-layer (surface layer) of glycoproteins or proteins, such grossly under-represented in the literature.
as those found in some Crnearchaeota. By cross-linking, the
The Archaea comprise two large phyla, the Crenarchae- bacteria and using bacterial metabolic products as a substrate
ota and the Euryarchaeota, as well as several basal lineages. for methanogenesis. The Nanoarchaeota were the first to be
The Crenarchaeota are thermophilic and sulphur-depend- identified microscopically, although the molecular analysis
ent whereas the Thaumarchaeota are mainly comprised of of this group was initially not possible because their DNA se-
mesophilic, aerobic, ammonium-oxidising species. The spe- quences varied so strongly from known sequences that stand-
cies Caldiarchaeum subterraneum is genetically so different ard PCR sequence primers could not bind to them. Their
from other Archaea that the separate lineage ‘Aigarchaeota’ phylogenetic relation to other Archaea could only be eluci-
has been proposed for it. The Korarchaeota include thermo- dated using large-scale gene sequencing techniques. The only
philic, anaerobic taxa, mostly inhabiting hydrothermal vents. formally described species of Nanoarchaeota, Nanoarchaeum
The Thaumarchaeota, the Aigarchaeota, the Crenarachaeo- equitans, has a strongly reduced genome and depends on vari-
ta, and the Korachaeota are together known as the TACK- ous metabolic products of other organisms. It is likely that
Archaea. its traits apply to all members of the Nanoarcheota, namely,
The Euryarchaeota include both mesophilic, thermophil- living in association with other Archaea, a likely previously
ic and psychrophilic taxa, including acidophiles, alkaliphi- parasitic relationship which was fundamental to the reduc-
les, and halophiles. The methanogenic Archaea are also in- tion of its genome and presumably preceded the divergence
cluded within the Euryarchaeota, living in associating with into different marine and terrestrial lineages.
acidophile: preferring low pH conditions psychrophilic: preferring low temperatures (from –20 °C to
alkaliphile: preferring high pH conditions 10 °C)
halophile: preferring high salt concentrations thermophile: preferring relatively warm temperatures, i.e. be-
isoprenoids: natural compounds arising from isoprenes (2-me- tween 45–80 °C; hyperthermophiles prefer temperatures over
thyl-1.3-butadiene) 80 °C
mesophilic: preferring moderate conditions (mostly in respect
to temperature and humidity)
See also: Origin of Eukaryotes: 2.2.2.5; Long-term global warming and extremophiles: 2.3.5.8
The Euryarchaeota include methanogenic, halophilic, and thermophilic The Crenarchaeota mainly comprise thermophilic and acidothermo-
taxa. The methanogenic Euryarchaeota produce methane and are of- phile taxa. They are commonly found in the terrestrial hydrothermal
ten found in the digestive tract of various Metazoa. The Halobacteri- fields around sulphur springs
ales (top: Halobacterium salinarium) live aerobically or anaerobically in
nearly or completely saturated salt solutions. The Thermoplasmatales
are acidophilic; most of them lack cell walls
a
ot Cr
ae
rch
en
ar
rya
ch
inale
Eu
Halobacteriales
ae
s
iale
arac
o
ta
ob
Ara
anos
mir
Th
che
er
no
m
ogl
Meth
op
tha
les
la
ob
ba
sm
Me
The s
us
e
cal
lo
at
rm
lfo
oc
al
oco
oc
es
Su
cca fur
les sul
De s
teale
Methano mopro
pyrales Ther
Thaumarchaeota
Methanobacteriales
Thaumarchaeota
ales
occ
noc
tha Eukarya
Me Bacteria Kor
arch
a eot
eota a
ha
arc
no
Na
Kora
rc h
predominantly mesophilic taxa

ta
aeo
ae o
predominantly thermophilic taxa

ta
mesophilic and thermophilic taxa

a rch
predominantly aerobic taxa

no
predominantly anaerobic taxa

Na
aerobic and anaerobic taxa

methanogenic taxa
The Korachaeota and Nanoarchaeota comprise thermophilic taxa. Whereas diversity is

relatively low in the Korachaeota, the Nanoarchaeota include only the type species Nano-
archaeum equitans. The phylogenetic position of both groups remains unresolved. How-
ever, based on archaeal 16S rRNA sequences, these taxa belong to their own phyla. The
Thaumarchaeoata (here: Nitrososphaera viennensis) are widespread in marine habitats
but likely also play a role in other mesophilic areas
254 Megasystematics
4.1.2.3
Eukarya
The domain Eukarya comprises the Unikonta (=Amor- comprise all land plants. Secondary plastids are surround-
phea), which includes animals and fungi, the Archaeplasti- ed by three or four membranes. The secondary plastids of
da, which includes plants, as well as the Excavata, Rhizaria, Alveolata, Stramenopiles, and Hacrobia are the product of
Alveolata, Stramenopiles, and Hacrobia. the endocytobiosis of a red algae (Rhodophyta) and possess
The eukaryotic cell is characterised by the presence of chlorophyll a and c (shown in red in the figure). The sec-
organelles, although the presence of these differs by line- ondary plastids of Euglenozoa and Chlorarchinophyta come
age. All eukaryotes possess either mitochondria or reduced from the endocytobiosis of a green algae and possess chloro-
modifications of such organelles. Plastids are only found in phyll a and b (shown in green).
some lineages, but these are not necessarily closely related to Some organisms possess organelles that have shared
each other, and the structure of these plastids differs between origins with mitochondria or plastids but that have been
groups. reduced to possess only a few metabolic pathways, for ex-
Plastids can be divided into two categories. Primary plas- ample, the apicoplast of the malaria parasite Plasmodium
tids are surrounded by two membranes and contain either (Apicomplexa). This secondary plastid is no longer capable
chlorophyll a or chlorophyll a and b. They are found in the of photosynthesis but still performs other essential metabolic
Archaeplastida, i.e. the Glaucocystophyta, the Rhodophyta, pathways, such as the biosynthesis of fatty acids.
the Chlorophyta, and the Streptophyta. The Streptophyta
In addition to the secondary plastids derived from red al- phores, which are double-membrane-bound organelles. Al-
gae, which are common in alveolates, some dinoflagellates though these resemble primary plastids, they can be traced
possess secondary plastids derived from green algae. Some back to independent endocytobiotic events. The genus there-
dinoflagellates even feature tertiary plastids, which originate fore displays the only known case of independent primary
from the endocytobiosis of other algae (Bacillariophyta, endocytobiosis.
Cryptophyta, Haptophyta). Plastids are the only known secondary and tertiary orga-
All plastids, including secondary and tertiary, can be nelles, since all mitochondria can be traced back to a single
traced back phylogenetically to a common ancestor. This primary endocytobiotic event. Mitochondria are absent in
seems at odds with the spread of plastids across a broad some eukaryotes, which instead possess hydrogenosomes
range of eukaryotic lineages. The distribution of plastids or mitosomes. The hydrogenosome enables ATP synthesis
across the eukaryotes is the result of multiple independent (energy production) under anaerobic conditions. Mitochon-
transfers between large lineages, a phenomenon that also ex- dria, however, can only carry out respiration in aerobic con-
plains the different membrane structures and pigmentation ditions. Mitosomes, in contrast, do not produce energy, but,
conditions. similar to mitochondria and hydrogenosomes, they remain
The genus Paulinella, affiliated with the Cercozoa, is important for the synthesis of iron-sulphur cluster proteins.
unique because members of this group contain chromato-
endocytobiosis: the term given to the absorption of prokary- organelle: a structurally distinct subunit within a cell with a spe-
otes by eukaryotic cells and their subsequent evolution into orga- cialised function; strictly speaking, an organelle is a cell compart-
nelles. This term is more precise than endosymbiosis because, in ment which is surrounded by a membrane formed from prokary-
the case of organelles, they are no longer independent organisms otes in a process of endocytobiosis: this narrower definition only
and therefore do not conform to the definition of symbiosis as includes plastids and mitochondria
being the association of cells of different species
See also: Hydrogenosom: 4.3.1

The plastids of Glaucocystophyta and Paulinella The plastids of Chlorarachniophyta and the Cryp-
have a peptidoglycan layer between their two tophyta have a nucleomorph between their in-
plastid membranes. Since peptidoglycan also a ner and outer plastid membranes. The nucleo-
component of bacterial cell walls, it is considered morph is a relic of the nucleus from an ingested
a relic of endocytobiosis eukaryotic algae, gained through secondary en-
docytobiosis
a
e p lastid Rhiz
aria
cha
Ar
ta
ella
hy
iop
aulin
Al
hn
era
rac
veo
nur P
inif
ora
ram
lata
h l
C
o
Streptop yta
F
ta
and
Chlo
Rhodophyta
Excava
ria
ea
roph ystop
Cercozoa
Gla
a
tin
hyta
Pe
t
ys
uc
rc
Aca
lyc
ol
oc
a
Eu oz ex
o
pl
P
o
or
gle
nid a
ph
m
a ico
lio
hy
Kineto
Ap merida
Ci
plastid
ta
a Chro
Jakobida Dinophyta
Parabasalia Bicosoecida
Peronospor
onada Bacilla omycetes
Diplom Ph riophycea
Op
La ida
Ch ae e
ali
by
rys op
Ha
oa
n
Apusoz a
rin
op hyc
pt
Cry
hy ea
th
s
Conoa
op
ce e
uli
pto
ae
hy
ose
da
ta
Lob onada
phy
piles
m a
ta
ano azo
Cho Met
i
ng
eno
Fu
am
Archaea
Str
Un
Bacteria
iko
a
nt
ia
crob
Ha
Mitochondria and plastids arose through the endocytobiosis of eubacteria. As a
result, genetic material is found not only in the eukaryotic nucleus but also in
some organelles. The genome of eukaryotes therefore contains a portion encoded
in the nucleus (the nucleome), the mitochondrion (the chondrome), and in the
plastids (the plastome). The overall genome of eukaryotes can therefore be traced
back to a number of different organisms; it is therefore a chimeric genome The outer plastid membrane of Haptophyta,
Cryptophyta, and Stramenopiles contains ribo-
somes. It forms a continuum with the nuclear
Organelles and their modifications:
membrane and endoplasmic reticulum. These
structures are therefore referred to as the chlo-
roplast endoplasmic reticulum (CER)
mitochondrion mitosome hydrogenosome primary plastid secondary plastid
256 Megasystematics
4.1.2.4
Eukarya: Cellular structures
hydrogenosome
mitochondria
mitosome
cell wall (outer membrane) energy storage poly-
flagellation plastids
material saccharide
nucleomorph
membranes
chlorophyll
secondary
primary
tertiary
accessory
CER
pigments
Unikonta (= Amorphea)
Apusozoa x glycogen bikont
extracellular matrix or lorica
Choanomonada of cellulose or silica
x glycogen unikont
Metazoa x x glycogen unikont

Microsporidia chitin x unflagellated
Chytridiomycota chitin x x glycogen unikont gametes
Zygomycota chitin x glycogen unflagellated
Glomeromycota chitin x glycogen unflagellated
Ascomycota chitin and β-glucan x glycogen unflagellated
Basidiomycota chitin x glycogen unflagellated
Tubulinea and
x glycogen unflagellated
Discosea
Conosa x x glycogen unflagellated to many
Archaeplastida x
starch phycobillins:
Glaucophyta cellulose x (extra-plastid in bikont x a phycocyanin 2
cytoplasm) allophycocyanin
floridean starch phycobillins:

Rhodophyta cellulose x (plastid surface or unflagellated x a phycocyanin 2
cytosol) phycoerythrin
starch a
Chlorophyta cellulose x
(in plastids)
bikont x
b
carotinoids 2
starch a
Streptophyta cellulose x
(in plastids)
bikont x
b
carotinoids 2
Excavata
Percolozoa x x unflagellated to many
Jakobida x bikont
Fornicata x x x glycogen mostly four or eight
Parabasalia x glycogen none, four, or eight
Preaxostyla glycogen four
β-carotene,
paramylon a neoxanthin,
Euglenida pellicle x
(extra-plastid)
bikont G
b diadinoxanthin,
3
xanthophyll
Kinetoplastea x mannan bikont, some unikont
Overview of the cellular structures of eukaryotic organisms: These figures are only a rough guide, as a number of different characteristics can often be
found across many taxonomic groups. In addition, the specified flagellation is often pronounced only in certain life cycle generations or stages of develop-
ment. CER: chloroplast endoplasmic reticulum; R (secondary and tertiary plastids): plastids that can be traced back to red algal origins; G (secondary and
tertiary plastids): plastids that can be traced back to green algal origins; x: present (in some cases but only in some taxa of each group)
chrysolaminarin: a storage polysaccharide found in strameno- paramylon: a storage polysaccharide in Euglenida and Hapto-
philes; β 1-3- and β 1-6-glycosidic bonds phyta. In contrast to starch in plants and red algae, paramylon is
glycogen: reserve polysaccharide in unikonts; linked by α (1- made from β 1,3-glucan
3) and α (1-6) glycosidic bonds; similar to but more extensively starch: reserve polysaccharide in Archaeplastida and Alveolates;
branched than starch α (1-3) and α (1-6) glycosidic bonds; similar to but less branched
mannan: β (1-4) linkages than glycogen
hydrogenosom
mitochondria
mItosome
cell wall (outer membrane) energy storage
flagellation plastids
material polysaccharide
nucleomorph
membranes
chlorophyll
secondary
primary
tertiary
accessory
CER
pigments
‘Core-Chromalveolata’ (Alveolata and Stramenopiles)
Ciliophora alveoli x x starch many cilia
a,c 3/
Dinophyta alveoli with cellulose plates x bikont R R
a,b
fucoxanthin, peridinin
4
Apicomplexa alveoli x x starch unflagellated R 4
Chromerida x bikont R a isofucoxanthin 4
Bicosoecida x bikont
Labyrinthulida polysaccharides x bikont
Opalinida x many cilia

cellulose and hemicellulose,
bikont
Peronosporomycetes also chitin in the Leptomi- x β-glucan
zoospores
tales group
cell wall mostly made of bikont a
Bacillariophyceae silicium oxide
x chrysolaminarin
gametes
R
c
fucoxanthin 4 x
scales of silicate or cell wall β-carotene, fucoxanthin,

a
Chrysophyceae of cellulose, lorica of chitin x chrysolaminarin bikont R
c
violaxanthin, anthaxan- 4 x
or silicate thin, neoxanthin
β-carotene, fucoxanthin,
bikont a
Phaeophyceae cellulose, alginic acid x chrysolaminarin
gametes
R
c
diadinoxanthin, diatox- 4 x
anthin
Hacrobia
starch phycobilins: phyco-
a
Cryptophyta periplast x (in periplasmic bikont R
c
erythrin, phycocyanin, 4 x x
space) α-carotene
scales of polysaccharides,
mostly cellulose, in the
fucoxanthin, β-carotene,
order Coccolithophorales chrysolaminarin, a
Haptophyta the scales are calcareous
x
rarely paramylon
bikont R
c
diadinoxanthin, diatox- 4 x
anthin
(coccoliths), Phaeocystis
contains chitinous filaments
Rhizaria
Cercozoa (excluding
Chlorarachniophyta x bikont
and Paulinella)
β-carotene, xanthophylls
unikont a (neoxanthin, violaxan-
Chlorarachniophyta naked x paramylon
zoospores
G
b thin, lutein, loroxanthin-
4 x x
dodecanoat)
Paulinella x a 2
calcium carbonate or silicate bikont

Foraminifera cell skeleton
x
gametes
258 Megasystematics
4.2
Unikonta (= Amorphea)
The Unikonta (unikonts) are an exclusively heterotrophic secondarily reduced to the point that most Amoebozoa
group of organisms. Unikonts comprise the Opisthokonta appear not to have any flagella at all. An exception are slime
(opisthokonts), Amoebozoa, and the likely paraphyletic mould gametes, which have two flagella.
Apusozoa. Plastids are not found in any unikont species, Apusozoa are unicellular bikonts, having two flagella
though they may temporarily use plastids when some and living in terrestrial and aquatic habitats on the sediment
representatives live in close symbiosis with algae (corals, surface. The Apusomonadida, Planomonadida, and Manta-
sponges, for example) or temporarily after plastids are monadida make up the Apusozoa. The phylogenetic
ingested. relationship of these groups with each other and their
Ophistokonts are characterised by their posterior facing possible affiliation with the Hemimastigida is unclear. It is
flagellum (Grk: ophisto = posterior; kontos = pole, i.e. therefore possible that the Apusozoa are paraphyletic.
flagellum). The group is composed of the Holozoa, which Due to its variety of constituent bikont taxa, the Unikonta,
includes Eumetazoa (‘animals’ in the narrowest sense), named for the number of flagella each cell displays, are
Porifera, Choanomonada, and also Holomycota, which sometimes called the Amorphea, a name referring to the
includes chitinous fungi (Basidiomycota, Ascomycota, cells of most taxa in this cluster not having a fixed form
Chytridiomycota, Mucoromycotina), Microsporidia, and unless restricted by an external layer (e.g. cell wall, lorica,
Nucleariida. test, extracellular matrix).
In contrast with Opisthokonta, Amoebozoa are
characterised by a forward facing flagellum, in many cases
Unikonts usually have only one flagellum whereas other steps of the synthesis are the catalysis of the enzyme car-
eukaryotes generally have two (bikont). This characteristic bamoyl phosphate-synthase II, aspartate-transcarbamylase,
difference can be found throughout most unikonts (for ex- and dihydroorotase. In unikonts, the genes for these three
ample, sperm in Metazoa), although it is likely that they too enzymes are fused into one. Based on the three first letters
were originally biflagellate. The biflagellate Apusozoa and of these constituent enzymes, this fusion is known as the
the gametes of slime moulds (Amoebozoa), as well as the ‘CAD triple-gene fusion’. CAD is transcribed into one con-
presence of a second kinetosome in some unikonts, such as tinuous mRNA transcript. Upon translation, the gene prod-
choanoflagellates and flagellated metazoan cells, are often uct is a contiguous protein with three functions. In contrast
used as examples of the biflagellate origins of unikonts. with CAD, the unikonts have separate genes for the enzymes
Unikonts share a common molecular characteristic relat- thymidylate synthase and dihydrofolate reductase, while in
ing to the synthesis of uridine monophosphate: the first three other eukaryotes these genes are fused.
dynein: one of the motor proteins in eukaryotic cells which ena- mRNA (messenger RNA): molecule in cells that carries a por-
bles movement of the flagella and other functionst tion of the DNA code containing information for the synthesis
flagellin: a protein used as a building block for bacterial flagella; of proteins
in contrast to eukaryotic flagella, flagellin is not associated with synthesis: (Grk.: synthesis = composition) combination of vari-
motor proteins – independent movement is therefore not pos- ous components to form a new whole
sible tubulin: a protein, the main constituent of microtubuli
microtubules: protein filaments which, together with micro- uridine monophosphate: an intermediate product in pyrimi-
filaments and intermediate filaments, serve to maintain a cell’s dine biosynthesis
structure, to facilitate intracellular transport and the cell’s ability
to move
See also: Heterotrophy: 4.6.2.3; Phylogeny, Phylogenetic trees: 4.1.1.6; Symbiosis: 4.2.2.5
Unikonta: introduction to the Unikonta /Apusozoa 259
stida Rh
pla iza
Tubulinea ae
Viridiplant ta
ria
oa
h
rc
Rh
Amoebozoa
z
G
Cerco
odo
Discosea la
uc ta
ria
op Re
phy
Chr
hy
ae
Conosea Disc ta
Excavata
oba olata
oma
Alve
Apusozoa a Stra
lveolata
monad men
Apusozoa Meta
a Ha
opile
s
zo
oa ta
o pt
eb
Cry
soz on
op
mo
k
hy
o
A
pto
Eumetazoa
is t
ta
phy
Op
Apu
Porifera
ta
Holozoa Choanomonada Eubacteria Archaea
Ophistokonta basal Holozoa
Nucleariida
Holomycota Microsporidia
Mucoromycota
Chytridiomycota
Glomeromycota
Ascomycota
Basidiomycota
mitochondrion
flagellum
(cross section) pellicula
Apusomonas proboscidea Mantamonas plastica Fabomonas tropica

The Apusozoa are a group of colourless, gliding flagellates which feed on bacteria. The phylogenetic relationships between different apusozoan orders
are not yet known. However, the Apusozoa is considered to be a basal unikont group including orders Apusomonadida (left: Apusomonas proboscidea),
Mantamonadida (middle: the only known species, type Mantamonas plastica), and Planomonadida (right: Fabomonas tropica). The electron micro-
scope (right) of Fabomonas tropica shows the hardened dorsal pellicula and mitochondrial structure typical of Apusozoa
filament central (inner)

The eukaryote flagellum is flexible. Motion of cilia and fla- microtubuli
flagellin
gella is created by the dynein-arms attached to microtu-
hook bules sliding past the neighbouring microtubule by using
the energy of ATP cleavage
dynein arm
outer membrane
L-Ring outer micro-
tubuli
P-Ring peptidoglycan
H+ Mot protein plasma membrane
Fli protein
MS-Ring flagellar base
cytoplasm membrane
C-Ring The bacterial flagellum is rigid and capable of an entire rota-
H+ tion. Protons flowing through the mot-protein result in an
electrostatic force which operates on the C-ring and the MS-
ring causing them to rotate. The rotation is regulated by the
Fli-proteins, which function as ‘motor switch’
Cilium/Flagellum
260 Megasystematics
4.2.1
Holozoa
Holozoa include the Metazoa and their basal sister groups sponse to increasing grazing pressure. With the widespread
Mesomycetozoa and Choanomonada. use of exoskeletons, the fossil record of metazoan species
The Metazoa (‘animals’ in the colloquial sense of the improved drastically: this sudden occurrence of metazoan
word) are a very diverse group of organisms: just the insects fossils from the beginning of the Cambrian is referred to as
alone comprise around one million known species, more the ‘Cambrian explosion’. However, the initial radiation of
than all other groups together. The Metazoa are also well- Metazoa must have taken place earlier, although it is hard
studied, in contrast to many other groups. to identify in the fossil record due to the absence of skeletal
The ontogenetic development and organisation of various elements. The first Metazoa were likely benthic marine or-
metazoan species differs widely; as a result, their phyloge- ganisms, their surface covered in ciliated cells, somewhat like
netic relationships are still unclear. today’s sponges.
Different metazoan lineages developed exoskeletons in
the late Precambrian and early Cambrian, likely as a re-
The Holozoa include a range of organismal groups with a Basal Metazoa include the Porifera (sponges), Ctenophora
number of differing life cycle configurations. (comb jellies), and the Placozoa (‘flat animals’). The Cnidar-
The Filasterea include unicellular free-living species and ia have traditionally also been linked to the basal metazoans.
parasitic species (which parasitise trematodes). The sponges still lack real tissue; all other Metazoa have at
The Ichthyosporea comprise unicellular species, mostly least two germ skin layers (ectoderm and endoderm) and are
fish parasites. therefore placed in Eumetazoa. The Eumetazoa are charac-
The Aphelidea include various species of intracellular terised by gap junctions between epithelial cells.
parasites of algae, whereas the Choanomonada are single- The Bilateria display bilateral symmetry (at least in the
celled colony-forming protists, that are important planktonic larval stages). All bilaterians except the cnidarians possess
bacterivores. three germ skin layers and are summarised as Triploblastica.
Metazoa have a multicellular body structure with special- While the Acoelomorpha do not possess a continuous intes-
ised cells and differentiated tissues. The adhesion and com- tinal system, the Neprhozoa (Eubilateria) are characterised
munication between adjacent cells play a special role in the by the presence of protonephridia and a continuous gut con-
organism’s functioning. Similar to choanoflagellates, many necting the mouth and anus. In Deuterostomia, the anus de-
metazoan cells possess a single flagellum. The oogenesis velops from the first body cavity, the blastopore, whereas the
and spermatogenesis (ophistokont sperm) processes also are mouth develops secondarily. In Protostomia it is the other
similar across Metazoa and Choanoflagellates. way round: the blastopore develops as a mouth and the anus
emerges secondarily.
adhesion: (Lat.: adhaesio = adhere) the way in which two cells, germ layer: in animals, the three embryonic tissue types (ec-
substances or particles cling to one another toderm, endoderm and mesoderm); in plants, cotyledons are
blastopore: embryonic mouth known as seed leaves
ectoderm: (Grk.: ektos = outside, derma = skin) the first or mesoderm: (Grk.: derma = skin) middle germ layer in embryo-
outermost germ cell layer which differentiates to form the skin, blasts; the mesoderm forms muscles, skeleton, vascular system,
nervous system and sensory organs excretive organs and part of the gonads
endoderm: (Grk.: endon = inside, derma = skin) inner germ cell protonephridia: simple excretory gland beginning with a ter-
layer which differentiates to form the respiratory system and the minal cell; a bundle of flagella create an outward current which
digestive tract leads to pressurisation which in turn removes waste fluids from
gap junctions: protein channels between the membranes of the animal
two adjacent animal cells
See also: HOX-genes: 4.2.1.3; Radiation, Mechanisms of speciation: 3.1.2, 3.2.1.2, 3.2.1.4
Unikonta: Holozoa 261
stida Rh
pla iza
basal Holozoa: Mesomycetozoa, Filasterea, Ichthyosporea, Aphelidea ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
Choanomonada oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa ta
o pt
eb
Cry
soz on
op
mo
ok
hy
basal Metazoa A
pto
st
ta
hi
phy
Op
Apu
ta
Eubacteria Archaea
Acoelomorpha
no continuous intestine
Deuterostomia
blastopore develops to the anus
Nephrozoa
continuous
intestine, mouth
and anus present,
Bilateria excretion system,
bilateral symmetry protonephridia Ecdysozoa
HOX-ParaHOX-cluster molting (ecdysis),
Triploblastica three-layered, organic
cuticula
triploblastic
Protostomia
blastopore develops to
the mouth
Spiralia
spiral cleavage,
trochophore larva
with ciliary crown
One of the major causes of mortality for all organisms is predation. To the end, one
of the most common evolutionary responses to predation is mobility: the ability to
flee from predators. However, this response relies on a motile lifestyle, common to
many metazoans and microalgae or protists. If prey species cannot flee to escape
predators, they must either accept feeding damage or develop mechanisms of pro-
tection against it, often by morphological adaptations. Many organisms are thus
able to survive despite losing body parts, demonstrated by land plants (top-right)
and sponges (top-left). Morphological protection against predation can be achieved
through an outer armour, exemplified in numerous plants and animals (middle-left:
turtle shell; middle-right: bark). Special structures, such as thorns and spines, also
serve to repel predators (bottom-left: porcupine; bottom-right: cactus). Different
groups of organisms have independently developed similar protective mechanisms.
Finally, land plants, unable to escape from predators, have developed morphologi-
cal and physiological/chemical protection mechanisms, as well as a tolerance to
feeding damage.
Protection from predation

262 Megasystematics
4.2.1.1
Choanomonada
Choanomonada (choanoflagellates) are unicellular or co- Choanoflagellates feed on bacteria and other smaller food
lonial protists, freely floating or attached to substrates in lim- particles. They are among the most important bacterivorous
nic and marine environments. There are about 150 known organisms in aquatic ecosystems. The flagellum creates a
species. Choanoflagellates have mitochondria but no plas- flow of water away from the cell, forcing a current down the
tids. They possess a single beating flagellum, which is used to cell’s sides and towards the microvilli collar. Small particles,
direct water currents away from the cell. Most other protists such as bacterial cells, are caught in the microvilli and trans-
possess two or more beating flagella, which produce a water ported towards the cell body, where they are ingested.
current towards the cell. In choanoflagellates the flagellum Some species possess an extracellular matrix or lorica
is surrounded by a characteristic collar of 30–40 microvilli, which is made of either cellulose or silica, whereas others
absent in other groups of protists. are ‘naked’. The systematic value of the lorica is unclear.
Choanoflagellates share several traits with the choano- metazoans need to be regarded as plesiomorphic (ancestral).
cytes of sponges (Porifera); the two structures are homolo- These considerations raise important questions about the
gous descending from a common origin. The systematic clas- morphology of metazoan ancestors amd about the appear-
sification of sponges and choanoflagellates and their relation ance of unikont ancestors in general. Specifically, a major
to the Metazoa was therefore a controversial and hitherto question relates to how many flagella the ancestral species
unresolved question for a long time. Molecular studies have had, i.e. whether the unikonts originally had one or two fla-
been used to decide whether sponges are simply an aggregate gella. The flagellated cells of choanoflagellates and metazo-
of colonial protists (choanoflagellates) or if they are unicel- ans have a single flagellum, whereas Apusozoa, which rep-
lular metazoans. According to these, sponges are affiliated resents a basal lineage within Unikonta, have two flagella.
with Metazoa, forming a sister group to Choanoflagellates. However, choanoflagellates and flagellated metazoan cells
However, it remains unclear whether the choanoflagellates have a second kinetosome next to the one by the flagellum.
are monophyletic or paraphyletic. It is therefore possibly that This distinct morphological trait is interpreted as an indica-
Metazoa emerged as a taxon within the choanoflagellates; tion of a second flagellum which existed but was reduced
in this case, the features common to choanoflagellates and during the course of evolution.
kinetosome: basal body of flagella; kinetosomes consist of a microvilli: membrane protrusions in cells with microfilaments
cylindrical array of microtubules; they serve as a nucleation site consisting of clusters of actin filaments
for the microtubules of flagella and cilia substrate: surface onto which sessile organisms can attach
lorica: shell-like, protective outer layer in various protists themselves
See also: Sponges: 4.2.1.2

stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a s
The choanoflagellates have one flagellum, which zo Ha
oa ta
o pt
eb
Cry
soz on
op
whirls water away from the cell. As in Metazoa, a mo
ok
A hy
pto
st
ta
second vertically standing basal body is located
hi
phy
Op
Apu
at the base of the flagellum, indicating that the
ta
ancestor of choanoflagellates and animals pos-
sessed two flagella. The flagella have a typical Eubacteria Archaea
structure of nine circularly arranged microtu-
bules surrounding two in the centre
The central flagellum is surrounded by 20–40

Monosiga ovata (top: cross-section of microvilli collar; microvilli. Water flows through these and is ‘fil-
bottom: longitudinal section through the cell body) tered’, so that food particles, such as bacteria,
are trapped and transported towards the cell
Food particles are ingested at the

base of the microvilli, where they
are taken up into food vacuoles
and shifted towards the cell inte-
rior. The food particles are digested
by enzymes in the vacuoles. Non-
digestible parts are subsequently
excreted
Some choanoflagellates have a lorica, an extra-

cellular goblet-shaped cell wall. The lorica may be
constructed of cellulose or silica
Filter-feeding organisms (left: water flea; right: flamingo) feed on prey

that is far smaller than themselves; for example, baleen whales feed on
krill, flamingos on unicellular algae, and water fleas on algae and bacteria.
Filtering organisms are able to process several different prey individuals
simultaneously, allowing them to absorb a sufficient quantity of food de-
spite the smaller size of prey organisms.
The difference in size between hunting organisms (left: copepod; right:
kestrel) and their prey is far smaller than in filter-feeders; they are usually
a maximum of ten times the size, or a maximum of about 1,000 times
heavier than their prey. For species that hunt in packs, the size difference
between each individual predator and prey is even lower. Size differences
between predator and prey vary accordingly across the variety of existing
Filter feeding: waterflea Filter feeding: flamingo
species, from protists to whales.
Prey capture: copepod Prey capture: kestrel
Size in predator-prey relationships

264 Megasystematics
4.2.1.2
Porifera
The sponges (Porifera) are metazoans with a simple body needles (spicules), formed by specialist spongocyte and scle-
structure. There are approximately 7,500 known sponge spe- rocyte cells.
cies, reaching a size of a few millimetres to over 3 m. Spong- The low cell differentiation and their plasticity (the abil-
es are benthic filter feeders and are mostly marine, with the ity to change specialisation), offers sponges a high regenera-
exception of some freshwater species. They lack muscle and tive capacity. They can tolerate damage from feeding and, in
nerve cells, gonads, and a digestive tract. However, they have many cases, parts of a sponge may grow into new individu-
mitochondria. As with all Metazoa, sponges do not have als.
plastids. Sponge cells are not as heavily specialised as in most Sponge larvae are planktonic and only attach themselves
metazoan species; the sponge body is made up of only a few to the substratum late in their life cycle. The metamorphosis
cell types and no real tissues can be identified. Pinacocytes of calcareous sponges (Calcarea) features an invagination or
are flat cells which cover the surface of sponges, including an immigration of cells similar to the process of gastrulation
the duct system covers. Choanocytes within each chamber in the embryonic development of higher Metazoa. Other
are very similar to choanoflagellates in morphology, with sponges have complicated parenchymula larvae, which are
20–40 filopodia surrounding the central flagellum and serv- similar to a gastrula. The sponge larvae are therefore consid-
ing to collect food captured externally and filtered towards ered to be a model for the evolution of the first metazoans
the cell. Sponge skeletal elements are made of collagen and (‘Gastraea hypothesis’).
Molecular data suggest that the sponges are a paraphyletic confirmed. The skeleton of the siliceous sponges (Demos-
group. If this is the case, several of their characteristic fea- pongiae) consists of silica spicules and the protein spongin.
tures must be interpreted as ancestral; notably, these include The calcareous sponges (Calcarea) have a skeleton made of
the development stage involving planktonic larvae as well calcite spicules, whereas glass sponges (Hexactinellida) have
as the sessile adult phase with a choanocyte-based filtration spicules made of amorphous silica (opal). The glass sponges
system. This would lead to the assumption that the ancestral are significant reef builders and in the Jurassic were as im-
species of the Metazoa was a filter-feeder and not a predator, portant in marine environments as corals are today.
as was conventionally thought. The Archaeocyathids are a group which became extinct
The various sub-groups of sponges (Calcarea, Hexactinel- in the Cambrian, thought to be associated with the sponges.
lida, Demospongiae), however, are each monophyletic. These organisms were significant reef builders during the up-
The Homoscleromorpha are usually classified within per Precambrian and lower Cambrian.
the Demospongiae, though this relationship remains to be
amorphous: unformed, shapeless parenchymula larvae: a type of larva which has a flagellated
benthic: benthic organisms live on or in the sediment at the bot- front section (later endoderm) and an unflagellated rear section
tom of a body of water (later ectoderm)
metamorphism: (Grk.: metamorphosis = transformation) al- planktic or planktonic: planktic organisms float or drift in the
teration of the composition or structure of rock, usually by heat, water column and cannot swim against the current
pressure, or other natural phenomena sessile: sessile organisms are attached to a substrate and cannot
move about independently, in contrast to motile organisms
See also: Filopodia: 4.2.3; Stratigraphic time scale of the Palaeozoic: 2.3.3
Plants and other phototrophic organisms are com- obtain their nutrients and energy from food, and
monly considered to be sessile, whereas animals therefore do not rely on contact with the surround-
and heterotrophic species are considered to be ing soil or water solution (with the exception of
motile. This view is overly generalised, biased to- osmotrophs). A motile lifestyle is possible both on
wards terrestrial ecosystems, and largely anthro- land and in the water. In contrast, a sessile hetero-
pocentric. The requirement to keep a large surface trophic lifestyle is not possible on land, as sessile
area available for taking up nutrients requires roots organisms can generally only catch prey through
or similar structures in terrestrial phototrophic or- filtration, which is only possible in aquatic environ-
ganisms and therefore allows only for a sessile life- ment. A visible consequence of these restrictions
style. Competition with other phototrophs for light is that relatively large terrestrial phototrophs are
promotes growth towards the light source. fed upon by relatively small herbivores, whereas in
However, aquatic phototrophy is different, since aquatic habitats, smaller phototrophs are largely
nutrients are in solution in the surrounding wa- consumed by larger (filter-feeding) herbivores.
ter. In order to maximise absorption capabilities, a
large body surface-to-volume ratio and therefore
small size is thus advantageous. Moreover, mobil-
ity is required in order to make the most of light in
the upper layers of the aquatic environment. Ter-
restrial phototrophs are therefore mostly sessile
and rather large, whereas aquatic phototrophs are
mostly motile and small. Exceptions exist, includ-
ing larger marine algae. Heterotrophic organisms
266 Megasystematics
4.2.1.3
Placozoa, Cnidaria, Ctenophora

The metazoans Placozoa, Cnidaria, and Ctenophora thread. Most cnidarian species display a radial symmetry at
(comb jellies) are characterised by two germ cell layers, the their adult stage. The Cnidaria include the Anthozoa (corals,
endoderm and ectoderm, and are therefore together known sea anemones) and the Medusozoa. Apart from a few fresh-
as the Diploblasta. These three groups all feature mitochon- water species, most of the approximately 9,000 known spe-
dria but not plastids. As with the sponges, the phylogenetic cies of cnidarians are marine, and are both sessile (polyps)
relationship of these groups with each other remains unclear. and planktonic (jellyfish). They have epithelia and a net-like
The Placozoa are 1–3 mm wide flattened animals with a nervous system.
dorsal surface epithelium (ectoderm), consisting of only one The approximately 100 known species of Ctenophora are
cell type, and a ventral digestive epithelium (endoderm, con- usually marine and pelagic. They are characterised by their
sisting of two cell types. They have no real epithelial cells epithelia and a reticular nervous system. Unlike the Cnidar-
and no nervous system or body symmetry. There are at least ia, they do not have any nettle cells. Instead, many cteno-
30 known placozoan species, of which only the type Trichop- phores have colloblasts, cells consisting of a coiled spiral fila-
lax adhaerens has been formally described. They are marine ment embedded in the epidermis and used to capture prey.
and feed on algae. Colloblasts rupture on contact with prey, releasing an adhe-
The Cnidaria are characterised by their specialised nettle sive substance which prevents it from escaping. Ctenophore
cells called cnidocytes, which are used for prey capture and are characterised by biradial body symmetry: the symmetry
defence from predators. The cnidocyte fires a thread contain- of the lower half of the body is offset by approximately 90º
ing toxins from a characteristic subcellular organelle called compared with the upper half. However, symmetry is not ex-
a nettle capsule. The nettle capsules are derived from the actly biradial as the body quadrants do not exactly match
Golgi apparatus and the flagellum developed into the cnido- each other.
cil – a hair-like structure triggering the ejection of the nettle
The affiliation of Ctenophora and Cnidaria with the of individual development (morphogenesis). As a result of
triploblast metazoa is still unclear. Older scientific literature their role, HOX genes have special significance in the recon-
often discusses the Cnidaria as model organisms for their ra- struction of phylogenetic relationships.
dial symmetry. However, recent studies show that cnidarian As a result of their soft tissue structures, the groups dis-
species are originally bilaterally constructed and that their cussed here are rarely found in the fossil record. In con-
radial symmetry is secondary. Evidence of their original bi- trast, fossil corals (Anthozoa, affiliated with the Cnidaria)
lateral symmetry can be seen in some Anthozoa (e.g. Nema- are common reef-building organisms since the Ordovician.
nostella sp.) as well as in the bilaterally structured nervous Coral taxa are distinguished according to their number of
system of the Planula larvae. Consequently, bilateral symme- gastric chambers as the Octocorallia (eight) and Hexacoral-
try evolved before the split of cnidara from the other bilate- lia (six). The fossil record features an important number of
rians. Thus, cnidarians belong to the bilaterians even though Hexacorallia: from the Ordovician to the Palaeozoic, these
they lack a third germ cell layer. were the Tabulata, which features undeveloped septa, as well
A close phylogenetic relationship between Cnidaria and as the Rugosa. The present-day most dominant coral groups
the triploblastic Bilateria is also supported by HOX gene have been in place since the Mesozoic, i.e. the Hexacorallia,
analyses, which target a family of regulatory genes whose including the hard corals (Scleractinia).
products control the activity of other genes during the course
epithelium: tissue which lines cavities; the outermost cell layer pelagial: open water zone
or layers in Metazoa planula: a free-swimming ciliated larva in various cnidarian spe-
HOX genes (homeotic genes): genes which are responsible cies
for controlling particular segment structures and the head-tail triploblastic: organism with three primary germ layers
axis
See also: Reef-building organisms: 2.3.2.2; Stratigraphic time scale of the Palaeozoic: 2.3.3
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa ta
o pt
eb
Cry
soz on
op
mo
ok
A hy
pto
st
ta
hi
Trichoplax adhaerens Dickinsonia sp.
phy
Op
Apu
ta
The Placozoa are animals with a simple body plan (left), which form a bulge due to the appearance of a
temporary digestive cavity (middle). As a result, they are model organisms for the Placula hypothesis, which
Eubacteria Archaea
postulates an alternative origin of Metazoa. Some Precambrian fossils, which are hard to interpret,such as
Dickinsonia from the Ediacarian probably belong to the Placozoa
medusa
The two body types of Cnidaria: Medusa The phylogenetic position of cteno-
epidermis
(top) and polyp (bottom). The gastro- phores (comb jellies) is controversial.
derm (endoderm) and epidermis (ec- gastrodermis tentacle The occurrence of muscle tissue and
toderm) surround the mesogloea, the gastrovascular cavity the fine structure of their sperm acro-
jelly-like substance which makes up the mesogloea some suggest they are closer to the
majority of the jellyfish body. triploblast Bilateria; however, HOX
gene analyses as well as a lack of real
bilateral symmetry support the idea
that they branched earlier than mor-
phology would suggest
Ctenophora have no polyps

polyp
Bilateral symmetry Animals without any symmetry are known as asymmetrical; this is
true of many Placozoa and sponges. Body symmetry is controlled by
regulatory genes. The simplest form of animal symmetry is spherical,
anterior posterior whereby the body can be divided through the centre into any num-
ber of mirror-image halves.
Organisms with radial symmetry can be divided into mirror-image
halves across more than one plane through the longitudinal axis. This
proximal distal type of symmetry is characteristic of ctenophores and cnidarians, for
example
dorsal
anterior posterior
ventral
Most animals show body symmetry; that is, the animal can be divided into
similar halves along a plane. Bilaterally symmetrical organisms can only be
divided once into two mirror image halves Radial symmetry
Symmetry and body structure

268 Megasystematics
4.2.1.4
Protostomia
Protostomia form a sister group to Deuterostomia and to- twist 45º around the macromeres and lie in the cleavage of
gether these make up the metazoan lineage Nephrozoa. Phy- the macromeres. However, certain Spiralia groups possess
logenetic relationships within the Protostomia remain un- alternative cleavage types.
clear, though molecular work suggests that the group is split The phylogenetic system presented above is contrasted by
into the Ecdysozoa, Lophotrochozoa, and the Platyzoa. The the overwhelming morphological similarity of annelids (Spi-
latter two groups form the Spiralia, sister to the Ecdysozoa. ralia) and arthropods (Ecdysozoa): both display a segmented
Ecdysozoans have a three-layered cuticula, whose moult- morphology with a (metamerically organised) rope-ladder
ing is controlled by a unique hormone called ecdysone. Lo- nervous system and longitudinal muscles. Metameric seg-
comotory flagella are degenerated; modified flagella are part ments usually contain the coelom, ganglia of the rope-lad-
of sensory organs and embedded in the cuticula, with no lo- der nervous system, metanephridia, and extremities. These
comotory function. The embryonic development of Ecdyso- structural similarities are the characteristics of the Articulata
zoa displays no clear spiral cleavage and they never have a (articulate animals).
trochophore larva. Protostomia do not contain plastids, but possess mito-
In contrast, the Spiralia derive their name from their clear chondria. They are cosmopolitan and colonise aquatic and
embryonic spiral cleavage. In the third equatorial division, terrestrial habitats at all altitudes. The insects, which also be-
four larger cells (macromeres) and four smaller cells (mi- long to the Protostomia, is the most species-rich taxon.
cromeres) are created, from which the smaller blastomeres
The morphological similarity between the annelids and Nevertheless, the morphological findings suggest that
the arthropods conventionally reinforced their phylogenetic these structures were convergently formed in both organis-
relationship. However, homology of their different struc- mal groups. This is quite plausible since the metameric or-
tures is questionable and has not been proven; therefore, it ganisation brings functional advantages and because genes
remains unclear whether the limbs of arthropods, known as for anterior-posterior organisation and structure occur in all
the arthropoda, and the extremities of the annelids, the pa- bilateral metazoan species. Further more, molecular data
rapodia, are homologous. Furthermore, it is unclear whether refute the ‘articulation concept’, meaning that metameric
the body cavities of arthropods and the coelom of annelids organisation must have arisen in both groups as a result of
correspond to each other. Despite the great organisational convergent evolution.
similarity of these two structures, serious doubts remain with
respect to their common origin.
coelom: (Grk.: koiloma = cavity) secondary body cavity com- metanephridia: excretory glands connected to the coelom by
pletely lined with mesodermal cells a ciliated funnel; filtration takes place by the blood vessels near
ecdysone: hormone in Ecdysozoa inducing moulting, metamor- the metanephridia using blood pressure; the nephron, as the
phosis and reproduction functional and anatomical unit in vertebrates, originates from
ganglion: a nerve cell cluster, also known as a nerve-knot the metanephridia
metamerism: having a series of repeated segments trochophore larvae: free-swimming, pear-shaped larvae with
several bands of cilia in various Spiralia
See also: Cuticula: 4.4.3.2

stida Rh
Subdivision of Protostomia pla iza
ae
Viridiplant ta
ria
oa
h
both arthropods and annelids have a front segment (akron), rear segment (pygidium), rc
Rh
z
G
Cerco
odo
and other, originally homonymous segments in between. The segments each have
la
uc ria
ta
op Re
phy
one pair of coelomic cavities, a pair of metanephridia, a pair of rope-ladder nervous
Chr
hy
ae
Disc ta
Excavata
system ganglia, and a pair of limbs or parapodia. Due to their large morphological oba olata
oma
Alve
and ontogenic similarity with each other, these groups have been grouped together a Stra
lveolata
Meta monad men
opile
as Articulata (articulate animals). However, molecular data contradict this grouping, zo
a Ha s
oa ta
o pt
suggesting insteadthat the Arthropoda belong to the Ecdysozoa and the Annelida to eb
Cry
soz on
op
mo
ok
A hy
the Spiralia
pto
st
ta
hi
phy
Op
Apu
ta
Eubacteria Archaea
Arthropoda: Octoglena sierra (top: Myriapoda) and a centipede from Annelida: Scolelepis squamata (top: Polychaeta) and Nereis succinea
Borneo (bottom: red Borneo centipede, Myriapoda) (bottom: Polychaeta)
Segmentation was an important step in the mor- The development of segments is controlled by
phological evolution of the Metazoa because it al- segmentation genes, divided into three different
lows for the specialisation of different sections of classes according to their function. The first, which
the body. Segmentation can be found in the anne- activate the process, are known as gap genes.
lids, arthropods, and vertebrates, and is thought to These divide the embryo into larger segments
have developed independently in all three groups. (head, thorax, and abdomen). The areas defined
Repeating identical or similar body sections are by the gap genes are divided into segments by
known as segments, metamers, or somites and are pair rule genes. Next, the pair rule genes activate
found in annelids, arthropods, and vertebrates. segment polarisation genes. These determine the Homonomous segmentation
Each body segment can display identical inner and orientation of the structures within each segment.
outer structure (homonymous segmentation).
On the other hand, the specialisation of individ-
ual body sections (heteronomous segmentation)
is what led, over evolutionary time, to complex
changes in the body and to more precise control
movement. For instance, different segments de-
veloped appendages for movement, feeding, re-
production and sensing. In some animals and in
humans, the segmentation of the body is hidden.
Heteronomous segmentation
Segmentation
270 Megasystematics
4.2.1.5
Ecdysozoa
Ecdysozoa and Spiralia form the major groups within peristaltic movements, as annelids can, and therefore exhibit
Protostomia (Metazoa). The Ecdysozoa (moulting animals), a wave-like locomotion.
which comprise Panarthropoda and Cycloneuralia, are char- Scalidophora are Cycloneuralia with a tripartite articu-
acterised by a multi-layered chitin cuticula and a hormone- lated body. The anterior end features a proboscis, known as
controlled moulting cycle. Locomotory cilia are reduced. the introvert, which it uses to guide its movements. Sensory
Ecdysozoa usually possess mitochondria but not plastids. organs are also located on the introvert, which is covered in
In Cycloneuralia, which inhabit both marine and terrestri- special scales known as scalids. The outer integument (endo-
al habitats, the central nervous system runs in a ring around cuticula) contains chitin.
the throat and dorsal and ventral strands run along the body The Scalidophora include the Priapulida, Loricifera,
axis. Some species are important parasites, for example, Loa and the Kinorhyncha, all benthic marine organisms. Unlike
loa and Wuchereria bancrofti. Cycloneuralia species do not Nematoida, Scalidophora lack protonephridia.
possess plastids but most have mitochondria. The three spe- The Panarthropoda are segmented Ecdysozoa with a met-
cies Spinoloricus nov. sp., Rugiloricus nov. sp., and Pliciloricus americ nervous system and demonstrating teloblastic growth
nov. sp. (Loricifera), inhabiting sediment in the hypersaline, at their body extremes. They share these characteristics with
anoxic, L’Atalante deep-water basin of the Mediterranean, the annelids, which, however, are affiliated with the Spiralia.
possess hydrogenosome-like organelles which allow them to However, only Panarthropoda possess antennae or modified
survive in such extreme conditions. These are the first known head limbs, paired claws, and yolk-rich eggs with partially
multicellular metazoan species living in the absence of oxy- superficial cleavage. In general, excretory functions are car-
gen. ried out by modified metanephridia; a coelom is established
Nematoida (including Nematoda and Nematomorpha) at least in the embryonic stage. The Panarthropoda compris-
are Cycloneuralia with unstructured, elongated bodies. Due es Onychophora (roughly 110 exclusively terrestrial species),
to their lack of circular muscle, the Nematoida cannot make the Tardigrada (roughly 800 marine and limno-terrestrial
species), and the Euarthropoda (several million species).
Tardigrades, also known as water bears or moss piglets, The misinterpretation of the single-gene genetic rela-
have an unusual morphology which makes them difficult to tionship between tardigrades and other groups is primarily
compare with other Panarthropoda. For example, they lack a caused by a phenomenon known as ‘long-branch attraction’,
coelom, nephridia, and trachea, with gas exchange occurring where results are skewed because target groups differ too
at their body surface. Each individual segment is also difficult much from the other species featured in the analysis. As a
to compare with those of other Panarthropoda. The assign- result, the reconstruction of phylogenetic relationships for
ment of tardigrates to Panarthropoda is based largely on mo- groups like tardigrades, where the separation of the closest
lecular rather than morphological findings. Genetic analyses known relatives occurred a relatively long time ago, remains
of single genes support their relationship with Nematoida, difficult.
whereas multi-gene phylogenetic studies groupsthem closer
to Onychophora and Euarthropoda.
chelicerae: mouth parts of the chelicerata the rear of the embryo and work their way forwards; teloblasty is
opisthosoma: posterior part of the body behind the prosoma common in all Articulata
pharynx: (Grk.: pharyngs = throat, gullet) in animals, the initial tracheae: (Lat.: trachea = wind pipe) in animals, tube allowing
part of the alimentary canal the passage of air to be transported to tissue; in plants, water-
prosoma: anterior part in Chelicerata conducting tissue
teloblastic growth zone: teloblasty is the term describing the
process in which new segments are formed in a growth zone at
See also: Trilobita: 2.3.2.5

body not segmented. Nervous system arranged in a ring around the pharynx in addition to a dorsal pla
stida Rh
iza
and ventral strand ae
Viridiplant ta
ria
oa
h
rc
Rh
z
Scalidophora body articulated, divided into a fore- G
Cerco
odo
la ria
C body, ‘neck’, and torso. The forebody
Priapulida uc
op Re
ta
phy
y
Chr
hy
ae
is formed by an eversible proboscis Disc ta
Excavata
oba olata
c
oma
Alve
(introvert)
l Loricifera a Stra
lveolata
Meta monad men
opile
o zo
a Ha s
oa ta
o pt
eb
n
Cry
soz on
op
mo
ok
A hy
pto
e
st
ta
Kinorhyncha
hi
phy
Op
u
Apu
ta
r
Nematoida long, thin body, with an unsegmented
a Nematomorpha Eubacteria Archaea
collagen cuticula. Longitudinal muscle
l present, though lacking circular mus-
i cle
a
Nematoda
Panarthropoda are characterised by a segmented body and ‘brain complex’ with a ventral nerve chord. The extremities possess paired claws
Number of cells is genetically fixed. Lacks a coelom and vascular system. Number of
Tardigrada head segments unclear, whereas total number of segments is low. Phylogenetic position
remains unresolved
possess tracheae, though these are not homologous to those in Euarthropoda. Possess
Onychophora
undivided leg stumps, with two claws at their extremities
P The Euarthropoda (‘true arthropods’) possess multiple-unit extremities, an exoskeleton as well as a

a modified number of segments forming functional body sections (tagmata)
n Chelicerata (horseshoe crabs, scorpions, spiders) have
a
Chelicerata tripartite chelicerae and are divided into a prosoma
r and opisthosoma
t
Trilobita are an extinct group of Euarthropoda with
h
Trilobita bodies divided into three tagmata (cephalon, thorax,
r
and pygidium)
o
Euarthropoda
p The Mandibulata have multiple head extremities, including two antennae, mandibles,
o and two pairs of maxillae
d
homonomous segments following a head capsule
a Myriapoda
made of several fused segments
Mandibulata Nauplius larvae, variable number of body segments,
Crustacea segmented legs, and two pairs of antennae are
plesiomorphic features
head made of six fused segments, thorax made of
Hexapoda three and abdomen made of 11 segments
The freezing and thawing of multicellular organisms often leads to their tering a state of cryptobiosis, an ametabolic state of life, whenever envi-
death. Most cells, for the most part, consist of water, which forms ice ronmental conditions are adverse. They can fully regenerate in minutes
crystals during freezing events, destroying the cell wall and internal com- in response to better conditions.
ponents. In addition, at the beginning of a freezing event, the concen- Two water bear species even survived in space at 270 km altitude for ten
tration of the solution within the cell increases, thereby increasing the days; where they were exposed to UV-rich sunlight, gamma radiation,
osmotic pressure within the cell which leads to fluid leaving the cell. Fi- and the range of other particles that make up general cosmic radiation.
nally, the freezing process also slows diffusion processes within the cell. Such extraordinary resilience was only previously observed in bacteria
With the help of cryopreservation, plant and animal (including sperm, and some lichen species.
egg, and embryonic) cells may be frozen and preserved for a longer pe-
riod of time. When this happens, metabolic processes are put on hold.
In order to prevent the formation of ice crystals, the cryopreservation
process involves a very rapid freezing of materials (e.g. in liquid nitro-
gen). In addition, antifreeze agents, such as glycerol or DMSO, can be
added to the mix.
A number of organisms are capable of withstanding freezing conditions
in nature. Water bears (Tardigradia) are particularly resilient, capable of
surviving for years in temperatures between +149 °C and –272 °C whilst
also being exposed to ionised radiation, lack of oxygen, food, osmotic
stress, and preservatives (ether and ethanol). They manage this by en- water bears
Freezing and thawing

272 Megasystematics
4.2.1.6
Spiralia
The second major Protostomia group is the Spiralia, com- and the paraphyletic Rotifera share a common jaw morphol-
prising around 150,000 known species. They have mitochon- ogy, and are therefore summarised as Gnathifera, a relation-
dria but lack plastids. ship that is also supported by molecular data.
Most organisms in this group are placed within Spiralia The second large spiralian lineage is Lophotrochozoa,
because they exhibit a characteristic spiral cleavage during including Brachiozoa and Trochozoa. The Trochozoa have
embryonic development. Deviations of this cleavage type trochophore-lavae, which are round or pear-shaped and have
can, however, also be found in some spiralian groups. Spi- two or more rows of cilia. They include Nemertea, anne-
ralia include the flatworms and related species (Platyzoa), lids, and molluscs. Brachiozoa exhibit a characteristic feed-
Trochozoa (which form trochophore larvae), and the Bra- ing organ known as the lophophore, which features a ring
chiozoa. Brachiozoa and Trochozoa are collectively known of cilia-laden tentacles around a mouth. The Brachiozoa in-
as Lophotrochozoa. clude the Brachiopoda and Phoronida. Molecular data also
The Platyzoa have a relatively simple acoelomate body support the Lophotrochozoa. However, the Ectoprocta and
plan and possess protonephridia. Apart from the flatworms Entoprocta also possess a similar organ and are therefore
(Platyhelminthes), most other platyzoan species are poorly grouped with Brachiozoa within Lophophorata. Molecular
studied and their phylogenetic relationships remain unclear. data, in contrast, suggest Ectoprocta and Entroprocta group
The Gnathostomulida, Micrognathozoa, Acanthocephala, with Platyzoa.
Although the different lineages affiliated with Lophotro- The Aculifera (spiked molluscs) lack typical mollusc shells
chozoa are well supported, the internal systematics of the but may exhibit other shell-like body parts, such as chitons.
group and the phylogenetic relationship of most internal Spiked molluscs do not form a monophyletic group; in par-
lineages to each other are often unclear. We discuss the Bra- ticular, the vermiform Aplacophora are probably basal mol-
chiozoa, Mollusca, and Ectoprocta. luscs. The Ectoprocta are systematically difficult to classify
The benthic marine Phoronida are filter feeders with no because the two lineages (Phylactolaemata and Gymnolae-
shell. Brachiopoda, on the other hand, are shell-bearing ben- mata) exhibit distinctly different morphological characteris-
thic organisms, living in a similar way to mussels though, tics, which in part support their relationship with Entoprocta
instead of possessing a left and right shell, they are character- and further to Platyzoa, whereas other characters support
ised by upper and lower shell halves. Molecular and morpho- their relationship with the Brachiopoda and ultimately to
logical data, including studies relating to the construction of Lophotrochozoa. Even the few available molecular data are
brachiopod cilia, place Brachiozoa near the annelids. conflicting, supporting both a relationship with Entroprocta
The molluscs are also a species-rich group with unclear as well as with Brachiopoda, but also alongside Chaetog-
internal systematic relationships. naths as basal Protostomia.
The Conchifera form a monophyletic group and possess
typical mollusc shells. They comprise the Bivalvia (mussels),
Gastropoda (snails), and Cephalopoda (cephalopods).
acoelomate: not possessing a coelom (a fluid-filled, sealed sec-

ondary body cavity)
See also: Brachiopods and shells: 2.3.2.4; Cephalopods: 2.3.2.3

colony-forming sessile filter feeders. The stida Rh

pla iza
Ectoprocta ae
Viridiplant ta
ria
anus sits outside a ‘crown’ of tentacles
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
Entoprocta anus sits inside a ‘crown’ of tentacles op Re
phy
Chr
hy
ae
P
Disc ta
Excavata
oba olata
oma
Alve
small (0.3 mm) animals vortexing
l Cycliophora a Stra
lveolata
nutrients using a ‘crown’ of cilia Meta monad men
opile
a zo
a Ha s
oa ta
microscopic worm-like animals lacking a eb
o pt
Cry
t
soz on
op
Gastrotricha mo
ok
hy
body cavity or vascular system A
pto
st
ta
y
hi
phy
Op
Apu
z Plathelminthes flatworms have no central body cavity
ta
o
a jaw worms are marine worms lacking a Eubacteria Archaea
Gnathostomulida
body cavity
micromeres
Micrognathozoa systematic position remains unclear
Gnathifera
Rotifers are a paraphyletic group, charac-
Rotifera terised by a rotating wheel organ macromeres
spiny-headed worms are intestinal para-
Acanthocephala sites with mandatory change of host spiral cleavage of Spiralia
Phoronida Horseshoe worms possess a U-shaped tentacle apparatus,

known as a lophophore
Brachiozoa
Brachiopods have an upper and lower shell. They vortex
L Brachiopoda food using tentacles on their lophophores. They were eco-
o logically significant in particular during the Palaeozoic
p
h worm-like animals with a proboscis, they are amongst the
Nemertea
o longest animals (up to 35 m in length)
t segmented worms with a metameric coelom and nervous
r system. In contrast with the Polychaeta, the Clitellata pos-
Annelida
o sess a gland-rich thickened epidermis near the anterior end
c of their body
Trochozoa
h
Divided into a head, food, and visceral sac. Molluscs possess
o
a mantle with a mantle cavity and a reduced coelom. The
z internal systematic classification within Mollusca remains
o Mollusca unresolved. In general, the Mollusca are grouped into the
a shell-bearing lineages (Conchifera), including snails, clams,
tusk shells, ammonites, monoplacophorans, and shell-lack-
ing lineages (Aculifera), including chitons, solenogastres,
and the caudofoveata
After death, organisms decompose until only inorganic materials re- of fossilisation remains low since many factors contribute to the process.
main. Decomposition is carried out for the most part by bacteria and For example, the speed at which the organism is embedded is critical:
fungi, which also release inorganic materials into their natural envi- the faster the embedding, the higher the chances of fossilisation. To that
ronmental cycles. This process can be interrupted under certain condi- end, it is estimated that under 1 % of organisms become embedded in
tions; for example, when dead or dying organisms enter oxygen-poor sediment and that under 1 % of these survive as fossils.
sediment (such as in peatlands, sand dunes, swamps, or lakes), which
prevents them from decomposing. In addition, fossils usually only occur
in areas with low Earth crust activity, which tends to deform or destroy
fossils over time. Fossilisation is only possible when these conditions are
met (right: Priscacara liops fossil from the Eocene). Several fossil types
exist, characterised by the fossilisation process. Fossilisation may occur
by way of mummification by dehydration or embedding in peat lands;
coalification by converting plants into peat, lignite, or coal under pres-
sure and anoxic conditions; preservation of hard parts such as scales,
teeth, bone fragments, or enclosures; petrification after the decomposi-
tion of organic matter and subsequent filling out of cavities with lime
or silica; imprints or footprints of, for example, a plant in sediment; and
entrapment within liquid resin (amber), salt, or ice. While there are sev-
eral ways to preserve an organism over millions of years, the probability
Priscacara liops from the Green River-Formation
Why can some fossils not be found?

274 Megasystematics
4.2.1.7
Deuterostomia
The Deuterostomia, along with Protostomia, make up sea lilies and wild feather stars) as the only recent group of
Nephrozoa. The approximately 60,000 known species of Pelmatozoa, the Asterozoa (Asteroidea – sea stars; Ophi-
Deuterostomia are cosmopolitan, colonising aquatic and ter- uroidea – brittle stars) and the Echinozoa (Echinoidea – sea
restrial habitats. They even occur in the atmosphere. urchins; Holothuroidea – sea cucumbers). All echinoderms
During embryonic development of Deuterostomia, the are characterised by their ambulacral system (water vascular
first opening, the blastopore, develops to the anus. The system); the appendages of this channel system are used as
mouth opens secondarily from a primitive gut in a process suction feet for locomotion and as tentacles for the acquisi-
called deuterostomy. Deuterostomia comprise Chordata tion of food.
and Ambulacraria, which includes Echinodermata (echino- Chordata are characterised by their dorsal axis rod, the
derms) and Hemichordata. notochord, a nerve cord lying above the chorda, a neural
The Hemichordata were previously grouped within Chor- tube, as well as the anterior pharynx showing gills. In higher
data as a result of their gill slits, although their larval mor- vertebrates, this structure is converted to gills. The notochord
phology and more recent molecular findings reinforce their (chorda dorsalis), serves as an endoskeleton and arises ontoge-
relationship with echinoderms. Hemichordata include vari- netically from the mesoderm. This structure is found in Bra-
ous recent worm-like organisms, including Enteropneusta as chiostoma as well as in the larvae of Urochordata and of
well as the extinct graptolites. lampreys.
Echinoderms, on the other hand, are exclusively marine,
and include the Pelmatozoa including the Crinoidea (sessile
The Cephalochordata (Acrania) are a significant fossil In Craniata (Vertebrata), the front part of the neural tube
group that today is only represented by the Amphioxiformes is differentiated into a brain. This, as well as the larger sen-
(lancelets). They eat and breathe through specialised gill in- sory organs, is encapsulated within a neurocranium. Crania-
testine organs. Incoming water is filtered by the gills and in- ta also possess skeletal elements which, in primitive groups,
testine in Brachiostoma lanceolatum, with planktonic food thus were small and limited to only a few areas. Craniata include
entering the digestive tract. the hagfish (Myxini), lampreys (Petromyzontida), and gna-
The Urochordata (Tunicata) are a strongly derived sister thostomes (Ghanthostomata).
group of Craniata. Together, these lineages are summarised The jawless taxa were previously classified as ‘agnatha’
as Olfactores, based on a number of apomorphies, including (jawless); however, since this is a polyphyletic group, this
the presence of tight junctions. However, the exact relation- classification is no longer in use.
ship of the Cephalochordata with Urochordata and Craniata
remains unknown.
branchial gut: part of the foregut containing gill slits. The gill neural tube: first stage in the formation of the central nervous
slits enable the animal to breathe as well as extract particles of system in the embryonic development of chordates
food from water through a process of filter-feeding neurocranium: part of the skull protecting the brain
chorda dorsalis: notochord; internal axial skeleton of all chor- notochord: cartilaginous skeletal rod supporting the body in all
dates embryonic and some adult chordate animals (=Chorda dorsalis)
endoskeleton: (Grk.: endon = inside, skeletos = frame) inner tight junctions: cell-to-cell conjunctions with no gap between
support structure (e.g. bones in vertebrates) epithelial cells, forming a barrier to diffusion
See also: Evolution of vertebrates: 2.3.2.8; Skeletal elements: 2.3.3.2

Graptolith Enteropneusta pla

stida Rh
larval development similar to that of ae
iza
Viridiplant ta
ria
oa
h
rc
Rh
Hemichordata echinoderms, though gill slits suggest
z
G
Cerco
odo
la ria
a relationship with the Chordata uc ta
A op Re
phy
Chr
hy
ae
m Disc ta
Excavata
oba olata
oma
Alve
b include filter-feeding sea lily a Stra
lveolata
monad
u Pelmatozoa and the secondary free-living
Meta
a Ha
men
opile
s
l zo
oa ta
o pt
feather star eb
Cry
soz on
op
mo
a
ok
A hy
pto
st
ta
c Echinodermata
hi
phy
Op
Apu
r
ta
include starfish and
a Asterozoa
brittle stars
r Eubacteria Archaea
i
a
Echinozoa include sea urchins and sea cucumbers
The Amphioxiformes (lancelets, families

Cephalochordata (Acrania) Asymmetromonidae and Branchiostomidae) are
the only extant acranians
notochord and neural tube only found in larvae, whereas these

Urochordata
are reduced in adults. Lack an excretory system, with excretory
(Tunicata)
C functions taken over by the nephocytes
h
o
r Olfactores
d skeleton of cartilage or bone tissue, multilayered skin
a
t hagfish skeletal elements limited to some cartilaginous
a Myxini structures in the head and cartilage threads along the
notochord
Craniata
(Vertebrata)
lamprey larva similar to those of lancelets, also filter-
Petromyzontida feeding in the sand. Adult forms mostly parasitic on fish.
Possess a cartilaginous skeleton
jawed vertebrates. Characterised by solidified and

Gnathostomata
articulated mouth edges
UV radiation comes from the portion of the solar spectrum with a photolyase, an enzyme, repairs tissues damaged by UV radiation; epi-
wavelength between 200–400 nm, between X-ray radiation and visible cuticular waxes provide a physical barrier to radiation; anti-oxidative
light. UV is further divided into three regions: UV-A at a wavelength of agents, such as vitamin E, can also protect against UV; finally, the mor-
320–400 nm, UV-B at 280–320 nm, and UV-C at 200–280 nm. UV-A, the phology of leaves may also minimise exposure to radiation.
lowest energy radiation within the spectrum, is only slightly filtered out
of the atmosphere. UV-B radiation, for the most part, is absorbed by the
ozone layer, whereas UV-C is completely absorbed by the atmosphere.
UV radiation may affect life in a range of ways, including by stimulating
the formation of vitamin D.
However, it is also known to damage genetic material and many land
animals protect themselves by using special shields on their body, such
as feathers on birds, the fur of mammals, and the scales on reptiles. In
humans, however, lacking the protective fur of other mammals, UV pro-
tection has developed differently, through a thickening of the epidermis
and epidermal pigmentation as a result of increased melanin production
in the deep epidermis (sun tanning). Melanin protects against UV radia-
tion by converting a majority of the radiation energy into heat. Left: UV protection via reflection – the skin of a Gila monster, flower of
Plants, on the other hand, protect themselves using other mechanisms the silver thistle; right: UV protection via hair growth – snow leopard
of UV-protection: screen pigments absorb radiation in the UV region; coat, edelweiss flower
Protection from UV radiation

276 Megasystematics
4.2.1.8
Gnathostomata
The Gnathostomata, along with the Myxini and Petromy- (dogfish sharks), only some skeletal elements are ossified,
zontida form Craniata, a group within the Chordata. especially in the area around the skull and vertebrae. The
In Gnathostomata, mouth edges are comprised of artic- skeletons of the Euteleostomi are, however, ossified.
ulated bone clasps. In fish, amphibians, reptiles, and birds, The bony fish (Osteichthyes) are a paraphyletic group, in-
these are held together by temporomandibular joints. Jaws cluding all Euteleostomi with the exception of Tetrapoda.
presumably arose from the modification of the third and Bony fish therefore include the ray-finned fish (Actinop-
fourth branchial arches. The original function of this modi- terygii) as well as the flesh-finned fish (Sarcopterygii), which
fication was likely in order to more effectively pump avail- do not belong to Tetrapoda. The paired fins of fleshy, bone-
able water through the gills. The associated enlarging of the finned fish have a single, mono-basal, bony axis running from
mouth and stabilisation of the mouth rim led to the develop- the body, connected to the shoulder and the pelvis bone. This
ment of a real jawbone. bone is homologous to the upper arm bone (humerus) and
In the Placodermi, the jaw is made of just one gill arch the thigh bone (femur) of tetrapods.
(shown in red in the figure opposite), whereas in cartilagi- The four-legged vertebrates are summarised as Tetrapoda.
nous fish (Chondrichthyes) and the Teleostomi this is made These include Lissamphibia (amphibians) and the Amniota.
of two arches. The Teleostomi have four pairs of gills and a The embryonic development of amphibians is highly water-
gill slit and operculum. dependent, whereas the Amniota overcome this dependence
The skeletons of cartilaginous fish are largely deossified. through the development of the embryo within a liquid-
In the extinct sister group of Euteleostomi, the Acanthodii filled, membrane-bound amnion.
The placoderms (Placodermi) were the first large preda- sequence, the internal skeleton became more important as a
tory fish with strong jaws. In addition, their heavy armour stabilising element and a point to which muscle could attach.
provided protection against predators, although at the same Land vertebrates evolved the ability to breathe air, as
time this restricted their mobility. With the evolution of more can be seen in lung fish. Important transformations also ap-
efficient jaws in predatory fish, the ability to be highly mo- peared on the fins of fish, as in coelacanths and lungfish.
bile and to respond rapidly become vital for prey compared Teleost fish are a paraphyletic taxon. Lungfish and coe-
with further developments to their outer armour. As a con- lacanths group with the tetrapods, forming Sarcopterygii, as
they are more closely related to these than to ray-finned fish.
desmin: homopolymer, constituent of a cytoskeleton
See also: Evolution of tetrapods extremities: 2.3.3.7; Water dependency of reproduction: 2.3.4.2
stida Rh
pla iza
‘Agnatha’ Gnathostomata ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa ta
o pt
The ‘agnatha’ (jawless) fish do not The Gnathostomata (gnathostomes) possess a primitive jaw, which has been eb
Cry
soz on
op
mo
ok
A hy
pto
have a jaw. Gills emerged in the formed from a gill arch (left) and is found in extinct placoderms. A jaw made
st
ta
hi
phy
Op
filtration openings of earlier chor- of two gill arches (right) can be found in the Chondrichthyes and the Teleos-
Apu
ta
dates tomi. The primary jaw joint is replaced by a secondary jaw joint in mammals
Eubacteria Archaea
extinct class of prehistoric fish characterised by

bone plate armour on their head and body. Lived
Placodermi mostly during the Devonian and were amongst the
first jawed vertebrates
cartilaginous fishes. All species reproduce by way

Chondrichthyes of internal fertilisation
G
n
a The extinct spiny sharks were characterised by a cartilaginous
t Acanthodii
skeleton and an only partly ossified skull
h
o Teleostomi Actinopterygii (ray-finned fishes)
s
t
o
m
a
t Euteleostomi
a Members of this group have Coelacanthimorpha (coelacanths)
an ossified skeleton Sarcopterygii
(lobe-finned fishes) Dipnoi (lungfish)
Eggs lack an amnion. As a result,

Lissamphibia early development is strongly
water-dependent
Tetrapoda
Embryonic development takes
Amniota
place within the amniotic cavity
The angiosperms appeared for the first quantities of plant matter to survive. The
time during the early Cretaceous (around radiation of angiosperms was further
135 mya) in northern Gondwana. Many stimulated by increases in atmospheric CO2
studies assume that the origin and early ra- around that time.
diation of angiosperms is linked to behav-
ioural changes in larger dinosaurs, which
fed on plants. The angiosperms were ini-
tially rare and up to the upper Cretaceous
formed no significant biomass on the ter-
restrial surface.
As a result, it is unlikely that they constitut-
ed an important part of the dinosaur diet;
rather, these findings suggest that there is
no link between dinosaur evolution and
the radiation of angiosperms.
Most likely, pollination by insects and
frugivorous animals was responsible for
the development and diversity of an-
giosperms, since dinosaurs required large
The development of dinosaurs and angiosperms

278 Megasystematics
4.2.1.9
Amniota
The Amniota and Amphibia belong to the Tetrapoda (land ral window in their skull, but molecular studies suggest they
vertebrates). Amniota are terrestrial vertebrates with embry- are related to the diapsids, possibly as a sister group to the
os that develop in liquid (amniotic fluid) within an amniotic Archosauromorpha.
cavity surrounded by an embryonic sac (amnion). Vitally, Apart from mammals and possibly turtles, all other Am-
their development is therefore independent of aquatic habi- niota alive today belong to the diapsids. The subgroup Ar-
tats. Amniota include birds, mammals, and the paraphyletic chosauromorpha (archosaurs) includes birds, crocodiles,
reptiles. Their cells lack plastids but contain mitochondria. and various saurian groups. The birds are a sub-group of
The Amniota are divided into the Synapsida and Saurop- the Dinosauria, which belong to the Ornithodira, while the
sida, which are in turn subdivided into Anapsida and Di- crocodiles belong to the Crurotarsi. The two groups differ
apsida. These groups differ from each other morphologically markedly through their ankle anatomy but have the condont
by the number of openings, or holes, that they have on their (socket) teeth, though these are secondarily reduced in birds.
skull. All other living reptiles (snakes, tuataras) belong to the
The synapsids include mammals and their ancestors. The Lepidosauria. These are acrodont or pleurodont, but are
anapsids include a number of extinct reptiles whereas the never thecodont. The Lepidosauria are characterised by the
diapsids comprise modern-day reptiles and birds, as well as spreading of their extremities, which affects locomotion –
their extinct relatives. The position of the turtles in relation carried out by lateral undulation of the spine.
to anapsids or diapsids remains unclear: they have no tempo-
The only extant representatives of the synapsids are mam- Several Amniote groups have developed homeothermy, a
mals (Mammalia). The Protheria are represented only by form of ‘warm-bloodedness’, or the ability to thermoregu-
one extant group, the egg-laying monotremes, which include late and thus maintain a stable internal body temperature
the spiny anteaters (echidnas) and the platypus. regardless of external influences. Homeothermy is present
In contrast, the Theria are viviparous, meaning they bring in synapsids and the birds, and presumably the dinosaurs
forth live young which have developed inside the body of and ancestors of modern-day crocodiles were also capable
the parent. Unlike the Protheria, the Theria possess teats as of thermoregulation in a similar manner. To that end, evi-
well as a perineum, which separates the urinogenital system dence from a number of fossil and extant groups within the
from the anus. They also differ from the Protheria in their Archosauromorpha suggests they were homeothermic; for
bone structure, including in their skull and shoulder. Their example, the crocodiles have anatomical features that are
shoulder girdle is made up of only a shoulder blade (scapula) otherwise only found in warm-blooded animals, including
and collarbone (clavicle). modifications of the heart anatomy (four-chambered), pul-
The Theria are divided into the Metatheria (marsupials) monary ventilation, and the secondary palate. In addition,
and Eutheria (placentals, or higher mammals). In marsupi- a conversion of the hip joint allowed the archosaurs to walk
als, offspring are born in an early embryonic-like state before upright, which in turn required a higher body temperature
continuing their development inside their mother’s pouch. and suggests that homeothermy developed as early as in the
archosaur ancestors.
acrodont: dentition in which the teeth have no roots and are thecodont: possessing dentition consisting of teeth set in bony
fused to the jaw bone at their base sockets in the jawbone
homeothermy: the ability to maintain a stable body tempera- viviparity: term describing organisms which produce their off-
ture spring in live births (as opposed to laying eggs); both fertilisa-
pleurodont: dentition consisting of rootless teeth that are tion and the development of the embryo take place inside the
fused to the jaw bone by their outer surface mother’s body
See also: Amnion: 2.3.4.2; Sauria: 2.3.4.4

stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
Protheria Monotremata rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
Metatheria a Stra
lveolata
Meta monad men
Synapsida: one temporal window a Ha
opile
s
zo
oa ta
Theria eb
o pt
Cry
soz on
op
thecodont teeth, differenti- mo
ok
A hy
pto
st
ta
hi
ated into incisors, canines,
phy
Op
Apu
and molars (or secondarily Eutheria
ta
toothless)
Eubacteria Archaea
The Anapsida are extinct. Most

Anapsida members were alive in the Car-
boniferous and Permian
Anapsida: no temporal window

remains unclear whether turtles belong
Testudines
to the Anapsida or Diapsida
comprise a number of differ-

S Lepidosauromorpha teeth
Sauropterygia ent extinct groups of aquatic
a are acrodont or pleuro-
dont reptiles
u
r
o extant reptiles excluding
Lepidosauria
turtles and crocodiles
p
s
i
d
Diapsida: two temporal windows
a
The mesotarsal ankle joint of the Ornithodira runs

Archosauromorpha possess between the proximal and distal tarsals
thecodont teeth (or are
secondarily toothless)
The crurotarsal ankle joint of the Crurotarsi is a pivot joint along

the longitudinal axis between the calcaneus and talus bones
In an evolutionary context, increases in size depend on the availability of food, space, extinct rhinoceros-like Indricotherium transouralicum
and prevailing climatic conditions. The size and growth rates of organisms are therefore was the largest known land mammal, weighing around
limited by a range of factors. 17 tonnes and measuring 8 m in length.
Large bodies can retain heat better, and larger organisms digest their food more slowly
and have fewer overall predators. Mammal body size is limited by the relatively warm
climate and the size of the land area.
Other factors favour smaller individuals; for example, if food is scarce or if mobility is a
particular advantage. Physiology and genetic factors also impose size limits.
The largest land-dwelling organisms in Earth’s history were the dinosaurs. They reached
a body length of up to 40 m and a height of up to 17 m. They were able to reach these
immense proportions for a number of reasons: they did not chew, saving not only time
but also on the need for specialised teeth. This made their head lighter and thus allowed
them to have a longer neck. Their bird-like pulmonary systems, comprising a system of
airbags, also facilitated breathing despite their longer necks. Dinosaurs also grew quickly
as a result of their high metabolic rate. In addition, dinosaurs laid eggs, therefore sav-
ing energy on breeding, allowing for a high number of offspring and in turn guarantee-
ing a stable population. After the dinosaurs died out, around 65 mya, mammals, until
then only the size of present-day rodents, began to increase in size. The mammals were
then able to successfully occupy ecological niches that the dinosaurs left behind. Within
25–30 mya, the body size of mammals continuously increased on all continents. The
Size and dimensions

280 Megasystematics
4.2.2
Holomycota
The unikont kingdom Fungi comprises approximately plants (mycorrhizae), algae, and cyanobacteria (lichens), as
70,000 known species, classified into the following groups: well as animals (for example, leafcutter ants). Many fungal
Nucleariidae, Microsporidia, Chytridiomycota (plus Neocal- species also live parasitically on a variety of host organisms,
limastigomycota and Blastocladiomycota, recently excluded and are able to shift easily between mutualistic and parasitic
from the Chytridiomycota), Glomeromycota in the strict relationships.
sense, the polyphyletic zygospore-forming Glomeromycota Fungi include the largest living organisms on Earth, be-
(previously known as Zygomycota), Ascomycota, and Ba- longing to the species Armillaria ostoyae (honey mushrooms).
sidiomycota. This organism, which weighs around 600 tonnes, occupies a
Fungi have mitochondria but no plastids and form charac- 9 km² area of forest in Oregon, USA, and is likely over 2,400
teristic cell walls made of chitin, cellulose, and glucans. Like years old. The fungus Formitiporia ellipsoidea forms the largest
bacteria, fungi are ecologically vital components within the fruiting body, over 10 m long, 80 cm wide, and around 5.5 cm
decomposition process in both terrestrial and aquatic ecosys- thick. In comparison, the largest plants on Earth, the gi-
tems, freeing carbon dioxide and nutrients from degrading ant redwoods (Sequoiadentron giganteum), are approximately
organic material. 120 m tall and weigh around 1,250 tonnes each. The largest
Fungi also play an important role in the supply of nu- living animal is the blue whale, measuring around 33 m in
trients to plants, as well as in symbiotic relationships with length and weighing 140 tonnes.
Because of their cell walls, lack of a phagotrophic diet, is absent in plant cell walls, which are generally composed
and sessile lifestyle, the fungi were classified as plants for of cellulose. The so-called ‘cellulose fungi’ (Peronosporomy-
a long time. Molecular data, however, show that the fungi cetes) are not truefungi, but belong to the Chromalveolata.
belong to Unikonta and are therefore more closely related Likewise, the plasmodial slime moulds (Myxogastria) belong
to animals. Morphological features also support this rela- to the Unikonta, but to the Amoebozoa and not to the Ophis-
tionship: although higher fungi have secondarily reduced tokonta.
flagella, basal groups still have an ophistokont flagellum. The Nucleariidae are amoebae with filose pseudopodia,
Furthermore, their cell walls contain chitin, which is also though they are not affiliated with Amoebozoa but, rather,
found in the exoskeleton of arthropods. In contrast, chitin with Ophistokonta as a sister group of fungi.
decomposers: organisms that live on dead or decaying organ- pseudopodia: temporary projections of plasma to enable
isms and which are involved in the process of decomposition movement or attachment to a surface; also used for ingesting
glucan: glucose-based polysaccharide nutrients
plasmogamy: the fusion of the cytoplasms of two cells septum: dividing wall in hyphae, basidia, spores and konoids
See also: Phagotrophy: 4.6.2.3; Pseudopodia: 4.2.3; Sister group: 4.1.1.6

Unikonta: Holomycota 281
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
The Nucleariidae are amoeboid organisms
Chr
hy
ae
Disc ta
Excavata
inhabiting mostly freshwater habitats oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa ta
o pt
eb
Cry
soz on
op
mo
ok
A hy
pto
st
ta
hi
phy
Op
Apu
The Microsporidia are exclusively parasitic. Their
ta
inner spore wall is made of chitin
Eubacteria Archaea
The Chytridiomycota are mostly unicellular and flagellated
The polyphyletic zygospore-forming fungi do not form septa. The hyphae are
multinucleated. The Mucoromycotina, Entomophthoromycotina, Zoopagomy-
cotina, and the Kickxellomycotina form zygospores
In addition to a few zygospore-forming fungi, the Glomeromycota include for the

most part symbionts of plants (arbuscular mycorrhiza), forming multinucleated
hyphae without real septa
Basidiomycota
The Basidiomycota and Ascomycota form true
septa within their hyphae. They all have at
least some dikaryotic hyphae, meaning those in
which cells contain a haploid nucleus from each
parent rather than a single haploid or diploid
nucleus. As a result, these two fungal groups are
collectively known as the Dikarya
Ascomycota
CH2OH CH2OH
Cell walls are found in a variety of organisms. the cellulose, β-1,4-glycosidic. In contrast with Cellulose CH2OH CH2OH
However, the chemical composition of these glucose, acetylglucosamine has an acetamino O O
walls may differ from group to group. Neverthe- group at position 2. OH O OH
less, the most important components – cellu- Peptidoglycan (murein) is the main component
lose, chitin, and peptidoglycan – have a similar of prokaryotic cell walls. It consists of the sugar- glucose
OH
glucose
OH
structure. derived molecule N-acetylglucosamine and N-

The cellulose present in plant cell walls is a poly- acetylmuramic acid. Here again, the monomers Chitin CH2OH CH2OH
O O
saccharide made of β-D-glucose molecules (cel- are β-1,4-glycosidic linked to polyglucan chains. O
OH OH
lobiose). Cellobiose consists of two β-1, 4-glyco- These are cross-linked at the lactyl residue of
sidic linked glucose molecules. The connection the acetylmuramin with amino acids by peptide NHCCH3 NHCCH3
=
is effected by covalent compounds in which two bonds. O O

hydroxyl groups (-OH) form a water molecule acetylglucosamine acetylglucosamine
(H2O) and the remaining oxygen atom connects Peptidoglycan CH2OH CH2OH
the ring-shaped basic structure (pyran ring) of O O
two cellobioses. In addition, there are intramo- O
O OH
lecular hydrogen bonds.
Chitin, which is a main component of cell walls CH2 NHCCH3 NHCCH3
in fungi, is synthesised from acetylglucosamine.
=
H3CCH O O
The acetylglucosamine units are linked, as in acetyl
CO
muramic
R acid acetylglucosamine
Cell wall materials

282 Megasystematics
4.2.2.1
Microsporidia and Chytridiomycota

The Chytriodiomycota are mostly single-celled fungi Neocallimastigomycota and Blastocladiomycota. The Neo-
comprising around 700 known species grouped within either callimastigomycota have no mitochondria, but do have hy-
the Chytridiomycetes or the Monoblepharidomycetes. They drogenosomes. The Blastocladiomycota are a group that is
are the only fungal group to form flagellated cells (zoospores predominantly based on molecular data alone.
and gametes). The Chytridiomycota have mitochondria but The unicellular Microsporidia comprise about 1,200 spe-
no plastids. They are predominantly aquatic but may also cies, all of which are intracellular parasites that are usually
colonise shores of lakes and rivers and even drier soils (in- found within the intestinal epithelium of fish and arthro-
cluding desert soils). They live as parasites, mutualists, and pods. Some may also infect humans. Microsporidians, which
saprophytes. Anaerobic species of Chytridiomycota are in- have neither mitochondria nor plastids, reproduce by passing
volved in the degradation of plant materials within the diges- on spores. They are divided into two groups: Apansporoblas-
tive tract of sheep and cattle. tina and Pansporoblastina.
Many anaerobic species were excluded from Chytridi-
omycota and placed in the recently established groups
Some Chytridiomycota species form hyphae, usually not known as the polar tube. It can be up to 400 µm in length and
separated by septa. The hyphae are multinucleate and only is used when Microsporida infect a host cell: within the intes-
the sporangia are separated from the rest of the fungal body tine of the host, the polar tubes are ejected based on a chemi-
by a cell wall. cal signal triggered by increasing pressure within the spore.
In asexual reproduction, the sporangia release flagellated The polar tubes attache themselves to the host’s intestinal
spores which germinate upon contact with a source of nutri- epithelium and the sporoplasm enters the host cell through
tion. In sexual reproduction, flagellated germ cells (gametes) the tube. Two groups can be distinguished depending on
are released. Some species also display somatogamy, where the design of the extrusion apparatus, the Microsporea and
two hyphae merge and the zygote develops into a spore. Rudimicrosporea. Asexual reproduction (merogony) takes
Microsporidia lack kinetosomes, centrioles, and flagella. place within the host cell, finally forming new spores (sporo-
They also lack mitochondria and have strongly reduced ge- gony) asexually. The newly-formed spores leave the host
nomes, among the smallest observed genomes of eukaryotes. through faeces or during decomposition.
Their spores are between 1–40 µm in size, surrounded by two Nosema apis is of particular economic importance, as it is
cell wall layers, the inner layer (endospore) made of chitin the trigger of nosemosis, the most common disease in adult
and the outer layer (ectospore) made of proteins. They also bees. These transfer from one bee community to another
feature a characteristic coiled polar filament inside the spore, through either predatory insects or on individual bees.
anaerobe: (Grk.: an = not, aer = air, bios = life) processes or saprophytes: heterotrophic organisms which feed on dead or-
organisms which can survive without molecular oxygen ganic matter and in doing so break it down into its constituent
centrioles: cell structures involved in forming the spindle ap- parts
paratus septum: dividing wall in hyphae, basidia, spores and konoids
hypha: filamentous structure in fungi which grow at the tip and sporoplasm: cell plasm in a spore
remain unbranched or branch laterally zygote: (Grk.: zygotos = yoked together) the cell formed from
two gamete cells in sexual reproduction
See also: Mutualism: 4.2.2.5

stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa ta
o pt
eb
Cry
soz on
op
mo
ok
A hy
pto
st
ta
hi
phy
Op
Apu
ta
Eubacteria Archaea
The Chytridiomycota are mainly aquatic and mostly unicellular fungi. In contrast with other fungal groups, they
form flagellated swarmers. Chytridiomycota live as saprophytes or parasitically on various organisms. Above is a
parasitic chytrid on filamentous green algae (left) and a saprophytic chytrid of genus Rhizidium on pollen grains
(right)
The nucleus-containing sporoplasm passes through
Dab (Limanda limanda) in- the polar filament cell infecting intestinal epithelial
fected by the microsporidian cells of the host. Inside, the microsporidian under-
Glugea stephani goes asexual reproduction and forms cysts.
Chemical stimuli within the intestine of the host

induce a rapid discharge of the polar filament
mediated by the lamellar membrane system and
the vacuole. The polar filament is anchored to a
plate within the spore and serves as conduit for
sporoplasm passage
Microsporidian spores contain either one or two nu-

clei. The polar filament is wound within the spore. The
plasma membrane is surrounded by an outer exospore
of protein and an inner endospore of chitin
Infections not caused by viruses or bacteria but by Babesiosis – development of Babesia sp. sulting merozoites can asexually multiply or
parasitic unicellular protozoa (for example, Plasmo- (Apicomplexa): a multinucleated sporo- make up gametocytes. These are taken up
dium (malaria), Toxoplasma (toxoplasmosis), Leishma- blast forms from the kinete, from which by a sucking tick, before forming gametes,
nia (leishmania) or parasitic worms (e.g. Schistosoma the sporozoites emerge. These are trans- which fuse to the zygote. The zygote forms
= schistosomiasis) are known as parasitic diseases. ferred through blood-sucking parasites haploid kinetes through meiosis.
These often take place through the ingestion of con- and penetrate the erythrocytes. The re-
taminated food or droplets. Protozoa can also infect
through insect bites. Among ectoparasites (external merozoites
sporoblast
parasites) are lice, fleas, mites, and flies, which lay sporozoites
their eggs in open wounds. merogony
Many parasites go through a generational cycle, either (asexual reproduction)
developing in one or several hosts. Sexual reproduc-
tion takes place in the definitive (final) host, whereas kinetes
the larval (juvenile) form of the parasite may develop intermediate
in intermediate hosts. After asexual reproduction they zygote final host host
are transferred back to the definitive host. gametes (tick)
gametocytes
gametogenesis
Generational shift in parasites

284 Megasystematics
4.2.2.2
Glomeromycota: arbuscular mycorrhizal fungi

The arbuscular mycorrhizal fungi, now known as Glom- etrate plant root cortical cells, forming tree-like branches of
eromycota, were formerly grouped with the zygospore-form- hyphae (arbuscules) through which they can move nutrients.
ing taxa as Zygomycota. Recent molecular phylogenies show This process also enables plants to better absorb dissolved
that Glomeromycota form a distinct lineage, which includes nutrients from the ground. Conversely, the fungus is also able
the arbuscular mycorrhizal fungi as well as some zygospore- to obtain carbohydrates from the host plant. Storage vesicles
forming taxa. The Glomeromycota are a rare and species- can form at the ends of the hyphae, which are multinucleate
poor group of chitinous fungi, important in an ecological and contain lipids.
and evolutionary context. As with other members of the This type of symbiosis is known as arbuscular mycorrhi-
mushrooms, they do not contain plastids but possess mito- zal (AM) and, as a result, the Glomeromycota are also called
chondria. AM fungi. AM fungi are not host-specific and, consequently
All Glomeromycota species live in obligate symbiosis with up to 80 % of land plants live in symbiosis with such fungal
mosses, ferns, and seed plants, playing a central role in the species. Around 160 different AM fungi species have been
nutrient supply of land plants. The hyphae of the fungi pen- described.
The oldest known terrestrial fungi fossils are AM fungi ably time around 900 mya. It is unclear how these fungi
from the Ordovician, around 440 mya. The symbiosis be- lived before land plants existed on Earth, though possibly in
tween Glomeromycetes and land plants developed with the symbiosis with cyanobacteria. This hypothesis is supported
emergence of land plants in the Silurian, the two co-evolving by a single known endosymbiosis between a fungus and a
since then. This relationship was likely vital in the colonisa- cyanobacterium: cyanobacteria of genus Nostoc live endos-
tion of terrestrial habitats by plants. ymbiotically with the glomeromycete of the genus Geosiphon
However, the radiation of fungi dates back to a much pyriformis. In this relationship, the cyanobacteria live within
earlier, with the emergence of Glomeromycota, presum- vesicles formed by the fungus.
endosymbiotic bacteria: symbiotic bacteria living in other or-

ganisms
See also: Colonisation of terrestrial environments: 2.3.3.6; Stratigraphic time scale of the Palaeozoic: 2.3.3
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa ta
o pt
eb
Cry
soz on
op
mo
ok
A hy
pto
st
ta
hi
phy
Op
Apu
ta
Arbuscular mycorrhizae (blue) in root cells of violets (Viola sp.) Eubacteria Archaea
The glomeromycetes form asexual multinucleate

spores, which are up to 800 µm in size. Sexual repro-
duction is not known in glomeromycetes
Fungal hyphae grow into the bark of roots, and some

grow into the root cells before ramifying like trees
(arbuscules). In this area, the cell walls are greatly re-
duced, simplifying the exchange of nutrients and me-
tabolites
The fungus stores metabolites in ves-

icles, both within the root bark and
on the outside
The soil is penetrated by plant roots (yellow) and fungal hyphae (blue). The hy-
phae form fine branches which are able to penetrate a larger volume of soil than
the plant roots. Using the fungal mycorrhizae, the plant therefore has better ac-
cess to the soil’s dissolved nutrients
Mycorrhizae are the product of a symbio- ships are found in a number of herba-
sis between fungi and plants, thoughdif- ceous plants and are critically important
ferent types of this relationship exist. In for the development of orchids.
ectomycorrhizal relationships, the fungus Arbuscular mycorrhizae are the most
grows between the cells and root rings, common mycorrhizal form, present in ap-
with the mycelium winding around the proximately 80 % of land plants. Here, the
roots. It does not penetrate the cortical fungus penetrates the root cortex cells
cells. Typically, ectomycorrhizal relation- and branches off into hyphae structures
ships can be seen in trees affiliated with (arbuscules), which enable the exchange
the Betulaceae, Fagaceae, Rosaceae and of nutrients.
Pinaceae. Interactions such as those enabled by my-
In contrast, endomycorrhizae emerge corrhiza are not necessarily mutualistic
when a part of the hyphae enters the root (advantaging both partners) and are com-
of the host tree, lacking the external hy- monly transitions to parasitic relation-
phal net characteristic of ectomycorrhizal ships, such as in chlorophyll-free parasitic
relationships. Endomycorrhizal relation- plants.
Pictures: Coenococcum sp. on oak roots (top-left), Lactarius rufus (top-right), Acephala
sclerotica (middle), Tomentella cortinasia (bottom)
Mycorrhiza
286 Megasystematics
4.2.2.3
Zygospore-forming fungi
The zygospore-forming fungi were previously grouped as maturing into spores. These are then released by the rupture
Zygomycota (zygote fungi), making up around 1,000 known of the sporangium, subsequently forming a new mycelium.
species. They have no plastids but contain mitochondria. Zygospore-forming fungi are mainly terrestrial and can be
Molecular data show that the group is polyphyletic, with found on every continent apart from Antarctica. They live
some taxa belonging to Glomeromycota as well as to four saprophytically, symbiotically, or parasitically on animals,
sub-lineages of unclear affiliation: Mucoromycotina, En- plants or other fungi.
tomophthoromycotina, Zoopagomycotina, and Kickxello- The most well-known representative of the zygote-form-
mycotina. ing fungi is the bread mould Rhizopus stolonifera, which be-
The hyphae of zygospore-forming fungi do not have longs to the Mucoromycotina and usually grows on bread,
any real cell walls (septa), with the exception of sporan- fruit, and other wet, carbohydrate-rich food. Preservatives
gia. Zygospore-forming fungi produce zygospores during such as calcium propionate and sodium benzoate can inhibit
sexual reproduction, where two hyphae of different mating the growth of this fungus. In this fungus, stolons, specialised
types grow together, forming a multinucleate gametangium. hyphae, form at the mycelium and stretch in the direction of
Gametes are not formed but, instead, the gametangia merge the foodstuff surface. When the stolons hit the surface mem-
(plasmogamy) into a multinucleated zygospore. Within the brane, rhizoids grow and asexual sporangiophores are pro-
zygospore, nuclei from two mating types come together first duced. At the point when sporangiophores with black spo-
undergoing karyogamy and then meiosis. At the moment of rangia develop, the mycelium is already deeply penetrated
zygospore germination, a sporangiophore forms at the hy- into the food (for example, bread). Sexual reproduction takes
phal tip. The nucleii migrate towards this sporangium before place in adverse environmental conditions (such as nutrient
shortage and drought).
The Mucoromycotina include saprotrophic, parasitic, spore capsule to be shot in the direction of a light source to
and ectomycorrhiza-forming fungi. The group also contains up to 2 m away.
human pathogenic agents, including the common moulds The Zoopagomycotina include endo- and ectoparasites
belonging to the genus Mucor (type species of the Mucoro- of small metazoans and fungi. This includes the carnivorous
mycotina). This fungus and other Mucoromycotina (also fungi of the genus Zoophagus, including Zoophagus insidans,
Rhizopus) cause mucormycosis in immunocompromised peo- which obtains nutrients by trapping rotifers and other small
ple, a condition brought about when the fungus enters the animals within sticky hyphae. After entrapment, the fun-
lungs by inhalation and passes into the blood and other or- gus grows into its prey. Zoophagus tentaclum forms loop-like
gans, including the central nervous system. The tissue is sub- hyphae, which it slings around and traps nematodes before
sequently destroyed and necrosis sets in. When the fungus pulling its hyphae together upon mechanical stimulation and
enters blood vessels, oxygen and nutrient supply to tissues growing into its prey. Captured animals are digested enyzy-
are reduced and cells subsequently die, causing thrombosis matically.
and infarctus. As a result, mucormycosis progresses rapidly The Entomophthoromycotina include, except for a few
and often leads to death. Another particularity found in the saprotrophic species, predominantly obligate parasites of
Mucoromycotina is the ejector system, known as the ‘dung metazoans (arthropods, vertebrates) and plants.
cannon’ (Pilobolus crystallinus). The spore-bearing organ has The Kickxellomycotina include saprotrophic species, fun-
photoreceptors at its base. Turgor pressure causes the whole gal parasites, and obligate symbiotic forms.
carnivorous: (Lat.: carnivorus = meat eating) consuming meat mycelium: the entirety of hyphae; the vegetative part of a fun-
commensalism: symbiotic relationship between two organ- gus
isms from different species in which one partner benefits and the sporangium: (Grk.: spora = seed, aggeion = vessel) a structure
other neither benefits nor suffers any disadvantage in which one or more spores are formed
karyogamy: fusion of two nuclei spore: (Grk.: spora = seeds) asexual reproductive cell
See also: Perception of light: 4.3.2.1

stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa ta
o pt
eb
Cry
soz on
op
mo
ok
A hy
pto
st
ta
hi
phy
Op
Apu
ta
Eubacteria Archaea
The common feature of zygospore-forming fungi are Zoophagus sp. (Mucoromycotina) forms loop-like
the zygospores resulting from the fusion of gametangia hyphae, which it uses to entangle and penetrate prey
(here: Phycomeces blakesleeanus) (e.g. nematodes) before digestion
The spores germinate. Haploid multinucleate The multinucleate gametangia fuse and form a
hyphae emerge, since no real septa are formed. multinucleated zygospore. Within the zygospore,
Sexual reproduction is initiated when hyphae of the two nuclei of different mating types undergo
two different mating types grow towards each karyogamy and then eventually meiosis. Later, a
other. The multinucleated gametangia fuse (plas- sporangiophore and a sporangium grow out of
mogamy). Gametes are not formed the zygospore
Uninucleate spores are

formed in the sporangium
Sporangia may arise mitotically from

the hyphae without sexual recombi-
nation. Under optimal growing condi-
tions, this type of reproduction is pre-
dominant
Organisms are grouped according to different criteria. Their phylogeny, or evolutionary relationships, plays a central role. Especially in conventional
textbooks, organisms are grouped according to functional similarities or according to the complexity of their organisation, even if they have multiple
independently convergently evolved. Examples of such polyphyletic or paraphyletic groups are:
• Bryophyta: The mosses and hornworts are closer related to the • Algae: The photosynthetic eukaryotes, with the exception of land
ferns and seed plants than the liverworts; the Bryophyta are there- plants, are grouped together as algae. However, these organisms
fore a paraphyletic group. belong to a range of lineages (Chromalveolata, Rhizaria, Archae-
• Pteridophyta: The true ferns are more closely related to seed plastida, Excavata). If considered from an ecological standpoint,
plants than to the lycopods, the Pteridophyta therefore form a the photosynthetic cyanobacteria are also grouped with the algae.
paraphyletic group. • Reptiles: Phylogenetic data suggest that birds belong to reptiles,
• Fungi in the broader sense: Chitinous fungi are grouped with the with crocodiles more closely related to birds than to other reptiles.
Opisthokonta whereas cellulose fungi (oomycetes) group with However, due to the differential organisation of birds and reptiles,
Chromalveolates and the slime moulds with the Amoebozoa. birds are often considered separately from the consequently para-
These polyphyletic groups are referred to as fungi (in the broader phyletic)reptiles.
sense) mainly because of their osmotrophic lifestyle.
• Yeast: The term ‘yeast’ has been assigned to more than one group
of organisms. On the one hand, it is used to refer to a fungal taxon
and, on the other, to the level of organisation of unicellular fungi
(though many different groups of fungi are unicellular).
Organisational morphology and phylogeny

288 Megasystematics
4.2.2.4
Ascomycota
The Ascomycota (sac fungi) are the sister group of Basidi- medically important species belong to this lineage, includ-
omycota within the chitinous fungi. Both groups are char- ing the antibiotic-producing Penicillium chrysogenum, as well
acterised by a septation of the hyphae by cross walls with as the pathogenic lung parasite Pneumocystis, ergot (Clavicepts
a central perforation, binuclear (dikaryotic) phases after the purpurea), and powdery mildew. Various species belonging
merger of the cell plasma and the possibility of fusion of to the family Erysiphaceae (Pezizomycotina) are causative
sterile hyphae (anastomosis). The Ascomycota also contain agents of powdery mildew. Mildews infections affect a range
spore-bearing cells, the tubular asci. of plant species, with fruiting bodies forming on the top of
Around 30,000 species of Ascomycota have been de- leaves. The causative agents of downy mildews, which form
scribed, yet another 30,000 are known to live symbiotically fruiting bodies on the underside of leaves, are not related to
with algae in lichen. They are predominantly terrestrial, the ascomycetes but, rather, to the Oomycetes (strameno-
though a few species can also be found in freshwater and piles).
marine habitats. All Ascomycota lack plastids but possess A number of mould species (for example, the red bread
mitochondria. Their cell walls mostly contain chitin and mould Neurospora sitophila) as well as most Ascomycota with
β-glucan. large and conspicuous fruiting bodies, and the edible lorchel,
Ascomycota are divided into the Pezizomycotina, Saccha- morel, and truffle fungi, also belong to the Pezizomycotina.
romycotina, and the Taphrinomycotina. Furthermore, many lichen fungi belong to this group, includ-
Pezizomycotina are the largest lineage. Characteristic is ing the largest lineage of lichen fungi, i.e. the order Lecano-
the formation of asci from ascogenous hyphae which are rales, which comprises around 10,000 species.
combined within a fruiting body called ascocarp. Several
In addition to the Pezizomycotina, the Saccharomycotina research. Saccharomycotina also include pathogenic species,
and Taphrinomycotina also belong to Ascomycota. including the mucosal infecting Candida albicans.
The Taphrinomycotina are a diverse but relatively species- Sexual reproduction occurs mostly through gametangiog-
poor group. As with Saccharomycotina, they lack fruiting amy. In the ascus, i.e. the extension of the dikaryotic hyphae,
bodies (ascocarp or ascoma). the nuclei undergo karyogamy and subsequently meiosis,
Saccharomycotina have a simple morphology with short resulting in four or eight ascospores which are released and
or no hyphae. Their asci arise without the formation of an grow into new mycelia. The fruiting bodies are named ac-
ascocarp, after the joining of two haploid cells. After the for- cording to their shape: apothecium (peeling open), peritheci-
mation of the zygote, an ascus containing four ascospores um (bottle-shaped), and cleistothecium (spherically closed).
develops. The Saccharomycotina include most yeasts, in- Reproduction is predominantly asexual, occurring
cluding baker’s yeast (Saccharomyces cerevisiae). In addition to through the proliferation of mononuclear conidia, located
its commercial importance, this species, having been the first in the tips of specialised hyphae and distributed by animals,
eukaryotic organism to have its genome sequenced, is one wind, and water.
of the most important objects of genetics and cell biology
ascocarp ( = ascoma): fruiting body of the ascomycete gametangiogamy: growing together and fusion of two entire
conjugation: transfer of DNA to another cell by means of a gametangia
plasma bridge
See also: Downy mildew, Oomycetes: 4.6.2.1

In addition to the morel (shown below), stida Rh

pla iza
ae
Viridiplant ta
ria
truffles belong to Ascomycota
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa ta
o pt
eb
Cry
soz on
Many types of mould belong to mo
op
ok
A hy
pto
st
ta
Ascomycota
hi
phy
Op
Apu
ta
In Ascomycota, the layer in which meiosis and sporulation
take place, the hymenium, is characteristically organised as Eubacteria Archaea
either cup-shaped apothecia (here), closed cleistothecia,
or bottle-shaped perithecia and pseudothecia
Karyogamy and subsequently meiosis takes place

within the tubular asci. The haploid nucleus gen-
erally divides further through mitotic division,
forming eight haploid spores
The haploid hyphae can grow

into conidiophores, which pro-
duce conidia, asexual distribution
units (spores)
The fruiting body (ascocarp) grows af-

ter plasmogamy of two cells of different spores
mating types
conidia
Eukaryotic cells typically have one cell nucleus. However, many organ- divide is otherwise only observed in multicellular organisms such as
isms differ because they contain multinucleate cells, those with two or plants and animals, as well as in a few colonial protists, such as Volvox.
more nuclei. Multinucleate cells also form the plasmodium of slime moulds, which
In fungi, a heterokaryotic mycelium is formed just after plasmogamy comes about after the fusion of many individual cells in some taxa or by
(cell fusion), instead of the usual karyogamy (nuclear fusion) step. The multiple nuclear division of a single cell without cell division in others.
repeated synchronous division of the pairs of nuclei created from just Multinuclear cells are also found in many other groups of organisms.
one initial plasmogamy eventually allow for many independent meioses. Examples of such cells are human muscle fibres (from up to 100 myo-
This increases the chances for genetic recombination, even when the en- blasts), the neodermis of platyhelminths and nemathelminthes, as well
counter of sexual partners is rare. Another solution to this problem – al- as some algal species, such as the green algae Caulerpa.
lowing for a number of meiosis steps following just one plasmogamy – is The two or more nuclei may also play a fundamental role in the architec-
realised in many algae and plants by growing a gametophytic generation. ture of the cell. For example, diplomonads and some oxymonads have
Multinucleate states can also serve to protect the genome: some ciliates two or more nuclei, associated with the basal bodies of the flagella and
and foraminifera have two different types of nuclei: a small diploid nu- the structure of the cytoskeleton.
cleus used for reproduction (generative micronucleus) and a larger, poly-
ploid nucleus which controls the cell’s metabolism (somatic macronu-
cleus). As a result of these dimorphic nuclei, the somatic and generative
functions are separated in these protozoa. Without the micronucleus,
the organisms would no longer be capable of division. Such a functional
Multinucleate cells
290 Megasystematics
4.2.2.5
Basidiomycota
Basidiomycota comprise around 30,000 species, roughly spores are called conidia and serve vegetative, asexual repro-
a third of all known fungi, divided into three subphyla: the duction.
Agaricomycotina (standing mushrooms in the narrow sense, The Agaricomycotina (standing fungi) is the most com-
including most edible fungi), the Ustilaginomycotina (smut monly recognised fungal group, familiar to most of us as
fungi), and the Pucciniomycotina (rust fungi). mushrooms or toadstools. These mushrooms obtain nutri-
Basidiomycota are characterised by the presence of basid- ents saprophytically through their mycelium or symbiotically
ia, bottle-shaped cells that form haploid spores after meiosis. through mycorrhizae. About 90 % of the volume of each in-
Basidia are either unicellular (holobasidia) with four spores dividual is made up of underground mycelia. Fruiting bod-
or divided into four septa (fragmobasidia). In Fragmobasid- ies are formed above ground as a reproductive organ. The
ia, each septum contains a spore. basidia are formed in the hymenium, the area where spores
As with other chitinous fungi, plasmogamy, the fusion of are formed through meiosis. The standing fungi vary by their
cells, and karyogamy, the fusion of nuclei, are two separate organisational form, based on the position of the hymenium,
processes. Mycelia are therefore dikaryotic, containing two influencing the external shape of the fruiting bodies: in aga-
nuclei. Karyogamy, the fusion of the nuclei, takes place in rics, the hymenium sits on lamellae, whereas in tubular fungi
the hymenium immediately before meiosis. In addition to this organ sits on the inside of the tube. In gasteroid fungi
the meiotic spores produced in the basidia, the haploid hy- (Gasteromycetes), spores are formed inside the organism.
phae can build spores as well. These mitotically resulting
The Pucciniales or rust fungi (affiliated with the Puccini- The approximately 500 species of Ustilaginomycotina,
omycotina), are among the most dangerous phytopathogens. or smut fungi (Ustilaginales), are obligate parasites and also
They live mainly parasitically on plants and in the intercellu- cause disease in various crop species. The hyphae, which
lar spaces of plant tissues, penetrating into host cells through germinate from the basidiospores, are not infectious and are
the formation of a haustorium. Some species change host. single celled, similar to yeasts. The infectious dikaryotic hy-
Rust fungi form small fruiting bodies. Aside from basidi- phae arise only after fusing with a cell of another mating
ospores, rust fungi can be differentiated by their spore types: type. Infection can be detected on host plants through a black
they possess either the cold- and drought-tolerant, two-celled spore mass giving it a burned appearance. These spores, teli-
and thick-walled teliospores or the unicellular, haploid, dinu- ospores, are initially dikaryotic. Karyogamy and subsequent
clear aecidiospores and uredospores. Rust fungi are obligate meiosis occurs in these spores. Septate basidia, which form
plant parasites and include around 7,000 described species. the haploid, mononuclear basidiospores, appear in the spring
Over 300 species can infect wheat and grass species. Since of the year following germination.
some infections can lead to massive crop failures, they can
be used as tools for biological warfare.
conidia: type of spore in fungi (Ascomycota and Basidiomycota) hymenium: tissue layer where meiospores develop in
and in prokaryotes of genus Streptomyces; characteristic of basidiomycetes and ascomycetes
the biological dispersal of fungi; the spores are formed outside somatogamy: sexual reproduction in which the haploid
the sporangium after developing specialised hyphae, or on somatic cells (not gametes) from several organisms fuse together,
conidiomata creating a diploid cell
See also: Karyogamy: 4.2.2.3; Parasites: 4.2.2.1

stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa ta
o pt
eb
Cry
soz on
op
Rust fungus (Uromyces sp.) on less- mo
ok
A hy
pto
st
ta
er celandine (Ranuculus ficaria)
hi
phy
Op
Apu
ta
Eubacteria Archaea
Fruiting body Fairy ring
The bulk of mushrooms and toadstools grows underground, often
spreading from the centre in a ring-like formation. As a result, fruiting
bodies, only a small part of the organism, are arranged annularly (fairy
ring). The largest known organism is a honey fungus, which extends
Sedge (Carex sp.) infected by a across 9 km2
smut fungus (Anthracoidea sp.)
Karyogamy takes place within

the hymenium, followed by
meiosis and the formation of
four spores on the basidia
Plasmogamy, the fusion of two hyphal cells of different mating types, leads to
dikaryotic (binuclear) cells. The dikaryotic mycelium forms fruiting bodies for Spores are the dispersal units of Basidiomy-
sexual reproduction. However, fungi may also reproduce asexually through cota. After germination, they form haploid
the segmentation of hyphae hyphae
Relationships between organisms are diverse. other to survive, this relationship is known as
Most species depend directly or indirectly on ‘obligate mutualism’.
interactions with other species in relationships One of the most important symbiotic relation-
ranging from feeding and parasitism to obligate ships occurs between fungi and plants, and in-
mutualistic, i.e. advantageous and necessary volves mycorrhizae. In lichens, the mutualistic
for life to both partners. relationship goes so far that each individual
In the European literature, a relationship be- organism (lichens) actually corresponds to an
tween species that is advantageous to both association of two species (fungi and algae).
partners is referred to as ‘symbiosis’. In the In the event when organelles, such as mito-
American literature, however, this is called chondria or plastids, are reduced to such an
‘mutualism’, and ‘symbiosis’ refers to any form extent that they cannot be described as inde-
of social relationship between species, includ- pendent organisms and are certainly not inde-
ing parasitism. pendently viable, the term ‘endosymbiosis’ is
A symbiont can live within (endosymbiosis) or inadequate and thus replaced by ‘endocyto-
outside (ectosymbiosis) the body of its host. biosis’.
If a symbiotic relationship is not necessary
for life, it is known as ‘facultative mutualism’. The feeding relationship between ladybird
Conversely, when one or both species need the and aphids is also a mutualistic relationship
between plant and ladybird
Symbiosis / mutualism
292 Megasystematics
4.2.3
Amoebozoa
The Amoebozoa are the sister group of the Ophistokonta. comprise ‘naked’ forms (Amoeba, Chaos), shelled amoeba,
In these organisms, the shape of the cell is usually not fixed and slime mould forms. Flagella are usually reduced and the
but is, rather, amoeboid. However, amoebae, organisms char- pseudopodia contain no microtubules.
acterised by their amoeboid locomotion, can also be found The Amoebozoa were conventionally divided into Lo-
in many other groups of organisms as well. For example, bosa (with Tubulinea and Discosea) and Conosa. Neverthe-
largely amoeboid species occur in Rhizaria as well the Het- less, phylogenetic relationships within Amoebozoa remain
erolobosea (Excavata). The Amoebozoa therefore comprise unclear.
numerous but not all amoeboid organisms. Amoebozoa
The Lobosa (lobose amoebae) have blunt pseudopodia. The Flabellinia are flattened amoebae, which are discoid
Pseudopodia are used to characterise Lobosea subgroups as or irregularly triangular in shape. Their sub-pseudopodia
being either tubular (Tubulinea, or as Lobosa sensu stricto), or are never pointed. The Longamoebia comprise all flattened,
lacking, with a flattened, tubular body (Discosea). elongated, lobose amoebae. The Centramoebida (=Acan-
The Tubulinea are amoeboid protozoa that are naked thamoebida) have an extremely thin glycocalyx and a non-
or surrounded by a shell (test). They form tubular or ap- adhesive uroid, which moves by sliding in a fluid, non-jerky,
proximately cylindrical pseudopodia. Their cytoplasm flows manner.
within the entire cell or within a pseudopodium in only one The lobopodia are broad pseudopodia with flexible sub-
strand (uniaxially). Centrosomes are absent in Tubulinea. pseudopodia (acanthopodia) branching out into a tip. Rep-
Locomotion is based on an actin-myosin cytoskeleton. Cyto- resentatives of this group are the most common free-living
plasmic microtubules are, if present, rare and never grouped amoebae in soil and freshwater habitats. Some species can
in bundles. Flagella do not occur. cause disease, such as granulomatous amoebic encephalitis
Based on molecular analyses the Discosea is made up or acanthamoebiasis. Contrary to the Centramoebida and
of Flabellinea and Longamoebia. The latter comprise The- Thecamoebida, the Dermamoebida have a multilayered and
camoebida, Dermamoebida and Centramoebida (=Acan- thick cell wall. The Thecamoebida differs from Centramoe-
thamoebida). bida through its broad hyaline anterolateral membrane.
glycocalyx: capsule or plasma coating; coating on the surface microaerophiles: organisms that require oxygen to survive but
of the cell membrane or cell wall in smaller concentrations than are present in the atmosphere
uroid: posterior bulb in amoebae
See also: Excavata: 4.3; Heterolobosea: 4.3.2; Rhizaria: 4.5

Unikonta: Amoebozoa 293
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
Ha s
oa
oa nta
z pt
bo
Cry
e op
o
mo
ok
A hy
pto
Amoeba sp. (Euamoebida) The Arcellinida include amoeba with an organic or mineral shell, also known as
is t
ta
soz
h
phy
Op
a test. Left: a living specimen; right: an empty shell belonging to Nebela collaris
Apu
ta
Tubulinea: no flagella, tubular pseudopodia
Euamoebida (= Tubilinida): lacking a test, lacking adhesive uroidal structures Eubacteria Archaea
Leptomyxida: lacking a test, possessing adhesive uroidal structures
Arcellinida: organic or mineral extracellular test
Discosea: no flagella, pseudopodia not tubular
Flabellinia: fan-shaped or triangular, lacking pointed subpseudopodia
Dactylopodida: motile irregularly triangular cells, broad anterior hyaloplasm
Vannellida : motile fan-shaped cell, broad anterior hyaloplasm
Stygamoebida: flattened and oblong
Longamoebia: flattened, oblong, pointed subpseudopodia
Dermamoebida: elongated with broad triangular pseudopodia
Thecamoebida: elongated, without pseudopodia
Centramoebida (Acanthamoebida): flattened, with pronounced pseudopodia Ripella platypodia (Flabellinia:
Conosa: often flagellated Vannellida)
Multicilia
Phalansterium
Protosteliida: ‘slime molds’ – sporophore develops from solitary cell, unicellular amoeba
Schizoplasmodiida: ‘slime molds’
Archamoebae: partially reduced mitochondria
Entamoebidae: lacking flagella, possessing mitosomes
Mastigamoebidae: one rigid flagellum
Pelomyxa: multiple flagella
Cavosteliida: ‘slime molds’, amoeba, mono- to multinucleate
Protosporangiida: ‘slime molds’, amoeboflagellate
Mayorella sp. (Longamoebida:
Dictyostelia: ‘cellular slime molds’, fruiting bodies an aggregation of multiple cells, lacking flagella
Dermamoebida)
Myxogastria: ‘plasmodial slime molds’, fruiting bodies of multinucleate plasmodia, with flagella
A posterior bulb, the uroid (arrow), draws in the The outer unstructured region of the cytoplasm is Thecamoeba sp. (Longamoebida:
pseudopodia known as the hyaloplasm Thecamoebida): trophic cell (left)
and cyst (right)
The Amoebae are considered a general life form or organisational level Cercozoa, Chlorarachniophyta) and Heterolobosea (Excavata) species
rather than a taxonomic group. They form a large, diverse group of single- display the characteristic traits of amoeboid morphology. Amoeboid
celled organisms that have a changing body shape, emitting pseudopodia. locomotion is also prevalent in some chromalveolate algae.
Amoeboid life has developed independently in several lineages. Apart
from individuals within Amoebozoa, several Rhizaria (Foraminifera,
lobopodia lamellipodia filopodia reticulopodia axopodia
Pseudopodia
294 Megasystematics
4.2.3.1
Conosa
Along with Lobosa, the Conosa belong to Amoebozoa, modia by repeated nuclear divisions, without subsequent cell
together forming a group sister to Opisthokonta. Conosa divisions. Formation of fruiting bodies occurs when the plas-
comprise a number of flagellated taxa. Specifically, they in- modia switches from negative to positive phototaxis, moving
clude Archamoebae, a variety of slime moulds (polyphyletic towards a light source and developing fruiting bodies, known
group, partly making up Mycetozoa), as well as other taxa. as sporocarps, develop.
The genera Multicilia and Phalansterium, as well as other rep- In Dictyostelia, several amoeboid cells congregate to form
resentatives, make up the Variosea. a multicellular aggregation, known as a pseudoplasmodium.
The species Breviata anathema, formerly placed within The pseudoplasmodium undergoes a metamorphosis part-
the Mastigamoebidae, remains phylogenetically unresolved, ly forming a stem and partly a sorus, the latter containing
though it is currently classified within Breviata (not shown), spores.
which may be a sister group of all remaining Amoebozoa. The majority of the approximately 1,000 known slime
The slime moulds are characterised by numerous of mor- mould species live in terrestrial habitats, mainly on dead
phologically different stages during their life cycle. Multinu- wood but also on the bark of living trees and on decaying
cleate plasmodia arise during the transition to fruiting body plant material scattered across the ecosystem surface. How-
formation. ever, slime moulds have also been found in deserts and in
In the Myxogastria and Protostelia, the plasmodia devel- alpine habitats. They lack plastids.
op from mononucleate amoeboid cells to multinucleate plas-
The systematics of slime moulds remain unclear, though the species Entamoaeba histolytica, the cause of amoebic dys-
it is thought that Dictyostelia and Myxogastria are mono- entery, is an important human pathogen. Archamoebae lack
phyletic whereas the Protostelia are paraphyletic. The Vario- mitochondria and the Golgi apparatus is reduced in some
sea include flagellated forms within the genera Phalansterium taxa. They are characterised by the nucleus-basal body com-
and Multicilia as well as unflagellated groups with pointed, plex, which contains the nucleus, the kinetosome of the fla-
often branched pseudopodia. gellum, as well as the microtubules holding together these
The Archamoebae are anaerobic parasitic or commensal structures.
organisms living in the digestive tract of animals, of which
aggregation: (Lat.: aggregatio = accumulation) accumulation, sorus (pl. sori): cluster of sporangia (fungi, ferns)
clustering sporocarp: spore-forming fruiting body
See also: Microtubuli: 4.2; Phototaxis: 4.3.2.1; Polyphyletic: 4.1.1.6

Unikonta: Amoebozoa 295
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
Ha s
oa
oa nta
z pt
bo
Cry
e op
o
mo
ok
A hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
Fruiting bodies (left) and amoeboid single cells of Protostelium sp. (left) and plasmodia of Myxogastria (middle-
right: Brefeldia maxima, right: another species) Eubacteria Archaea
Myxogastria cells are haploid biflagellate. (1) These cells can reproduce
5 asexually by mitotic division. The merger of two such amoeboflagellates

results in a diploid zygote. (2) When multiple synchronous nuclear division
1
takes place without subsequent cell division, a multinucleate plasmodium
appears. (3) The multinucleate plasmodium is macroscopically visible and
may be as large as a several decimetres in size. The diploid plasmodium
may also divide back into several individuals. Stalked sporangia form under
unfavourable environmental conditions, such as dehydration or lack of
food. (4) Haploid spores are formed by meiotic nuclear division and the
reduction of cell walls
4
3 2 4 1
Individual cells of Dictyostelia are haploid and amoeboid. (1) These cells
can reproduce sexually to form a zygote and eventually a cyst. (2) As a
result of chemical stimuli (e.g. cAMP), these cells come together, aggregat-
ing into multicellular pseudoplasmodia. (3) The pseudoplasmodium can
3 2
move as a whole and, depending on environmental conditions, may also
futher split again into individual cells. The pseudoplasmodium grows into
a cellulose-containing fruiting body. (4) The cells of the stem die, whereas
surviving cells encyst and later develop into spores (5)
Communication and other interactions between cells, tissues, organs, senescence, abscission, and apical dominance, gravitropism and photot-
and organisms is vital to life. Furthermore, intracellular communication ropism, and as well as many others.
is a prerequisite for the healthy functioning of all cells within more com- Semiochemicals are substances that enable communication between
plex, multicellular organisms, where cells are specialised by role. Cell ad- different organisms. Of these, pheromones target organisms belonging
hesion molecules (CAMs) play an important role in the communication to the same species, whereas allelochemicals are used for communica-
process, allowing cells to stick together (cohesion) and communicate tion between individuals of different species. Pheromones are used, for
with each other. CAMs can be divided into two distinct groups, namely, example, in the marking of territories, finding sexual partners, or as an
those responsible for contact between two adjacent cells and those alarm signal. For instance, plants can better protect against herbivores
dealing with contact between the cell and the surrounding extracellular by increasing, tannin production following the detection of alarm phero-
matrix. mones from neighbouring plants.
Hormones act as biochemical messengers with a specific effect or regu-
latory function. They are formed in special cells and transported to the
target organ, where they bind to specialised hormone receptors. These
receptors often sit near the cell surface. After binding takes place, sig-
nals are triggered along the inner surface of the membrane. In plants,
hormones control and regulate the development of the plant, initiating,
promoting, or inhibiting growth and developmental processes. Phyto-
hormones have a broad range of effects, including responsibility for the
growth of the roots, shoots, and leaves; development of seeds or fruit;
Chemical communication and semiochemicals

296 Megasystematics
4.3
Excavata
The Excavata (excavates) are a major eukaryotic group Another feature that is typical of the excavates is the pos-
named after the characteristic shape of their mouthpart, or teriorly-facing flagellum, which beats to create a water cur-
cystosome, which has a pronounced groove. However, many rent that sweeps prey particles towards the cystosome.
excavates lack this feature, as it is secondarily reduced in
various groups.
The excavates include Metamonada (metamonads) and aerobically or microaerophilically; their mitochondria are
Discoba (discobids) among others. Many taxa within these reduced.
two groups, and especially Metamonada, live in anaerobic In contrast, with a few exceptions, the discobids have mi-
habitats and have highly reduced mitochondria (hydrogeno- tochondria. In the Jakobida, the mitochondrial cristae are
somes and mitosomes). These reduced organelles are no morphologically distinct (often tubular), whereas in the case
longer capable of oxidative phosphorylation and, therefore, of Heterolobosea and Euglenozoa, these structures are dis-
can not be used for generating energy by cellular respiration. coid. As a result of this morphological property, these two
Still, these structures biosynthesise proteins and fats in the groups are clustered together as Discristata, which include
same way as mitochondria. free-living forms as well as parasitic taxa.
Metamonads comprise mainly commensal and parasitic
taxa, as well as some free-living taxa. All species live an-
kinetid: structure in eukaryotic cells used for locomotion sociated with the parabasal filaments. The parabasal filaments
kinetoplast: network of circular DNA in the mitochondrium of grow out of basal bodies which are themselves not part of the
kinetoplastids parabasal apparatus. The parabasal bodies can possess up to 20
kinetosome: basal body of flagella; kinetosomes consist of a flattened vesicles known as cisterna
cylindrical array of microtubules; they serve as a nucleation site paraxonemal rod: protein structure running parallel to the fla-
for the microtubules of flagella and cilia gella
parabasal apparatus: equivalent to a specialized Golgi appa- pellicula: (Lat.: pellicula = little skin) hard but flexible layer (usu-
ratus consisting of parabasal bodies (dicotysomes) which are as- ally made of proteins) under the cell membrane
See also: Hydrogenosome: 4.3.1

Excavata 297
Metamonada: anaerobic or microaerophilic, mitochondria strongly modified (hydrogenosomes or mito-

somes) and lacking cristae, usually four kinetosomes per kinetid (flagellar apparatus)
Fornicata: one nucleus and kinetid or two nucleus-kinetid pairs, two to four flagella per
kinetid
Preaxostyla: four flagella per kinetid
Parabasalia: parabasal apparatus present, parabasal fibers connecting the Golgi apparatus to the fla-
gellar apparatus (kinetid). Kinetid with four or several (up to over 1,000) flagella
Discoba: taxon mainly defined based on molecular characteristics
Discristata: discoid mitochondrial cristae
Heterolobosea: mostly amoebae with emerging pseudopodia, certain dis-

tinct life cycle stages characterised by the presence of flagella
Euglenozoa: two flagella (rarely one) emerging from an apical pit
Euglenida: pellicula of proteinaceous fibers
Kinetoplastea: kinetoplast
Diplonemea: paraxonmal rod missing in the trophic phase
Symbiontida: anaerobic or microaerophilic, reduced mitochondrion, pellicula missing
Jakobida: mitochondria with tubular or flat cristae; two flagella emerging from the top of a
broad ventral feeding pit, within which the trailing flagellum beats
Phagocytosis (Grk: phagein = to eat; cyto = cell) is an active method of a mouth hole. Ciliates also have a cytostome: they feed by transporting
food intake common to protists and lower metazoans. It involves the ac- food through an undulating membrane of cilia towards the cytophar-
tive uptake of particles or prey cells. Along with pinocytosis, which is the ynx. Food particles are transported within the cell in vacuoles, initially
process of ingesting liquids containing dissolved substances, phagocyto- be acidified by acidosomes and subsequently digested by the help of
sis is a form of endocytosis. In receptor-mediated phagocytosis, particles lysosomes.
are ingested after binding to receptor molecules in the cell membrane. In multicellular animals, such as mammals, phagocytosis is an important
The process of phagocytosis starts when food particles or other organ- component of the immune defence system, serving to dispose of invad-
isms are surrounded by the plasma membrane, which has been either ing microorganisms. Detected invaders are surrounded by phagocytes,
reversed or tied off, forming a phagocytic vesicle, which is subsequently ingested, and digested. Phagocytes are also responsible for the disposal
transported into the cell interior and digested by lysosomal enzymes of dead cells.
(lysozymes). Nutrients are then transported through the vacuolar mem-
brane in the surrounding cytoplasm, with indigestible material excreted
from the cell via the process of exocytosis. Some organisms have devel-
oped specialised organelles for ‘catching’ food and transporting it to the
cell’s interior.
Many amoeba can perform phagocytosis through their pseudopodia
along any segment of their plasma membrane. Other protists, however,
can only take in food in certain areas of the cell, known as the cytos-
tome or cell mouth. Most members of Excavata have a cytostome with
Phagocytosis
298 Megasystematics
4.3.1
Metamonada
The Metamonada (metamonads) include Diplomona- sals within the gut of insects. For example, they play a vital
dida (diplomonads), Retortamonadida, Parabasalia, and role within the process of wood and cellulose degradation
Oxymonadida. Metamonads have no plastids and all taxa within the gut of termites.
are anaerobic and amitochondrial, meaning they lack mito- Some metamonads are also important pathogens, includ-
chondria. Their lack of mitochondria was previously falsely ingfor example the diplomonad gut parasite Giardia, which
attributed to the ancestral state, with metamonads accord- affects various vertebrates including humans. Giardia is a
ingly attributed as the earliest eukaryotes. However, meta- common pathogen in human drinking water, since cells are
monads have been shown to possess genes from an earlier particularly resistant to chlorination and UV-treatment pro-
mitochondrial state, in addition to organelles like mitosomes cedures. In areas with poor treatment facilities, up to 30 %
or hydrogenosomes, which are interpreted as reduced mito- of the human population may be infected. Ultrafiltration,
chondria. These organelles and the remaining mitochondrial however, has been shown to be completely effective against
genes indicate that metamonad ancestors possessed mito- Giardia. Trichomonads, which belong to the Parabasalia,
chondria. are also pathogenic, infecting the genitourinary tract. Tricho-
Today, metamonads live in a number of anaerobic habi- monas vaginalis causes around 160 million infections in hu-
tats and are particularly important in their role as commen- mans each year worldwide.
Diplomonads have two nuclei and two kinetids. Each ki- Parabasalids are endosymbionts, living, for example, in
netid usually has four kinetosomes and four flagella, three the digestive tract of termites, or endoparasites. They feed
of which are anteriorly facing and one faces in a posterior through phagocytosis and are important pathogens for ani-
direction, supporting the groove- or tube-like cytopharyngeal mals and humans. The parasite Trichomonas vaginalis can
apparatus. The cytopharyngeal apparatus and the nucleus cause trichomoniasis, a sexually transmitted disease which
are supported by fibres. Diplomonadida includes free-living infects the mucous membranes around the genitourinary
species, which occur in DOC-rich freshwater, as well as com- area.
mensals, which can be found in the digestive tract of various There are no free-living oxymonads, with almost all spe-
invertebrates and vertebrates. Diplomonads have mitosomes cies living as commensals or symbionts together with bac-
but no dictyosomes. teria. The commensals have a rostellum, an adhesive organ
Parabasalia (parabasalids) and Oxymonadida (oxymon- enabling them to attach themselves to the intestinal wall of
ads) are characterised by an axostyle, a collection of several a host; they feed phagocytotically. Oxymonads have no dic-
thousand microtubules which support the cell as a skeleton. tyosome and no mitochondria and, presumably, possess no
In oxymonads, the axostyle moves freely within the cell hydrogenosomes. Most species have one nucleus and four
whereas it is immobile in parabasalids. flagella.
Parabasalids are also characterised by the parabasal ap- Most Retortamonadida live as commensals and parasites
paratus, which is surrounded by specially arranged dicty- in the digestive tract of animals or free-living in an anaerobic
osomes and the kinetosomes of four to six flagella forming environment. A few species are pathogenic, with Chilomastix
a cluster with the nucleus. A trailing flagellum is directed to- mesnili and C. gallinarium causing diarrhoea in humans and
wards the cell’s posterior, while the remaining flagella face in fowl respectively. They have two or four flagella and, as with
an anterior direction. Another morphological form has four most metamonads, lack a dictyosome.
flagella (hypermastigote), arranged at the front tip of the cell.
axostyle: a sheet of microtubules forming a thin rod behind the parabasal apparatus: equivalent to a specialized Golgi appa-
main body ratus consisting of parabasal bodies (dicotysomes) which are as-
costa: rod-like structure consisting of proteins at the base of the sociated with the parabasal filaments. The parabasal filaments
undulating membrane, movable in some species grow out of basal bodies which are themselves not part of the
dictyosome: stack of cisterna enclosed in a sac – the totality of parabasal apparatus. The parabasal bodies can possess up to 20
dictyosomes constitutes the Golgi apparatus flattened vesicles known as cisterna
DOC: dissolved organic carbon pelta: a flat ascocarp having no rim
kinetosome: basal body of flagella; kinetosomes consist of a
cylindrical array of microtubules; they serve as a nucleation site
for the microtubules of flagella and cilia
See also: Phagocytosis: 4.3; Nuclear dimorphism: 4.2.2.4

Excavata: Metamonada 299
stida Rh
Fornicata: one nucleus and one kinetid or a pair of each, two to four flagella per kinetid pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la ria
M Diplomonadida: diplomonad cell organisation (a pair of kinetids and two nuclei) uc ta
op Re
phy
Chr
E hy
ae
Disc ta
Excavata
oba olata
T
oma
Alve
Retortamonadida: one kinetid and one nucleus
A Stra
lveolata
a
Meta monad men
opile
M Preaxostyla: four flagella per kinetid zo
a Ha s
oa nta
o pt
O eb
Cry
op
o
mo
ok
hy
Oxymonadida: intestinal symbionts, four flagella in two pairs, axostyle present (contractile or mo- A
pto
N
is t
ta
soz
h
phy
tile)
Op
A
Apu
ta
D
Trimastix: free-living, with four flagella and a central feeding groove
A Eubacteria Archaea
Parabasalia: parabasal apparatus present, parabasal fibers binding the Golgi apparatus to the flagellar ap-
paratus (kinetid). Kinetid with four or several (up to over 1,000) flagella
Oxymonadida
anterior flagella basal bodies (kinetosome)
pelta Oxymonadida: light microscope (left) and electron microscope (mid-
costa dle) micrographs of Pyrsonympha from the termite gut; right: slice
nucleus
through the preaxosyle (arrow) of Monocercomonoides
undulating hydrogenosomes
membrane
parabasal body
axostyle
parabasal fibers
Parabasalia: slice through the anterior end of a commensal Joenia
posterior flagellum annectens cell from the termite gut (left); parabasal bodies and hy-
drogenosomes of the same species (right)
diagram of a parabasalid trichomonad
Hydrogenosomes, described for the first hydrogenosomes and mitosomes possess

time in 1973, are organelles surrounded by enzymes for the assembly of the iron-sul-
a double membrane, approximately 1 µm phur cluster. In contrast to the mitochon-
in length. Like mitochondria, they produce dria, however, hydrogenosomes are missing
adenosine triphosphate (ATP). However, their own genome. However, the ciliate Nyc-
while mitochondria operate by aerobic totherus ovalis has a small hydrogenosome
respiration, hydrogenosomes allow for an- genome. Hydrogenosomes can be found
aerobic fermentation. The bi-products of in a number of unrelated species, varying
ATP synthesis under anaerobic conditions greatly in the degree to which they have
include acetate and hydrogen, from which been reduced and the nature of their meta-
the organelles took their name. Under aero- bolic pathways. Top-left and bottom-left: hy-
H2
bic conditions, hydrogen peroxide is pro- drogenosome; top right: enlarged image of a
duced instead of hydrogen. The substrate double membrane; bottom right: simplified Malat
is pyruvate and, in some cases, malate. The nutrient pathway for hydrogenosomes in N. H2 NAD + Malat
e‐
pathway shown here is a simplified repre- ovalis.
sentation of the conditions in Nyctotherus
H+ NADH Pyruvat
ovalis. Hydrogenosomes occur in many ATP
copies within each cell and divide indepen- Acetat
ADP
dently of the cell cycle. Like mitochondria, H + Acetat
Hydrogenosomes
300 Megasystematics
4.3.2
Discoba
The Discoba include Jakobida and Euglenozoa, as well The Heterolobosea include amoeboid protozoa which
as the Percolozoa. Due to their discoid mitochondrial cris- are not related to Amoebozoa. The two groups may also
tae, the Eugleonoza and Percolozoa are grouped together as be distinguished by their movement, which is dissimilar: in
Discicristata. The Jakobida, in contrast, have tubular cristae. the Heterolobosea, the biggest single pseudopod eruptively
Heterolobosea and their sister group comprising the gen- swells forth from the cytoplasm, whereas in Amoebozoa, the
era Stephanopogon and Percolomonas make up the Percolozoa. pseudopodia are formed more slowly and in a flowing move-
The genus Stephanopogon comprises marine and benthic ment. Some heterolobosean taxa also form flagellar stages,
flagellates with numerous flagella arranged in rows. The fla- with two or four flagella, arranged in parallel. Flagellate
gella are rooted in the surface of the cell and are supported stages are not usually capable of taking in particulate food;
by radially arranged microtubules. however, for some species, this can be carried out through a
The genus Percolomonas only includes the species Percolo- pit-shaped cell mouth (cytostome). Amoeboid Heterolobo-
monas cosmopolitus. Molecular data support the relationship sea are exclusively heterotrophic feeders.
within this group and to its sister group Heterolobosea.
Heterolobosea are divided into the Acrasidae and the are heterotrophic and feed on bacteria, other protists, or par-
Schizopyrenida. ticles of detritus.
The Acrasidae are cellular slime moulds, capable of aggre- Some species of genus Naegleria are facultatively patho-
gating within pseudoplasmodia where, unlike in real plasmo- genic. Their cysts can survive for several years. As a result of
dia, the cells do not merge together. Pseudoplasmodia form exogenous stimuli, individuals emerge at the flagellate stage
fruiting bodies (sporocarps), in which spores are formed. In though these are unable to feed. With the loss of the flagella,
contrast to the slime moulds affiliated with Amoebozoa, in- individual cells transform into amoeboid trophozoites. Naeg-
dividual Acrasidae cells do not die during the formation of leria is thermotolerant, able to reproduce even at 45 ºC, and
the stem of the fruiting body but, rather, form flagellar stages can survive at even higher temperatures, including naturally
later. The Acrasidae are benthic decomposers. warm waters as well as anthropogenically heated water. The
The Schizopyrenida include Vahlkampfiidae and the potentially pathogenic species Naegleria fowleri can enter the
Gruberellidae. Comprising only two genera (Stachyamoeba olfactory neuroepithelium through the nose before penetrat-
and Gruberella), Gruberellidae is the smallest heterolobo- ing into the brain through the human olfactory nerve after
sean group. Both genera do not form flagellated stages and exposure to infected lakes and swimming pools, or even in
fruiting bodies. Gruberella cells are multinucleate, colonising drinking water. Infecting cells penetrate the surface of the
marine habitats, whereas Stachyamoeba cells have just one brain, causing an acute inflammation (PAME: primary
nucleus and are found in freshwater and terrestrial habitats. ameobic meningoencephalitis), which may lead to death in
The Vahlkampfiidae, on the other hand, have amoebic only a few days. Naegleria fowleri is mainly found in tropi-
and flagellar stages, with the exception of genus Vahlkampfia, cal and subtropical climates in regions where drinking water
which has no flagellar stage. Vahlkampfiidae are unicellular may not be properly treated. In more temperate latitudes,
and do not form pseudoplasmodia or fruiting bodies. They N. fowleri may exist in artificially warmed waters or sewage,
which may infect humans if discharged near bathing waters.
detritus particles: (Lat.: detritus = rubbing away) small parti- to real plasmodia, in which a multinucleate mass of cytoplasm
cles of organic origin is formed
pseudo-plasmodium: aggregation of numerous cells to form
a grex; the individual cells retain their cell membrane in contrast
See also: Amoebozoa: 4.2.3, 4.2.3.1; Slime molds: 4.2.3.1

Excavata: Discoba 301
stida Rh
pla iza
Jakobida ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Dis ta
Excavata
tubular mitochondrial cristae co ba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa nta
o pt
eb
Cry
op
o
Discristata mo
ok
A hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
discoid mitochondrial cristae Eubacteria Archaea
Percolozoa
Stephanopogon sp.
This little known group reaches 20–50 mm in length. It is characterised by flagella arranged
in rows. Members of this lineage occur in aquatic environments at depths of up to 100 m
D Stephanopogon sp.
i
s
Percolomonas sp.
c This genus has just one free-living flagellate species, Percolomonas cosmopolitus
o
b P. cosmopolitus
a
Heterolobosea
Acrasidae
These unicellular amoeboids are able to come together to form a multicellular pseudo-
plasmodium
Naegleria sp.
Schizopyrenida
This group consists of the Vahlkampfilidae and Gruberellidae (only two genera)
Vahlkampfia sp.
Euglenida
Euglenozoa
Kinetoplastea
By adapting to host organisms and thereby heavily group species disease haploid
specialising, many parasitic species have lost a Genome
number of their original characteristics and gained in Mbp
some new ones. In particular, endoparasites live in a
Bacteria Escherichia coli 4.2
relatively stable environment (chemical properties,
temperature). Often, parasites have abandoned Protists Giardia duodenalis small intestine infection 12
properties that were used by their free-living ancestors;
Trypanosoma brucei sleeping sickness 25
for example, tapeworms lost an intestinal tract, since
their main method of food intake occurs via their cell Toxoplasma gondii toxoplasmosis 87
surface membrane. Some stationary ectoparasites, for
Plasmodium falciparum malaria tropica 25
example, have also reduced their locomotory ability,
or converted their appendages from legs to clamping Babesia bovis babesiosis 9.4
organs. Such changes can also be observed in the Metazoa Schistosoma mansoni (Trematoda) bilharyiasis 270
genome; in intracellular parasites, genome size and the
total number of genes is drastically reduced as the level Echinococcus granulosus (Cestoda) dog tapeworm 150
of specialisation increases. Haemonchus contortus (Nematoda) haemonchosis 50
Onchocerca volvulus (Nematoda) river blindness 150
Mus (mouse) – 2,700
Reducing of genome size in parasites

302 Megasystematics
4.3.2.1
Euglenozoa: Euglenida
The Euglenozoa are a sister group to Percolozoa. They largely reduced and formed only within the ampulla. Pho-
comprise Euglenida, Kinetoplastea, Diplonemea, and the toautotrophic species are distinguished by a basal swelling
Symbiontida. Euglenozoa have two flagella, of which one (paraflagellar body), which serves photosensory and orienta-
is often strongly reduced. A feature common to Euglenida tion functions.
and Kinetoplastida is the pellicula and the paraxonemal rod The euglenids mainly live in freshwater, although some
running in parallel to the axoneme of the flagella. Only the species can also be found in marine and brackish habitats.
Diplonemida are missing a pellicula and a paraxonemal rod. There are approximately 1,000 described species, of which
Due to the paraxonemal rod, the flagella appear to have a around a third have plastids. Chloroplasts, containing chlo-
thicker base. rophyll a and b, are surrounded by three membranes, with
For the most part, the Euglenida have no cell wall or solid the outer membrane separated from the endoplasmic reticu-
structure around their plasma membrane. One exception is lum and the nuclear membrane. The products of photosyn-
the genus Trachelomonas, which has a rigid cell wall made thesis are stored as paramylon in the cytoplasm. Phototro-
of iron- and manganese-containing minerals. The Euglenida phic euglenoids are known to play a prominent role in algal
are characterised by a pellicula under their plasma mem- blooms in lakes.
brane, composed of helically revolving microtubules and The Diplonemea include the two genera Diplonema and
other filaments. The pellicula may be rigid, as in the photo- Rhynochopus, which are both unicellular and dorsoventrally
autotrophic genus Phacus, or flexible, which allows for the flattened, free-living, phagotrophic flagellates. They live in
typical euglenoid movement, which is displayed specifically planktonic and benthic freshwater and marine environments.
by members of the group living in the substrate, as preda- The Diplonemea have no pellicula and no paraxonemal rod.
tors, or as parasites. At the front end of the cell, the pellicula The systematic position of the Euglenida and the Kineto-
converges into a channel complex, the ampulla, from which plastida remains unclarified.
the flagella emerge. In some taxa, the second flagellum is
The Euglenida comprise photoautotrophic and hetero- The ancestral euglenids are thought to have been phago-
trophic species. trophic, from which the primary osmotrophic euglenids, for
Heterotrophic euglenids have no functional chloroplasts exampale Distigma, have been derived. Similarly, the photo-
and are therefore entirely dependent on the uptake of or- trophic euglenids are also derived from phagotrophic ances-
ganic substances. They can be divided into two groups: the tors. Through secondary endocytobiosis, ancestors of this
phagotrophic euglenids (e.g. Peranema, Entosiphon, or Petalo- group took up a green algal cell through secondary endocy-
monas), which have a specific ingestion apparatus with which tobiosis.
they can take larger prey organisms, and the osmotrophic Secondarily, osmotrophic Euglenida, for example Euglena
euglenids, which have neither a chloroplast nor a specialised longa, are derived from phototrophic ancestors. These species
ingestion apparatus. have plastids which are no longer capable of photosynthesis.
paramylon: a storage polysaccharide in Euglenida and Hapto- paraxonemal rod: protein structure running parallel to the fla-
phyta. In contrast to starch in plants and red algae, paramylon is gella
made from β 1,3-glucan pellicula: (Lat.: pellicula = little skin) hard but flexible layer
(usually made of proteins) under the cell membrane
See also Osmotrophic, Heterotrophic, Photoautotrophic: 4.6.2.3; Dorsoventral: 4.2.1.3

stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Dis ta
Excavata
co ba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa nta
o pt
eb
Cry
op
o
mo
ok
A hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
Phacus sp. Trachelomonas sp. Distigma sp. Peranema sp. Eubacteria Archaea
OH
OH
long flagellum HO O
HO O O ...
eyespot (stigma) O
... O OH
OH
short flagellum
paraxonemalrod Paramylon chemical structure
chloroplast
pyrenoid
thylakoid
Golgi apparatus
paramylon
mitochondrion
nucleus
Electron micrograph of the flagellar

groove (bottom: longitudinal section)
pellicula
(surrounds the entire
cell body; here only
shown on the cell’s pos-
terior end)
Electron microscopic micrograph of the Euglena gracilis

pellicula
Light-sensitive sensory cells (photoreceptors) are found in various forms

in different organisms. These include simply constructed light-sensitive
intracellular structures, such as the eyespot (stigma) in unicellular or-
ganisms, to the highly sophisticated lens in the eyes of vertebrates and
cephalopods. More highly developed eyes can be divided into two types:
single-lens eyes of the camera type (top-left: human; top-right: croco-
dile) or as composite compound eyes, which work together as several
independent units (ommatidia) as in arthropods (bottom-left: horse fly).
A bee has around 15,000 ommatidia, which, together, form a mosaic im-
age. Although the spatial resolution of a compound eye is much lower
compared to that of vertebrates, its temporal resolution is much higher.
Therefore, movements can be perceived much more rapidly. Organisms,
such as Euglena, which possess only simple photosensitive structures
within their own cells (bottom-right: eyespot), are able to detect the di-
rection of incidence and the intensity of light, enabling the cell to either
swim towards the light source (positive phototaxis) or swim away, e.g.
when the light intensity is too high (negative phototaxis).
Perception of light
304 Megasystematics
4.3.2.2
Euglenozoa: Kinetoplastea
Together with the Euglenida, the Kinetoplastea make up cell body in others. Free-living Kinetoplastea are usually
the Euglenozoa. These, in turn, with Discoba and Meta- bacterivorous or live as endobiotic commensals. They are
monada, make up the Excavata. among the most common flagellate groups in many terres-
Kinetoplastea include single-celled flagellates that are trial and aquatic habitats.
either free-living or parasitic. An important collective char- The parasitic trypanosomatids have one flagellum (homol-
acteristic of the group is the kinetoplast, a DNA-rich body ogous to the anterior cilium of free-living taxa), which either
within the sole mitochondrion, which is often as long as the oscillates freely or is connected to the cell surface across sev-
entire cell. The kinetoplast is located near the basal body of eral adhesion points, thereby stretching the membrane itself
the flagellum, to which it is connected by the cytoskeleton. to become an undulating membrane. Many trypanosomatids
The Kinetopolastea are divided into the Prokinetoplastina reproduce exclusively inside insects, although some species
and Metakinetoplastina. The former group includes a num- may change host, generally from insects to vertebrates. The
ber of parasitic species, whereas the latter includes several pathogenic Leishmania spp. (leishmaniasis) and Trypanosoma
free-living lineages (Neobodonida, Parabodonida, and Eu- spp. (chagas disease, sleeping sickness and animal diseases
bondonida), as well as the parasitic Trypanosomatida. nagana and surra) belong to the Trypanosomatida. Some
The free-living Kinetoplastea usually have two heterokont species may also be plant pathogens (Phyromonas). Since the
and heterodynamic flagella, with single rows of cilia along surface proteins of the parasites are highly variable, drug
the anteriorly-directed flagellum. The posteriorly-directed treatments against these pathogens are often difficult.
flagellum is free in some taxa, whereas it is fused with the
The Prokinetoplastina include the two genera Ichthyobodo are phagotrophic or osmotrophic and can be either free-liv-
and Perkinsiella, which differ drastically from each other mor- ing, commensal, or parasitic.
phologically. Thus, characteristic morphological features for The free-living Eubodonida are phagotrophic. They pos-
the Kinetoplastea are hard to define and their systematic sess two flagella, the posterior flagellum bears tubular hairs.
classification is therefore based on molecular phylogeny. Per- Finally, the trypanosomatids are phagotrophic and os-
kinsiella spp. are endosymbionts of various amoebae whereas motrophic, possessing just one flagellum without mastigon-
Ichthyobodo spp. are ectoparasites of fish. emes. The kinetoplast-kinetosome-flagellar complex varies
The biflagellates Neobodonida contain a cytostome but between taxa as well as across generational stages. A distinc-
do not possess noticeable mastigonemes and their posterior tion can be made between the following forms: amastigote,
flagellum is either attached or free. They feed phagotrophi- promastigote, epimastigote, and trypomastigote. Promastig-
cally or osmotrophically. ote and epismastigote forms can be found mainly in inver-
On the other hand, the biflagellate Parabodonida do not tebrates whereas trypomastigotes are mostly found in the
always have a cystostome. They have no mastigonemes and blood of vertebrates. Finally, amastigote forms are usually
their posterior flagellum can be either attached or free. They found intracellularly in vertebrates.
basal body: centriole at the base of the eukaryotic cilium or heterokonts: term referring to differently shaped flagella,
flagellum especially in stramenophiles
cytostome: cell mouth in protists mastigonemes: (Grk.: mastigo = thread, whip) hairs which
cover flagella
See also: Flagellum: 4.2; Phagotrophy: 4.6.2.3

stida Rh
Prokinetoplastina ae
pla iza
Viridiplant ta
ria
oa
h
rc
Rh
fish ectoparasites or endosymbionts of amoeba
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Dis ta
Excavata
co ba olata
oma
Ichthyobodo sp. from fish gills Alve
a Stra
lveolata
Meta monad men
Metakinetoplastina a Ha
opile
s
zo
oa nta
o pt
eb
Cry
op
o
Neobodonida mo
ok
A hy
pto
is t
ta
soz
kinetoplast kDNA not in an single cluster but, rather,
phy
Op
Apu
scattered across several locations within the mitochondrion;
ta
two flagella lacking mastigonemes
Rhynchomonas nasuta Eubacteria Archaea
Parabodonida
kinetoplast kDNA not in a single cluster but, rather, divided
within the mitochondrium; two flagella lacking mastigonemes
Procryptobia glutinosa
Eubodonida
kinetoplast kDNA not in a single cluster but, rather, in
a parakinetosomal position; two flagella, the posterior
featuring tubular hairs
Bodo saltans
Trypanosomatida
kinetoplast kDNA in a single cluster associated with the
flagellar basal bodies; one flagellum, mastigonemes missing
mitochondrium
kinetoplast
pellicula (envelops
the entire cell)
Genera such as Trypanosoma (shown here in a hu-

Golgi apparatus man blood smear) or Leishmania undergo a change
of host between insects and vertebrates. Moreover,
nucleus the genus Phytomonas makes a host exchange be-
tween insects and plants, whereas other genera, such
as Crithidia or Leptomonas live within insects without
flagellum
changing hosts
undulating membrane
Amastigote (for example, Leishmania during the intracellular phase): Epimastigote (for example, Crithidia): the flagellum is attached
The flagellum on the cell apex does not emerge from the flagellar to the cell body along the anterior sector of the cell, with only the
pocket and remains invisible by light microscopy. rear segment free. The kinetoplast lies between the nucleus and the
posterior end of the cell.
Promastigote (for example, Leptomonas): The flagellum originates at Trypomastigote (for example, Trypanosomas in the blood of
the anterior end of a slim cell and does not lie in parallel with the cell vertebrates): The flagellum is attached along the entire length of the
body. The kinetoplast is located towards the anterior end of the cell. cell body. The kinetoplast is located in the posterior segment of the
cell.
Position of the kinetoplast-kinetosome-flagellar pocket complex

306 Megasystematics
4.4
Archaeplastida
The Archaeplastida include Glaucocystophyta, Rhodo- The only exception can be found within the genus Paul-
phyta, Chlorophyta, and Streptophyta. All representatives inella (Rhizaria), where the plastid (or chromatophore) can
are characterised by the presence of plastids with chlorophyll be traced back to an independent primary endocytobiosis of
a as the major pigment and starch as the storage polysac- another cyanobacterium.
charide. Plastids in some lineages may have been reduced or The phylogenetic relationships between these groups can-
lost secondarily in some groups; they usually have a cell wall not be properly displayed within the traditional framework
made of cellulose. The mitochondria have flat cristae. of the formally established taxonomic hierarchy levels (spe-
The plastids originate from the primary endocytobiosis of cies, orders, families, etc.). This is particularly important for
a cyanobacterium. Secondary plastids, such as those found the classification of land plants within Viridiplantae. Many
in other algal groups, can be traced back to an endocytobio- phylogenetic groups therefore have names that do not com-
sis of a eukaryotic algae affiliated with the archaeplastida. ply with the established taxonomic ranks and they therefore
Therefore, in phylogenetic analyses, the plastids cluster as a differ from these established group names.
monophyletic group within the cyanobacteria.
The Glaucocystophyta are a basal group within the Ar- tinguished as the only group to undergo a triple generational
chaeplastida. They differ from other groups within the change (gametophyte, carposporophyte, and tetrasporo-
Archaeplastida by the presence of carboxysomes and the phyte).
formation of peptidoglycan walls in their plastids. These The Viridiplantae are also known as the Plantae, Chloro-
properties have been reduced in other lineages. plastida, Chlorobiota, or Chlorobionta. This group contains
The Rhodophyta are the sister group of Viridiplantae. In the Chlorophyta and Streptophyta. Most green algae belong
contrast with the Viridiplantae and similar to the Glaucocys- to the Chlorophyta, whereas the monophyletic Streptophyta
tophyta, the thylakoids of Rhodophyta are not arranged in includes a paraphyletic collection of algae and land plants
stacks but side by side instead. Also, similar to the Glauco- (embryophytes). The latter comprise a paraphyletic selection
cystophyta, rhodophyte plastids contain only chlorophyll a. of mosses and a monophyletic lineage of vascular plants in-
The Viridiplantae, on the other hand, also have chlorophyll cluding club mosses, ferns, and seed plants, i.e. gymnosperms
b in their plastids. Furthermore, the Rhodophyta can be dis- and angiosperms.
phycobilisome: large protein complex associated with colour

pigments involved in photosynthesis; in contrast to chlorophylls,
the phycobilines absorb green and yellow light
See also: Paulinella: 4.5.1; Primary endocytobiosis: 2.2.2.5

Archaeplastida 307
Glaucocystophyta: plastids with pepti-

doglycan layer, as well as chlorophyll a and
phycobilisomes
Rhodophyta: plastids without peptidogly-

can layer, but with chlorophyll a and phy-
cobilisomes
A
R
C
H Viridiplantae: plastids without peptidoglycan layer and without phycobilisomes or chlorophyll a and b
A
E
P
L Chlorophyta: flagellar basal body without ‘multi-layered
A structure’
S
T
I
D Streptophyta: flagellar basal body with ‘multi-layered-structure’
A
The streptophyte algae are a polyphyletic group.

The closest relatives of land plants are probably
the Zygnematophytina
The land plants (embryophytes) are a sister line-

age of Streptophyta and include the bryophytes,
club mosses, ferns, and seed plants
Chlorophyll molecules comprise a porphyrin ring with an Mg2+ ion in although these possess a central iron ion rather than a magnesium ion.
the centre. The four pyrrole rings are connected to each other with a The different types of chlorophyll (a, b, c1, c2, d) differ from each other
methine-bridge and bound into a ring (tetrapyrrol). In their structure, by the number of side chains that they possess.
they resemble the haem group (haemoglobin, myoglobin, cytochrome),
chl a X: CH=CH2 Y: CH3

chl b X: CH=CH2 Y: CHO
chl d X: CHO Y: CH3
chlorophyll c1 chlorophyll c2 basic structure of chlorophylls a, b, and d
Chlorophyll
308 Megasystematics
4.4.1
Glaucocystophyta
The Glaucocystophyta are a species-poor and relatively display a number of similarities with cyanobacteria. To that
rare group of organisms, consisting of only a few genera end, each plastid has a peptidoglycan polymer between its
(Cyanophora, Glaucocystis, and Gloeochaete), making up a total two membranes, considered the remains of an ancient bacte-
of 13 species. For the most part, they are found in lakes and rial cell wall. Furthermore, their plastids contain chlorophyll
marshes in temperate zones. The group is particularly sig- a and phycobilins. Starch is stored outside of the plastid, in
nificant from an evolutionary perspective, since its plastids the cytoplasm.
Due to the broad similarities between plastids and cyano- nesis takes place by median cleavage without phycoplasts
bacteria – mainly due to the presence of a peptidoglycan and phragmoplasts. Asexual reproduction takes place by
polymer – the plastids of Glaucocystophyta are also referred zoospores or auto spores. Sexual reproduction is not known
to as cyanelles. In addition, photo pigments, including chlo- in Glaucocystophyta.
rophyll a and the accessory pigments phycocyanin and al- The genus Glaucocystis has two rudimentary flagella,
lophycocyanin found in the phycobilisomes, as well as the which are no longer capable of movement, with cyanelles
organisation of the phycobilisomes in unstacked thylakoids, arranged in a star shape. Vacuoles are clearly visible. Glau-
is similar to that observed in cyanobacteria. In contrast, the cocystis rarely appears as single cells but, rather, in groups of
Glaucocystophyta are missing the light-harvesting complex two, four, eight, or 16 autospores.
typical of land plants and many green algae. As in cyano- The genus Gloechaete has both motile (biflagellate zoo-
bacteria, a carboxysome is located in the centre of the chlo- spores) and sessile stages. Its cyanelles may be lost during
roplast. Glaucocystophyta store starch, a polysaccharide, cell division as well as through digestion by the host cell.
outside the plastids. The flagella have a 9+2 arrangement The genus Cyanophora has two cyanelles and two unequal
of supporting microtubules, which is typical of eukaryotes. flagella. Cyanophora paradoxa is considered a ‘living fossil’;
Glaucocystophyta also have flattened vesicles underneath the deciphering of its genome provided the first evidence
their plasma membrane, anchored by microtubules. These of primary endocytobiosis as a single event that occurred
structures are similar to the alveoli of the Alveolata. Cytoki- roughly a billion years ago.
autospores: daughter cells are formed within the mother cell phycobilisome: large protein complex associated with colour
wall; autospores resemble the mother cell pigments involved in photosynthesis; in contrast to chlorophylls,
cristae: (Lat.: crista = comb, crest) numerous folds on the inner the phycobilines absorb green and yellow light
membrane of mitochondria phycoplast: microtubuli assembled parallel to the cell plate
cytokinesis: (Grk.: cytos = cell, kinesis = movement) cell divi- during cell division; microtubule structure during cytokinesis in
sion members of the Chlorophyceae
phragmoplast: microtubuli assembled perpendicular to the cell transcriptome: the total set of all RNA molecules in a cell, in
plate during cell division tissue or in an organism during a given developmental stage
vesicle: (Lat.: vesicula = diminutive of bladder, blister)
See also: Light-harvesting complex and photopigments: 4.4, 4.4.2; Arrangement of flagellar microtubuli 4.2; Origin of plastids: 2.2.2.6
Archaeplastida: Glaucocystophyta 309
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
A
G
Cerco
odo
la
uc ria
op ta
Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
Stra
onada
lveolata
men
Metam opile
a Ha s
zo
oa nta
bo pt
Cry
oe op
o
ok
Am hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
Eubacteria Archaea
Cyanophora paradoxa Glaucocystis nostochinearum

peptidoglycan
circular DNA
dictyosome
thylakoid
80S ribosomes
70S ribosomes
Immunoelectromicroscopic cross-section of mitochondrion

starch grains
Cyanophora paradoxa plastids, with antibod-
ies (black spots) clearly visible attached to the
murein layer. Top-left: magnified details
Organisms with a complex organisational structure are often

thought of as ‘better adapted’ than those displaying a simpler
layout. This implies that they are in some way better adapted,
from an evolutionary point of view. However, all extant organ-
isms can be traced back to a common ancestor. Even though it
cannot be excluded that multiple viable body structures emerged
and continued reproducing in the early Precambrian, only one
of these survived. As a consequence, all life found today can be
traced back to one common origin and has survived and success-
fully reproduced through the same amount of evolutionary time.
It is therefore incorrect to speak of ‘better’ or ‘worse’ adapta-
tions; rather, these are different strategies of achieving the same
thing: survival.
Acineta tuberosa (Ciliophora), Echinoderes rex (Kinorhyncha), Giraffa

camelopardalis (Vertebrata)
Are higher-level organisms evolutionarily better-adapted?

310 Megasystematics
4.4.2
Rhodophyta
The Rhodophyta (red algae) are eukaryotes lacking fla- shelves. As a result of their accessory pigments (phycoco-
gella and basal bodies; instead, they have polar rings as mi- erythrin, which can absorb light in the ‘green window’ of
crotubule organising centres. Roughly 500 genera of red al- chlorophyll), red algae can survive at depths of over 250 m.
gae have been described, comprising a total of around 5,000 One particular example was found on the slopes of a marine
species. Most red algae are multicellular, predominantly fila- mountain at a depth of 268 m, where only 0.001 % of light
mentous, with intertwined or pseudoparenchymatous thal- from the surface was able to penetrate. Some representatives
lophytes. Their oldest appearance in the fossil record stem of the Rhodophyta are symbionts of benthic foraminifera,
from the Mesoproterozoic, around 1.2 billion years ago.Red whereas others may live – with reduced plastids – as obligate
algae contain primary plastids with chlorophyll a and phyco- parasites of other Rhodophyta. Some species deposit calci-
bilisomes. They possess mitochondria and primary plastids um carbonate (Ca2CO3) in their cell walls and are important
with two cell membranes as well as chlorophyll a. The cell within reef-building processes.
wall is made of cellulose. They are taxonomically divided Rhodophyta are of great economic importance. The poly-
into the Cyanidiophytina and Rhodophytina (red algae in saccharides agar and carrageenan, obtained from red algae
the narrower sense) lineages. like Chondrus crispus, are widely used in the biomedical, gas-
The vast majority of taxa are marine, though some can be tronomic, and cosmetic industries. For example, these sub-
found in freshwater and soil habitats. Some species use larger stances are used to clarify beer or custard, or to make agar
brown algae, seaweed, or shells of mussels and gastropods as plates in laboratories. The mineral deposits of Lithothamnion
a substrate on which to live. Interestingly, red algae exist in a spp. (algal limestone) are used as an agricultural fertiliser as
relatively narrow littoral zone at the edge of the continental well as a food substitute to increase calcium content.
As a result of primary endocytobiosis, red algae possess grow into a second diploid generation, the tetrasporophyte,
platids (rhodoplasts) containing phycocyanin and phyco- which is often morphologically identical to the gametophyte
erythrin. Rhodophyta are the only phototrophic protists that (isomorphic). The tetrasporophyte forms four haploid mei-
have phycoerythrin. As with Glaucocystophyta, red algal otic spores by reductive division, which germinate again to
thylakoids are arranged side by side (not in stacks). In con- produce gametophytes.
trast to most other organisms, their chloroplast DNA is not The Cyanidophytina form a sister group with all other
circular. The products of red algal photosynthesis are stored red algae. They are unicellular, with thick, proteinaceous
as floridean starch (α-1,4-glucan with structural similarity to cell walls that protect them in extreme habitats. They form
amylopectin) on the outside surface of the plastids in the cy- endospores and are sometimes able to survive heterotrophi-
tosol or in granules. At no point in their life cycle do red al- cally. The Golgi apparatus of the Cyanidiophytina is con-
gae possess flagella; the male gametes, which lack cell walls, nected to the endoplasmic reticulum.
may move around in an amoeboid manner. The Rhodophytina include three groups: the Rhodello-
Rhodophyta generally undergo three generations, with a phytales (unicellular or pseudofilamentous red algae), the
haploid gametophyte, a diploid karposporophyte, and a dip- Metarhodophytales (associated with biphasic alteration of
loid tetrasporophyte. The fully grown gametophyte possess generations; Golgi apparatus connected with the endoplas-
a female gametangium (carpogonium) containing the egg mic reticulum), and the Eurhodophytales (Golgi apparatus
cell and many male gametangia (spermatangia) containing connected with the endoplasmic reticulum as well as with
sperm. After fertilisation, the diploid zygote grows into a the mitochondria, with at least one generation displaying pit
carposporophyte, the first diploid generation, which remains plugs, i.e. plugs of proteins in the area of the pits). The Eu-
connected to the gametophyte and is nourished by it. The rodhophytales include the Bangiophycaeae and Florideophy-
carposporophyte forms mitotic diploid carpospores, which ceae, the largest and most commonly found red algal groups.
carposporophyte: formed by the fusion of haploid gametes in tetrasporophyte: the second sporophytic generation in red al-
the three-stage lifecycle of red algae gae formed from a carpospores
pseudo-parenchyma: tissue-like complex of cells; in contrast trichal: filamentous (branched or unbranched) organisation of
to real tissues, cell-to-cell structures such as plasmodesmata are algae
only connected by the individual (intertwined) cell filaments zoospore: asexual spore with a flagellum
See also: Alternation of generations: 2.3.3.11, 2.3.3.12, 4.4.3.3; Carposporophyte, Tetrasporophyte: 2.3.3.12; Bangiomorpha: 2.2.2.7
Archaeplastida: Rhodophyta 311
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
od
la
uc ria
ta
op
op Re
hy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
Stra
onada
lveolata
men
Metam opile
a Ha s
zo
oa nta
bo pt
Cry
oe op
o
ok
Am hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
Porphyridium purpureum Batrachospermum sirodotia Sphaerococcus coronopifolius
Eubacteria Archaea
The tetrasporophyte forms haploid

meiotic tetraspores, from which the
80S ribosomes Tetrasporophytes, the second gametophyte grows
floridean starch diploid generation, emerge from
rough endoplasmic reticulum the diploid carpospores, which
form from the carposporophyte.
nucleus
It is often isomorphic with the
gametophyte
mitochondrion

circular DNA
70S ribosomes
The zygote emerges from the carpo-

thylakoid
sporophyte, remaining on the gameto-
phyte and providing it with nutrients.
This is the first diploid generation
phycobilisomes
The carpogonium, the female
dictyosome gametangium, meets the game-
tophyte for fertilisation and the
formation of the zygote
When radiation hits a water surface, a small part is reflected and 0

the remaining energy is absorbed and scattered. Due to the par- chl b chl a
tial absorbance of light, a vertical light gradient is created, with a
light intensity decreasing exponentially with the depth of the water
body. Different wavelengths of light are absorbed differentially and 20
are therefore associated with different depths in the water column. green algae
Red light is the most strongly absorbed, therefore disappearing at
fucoxanthin chl a
water depth [m]
shallower water, whereas blue-green light penetrates deeper than

chl c
other wavelength. For photosynthesis, the visible wavelength range 40
of 400–700 nm is particularly important. The pigment composi-
tion of algae is adapted to the available light spectrum at different
depths. To that end, green algae do not survive at depths where red brown algae
light cannot penetrate, whereas red and brown algae can, meaning phycocyanin chl a
that these species dominate the deeper water zones. In addition 60
phycoerythrin
to chlorophyll, other photopigments are also used to absorb light
in parts of the spectrum where chlorophyll is not effective. These
other photopigments make it possible to survive in deeper waters.
Brown algae, for example, complement their chlorophyll with fucox- 80 red algae
anthin, which absorbs light in the blue-green range. Red algae, on 400 500 600 700 Dominant algal groups by depth (left) and the
the other hand, use phycobilins. wavelength [nm] absorption spectrum of their photopigments
(right)
Photo pigments and vertical ecological niches

312 Megasystematics
4.4.3
Viridiplantae
The Viridiplantae (=Chloroplastida, =Chlorobionta, forms during cell division: the two daughter nuclei move to-
=Plantae) is a monophyletic group of organisms, which is wards each other and, after the spindle apparatus collapses,
diverse in terms of morphology, cell architecture, life cycle, the microtubules organise themselves in parallel to the plane
reproduction, and biochemistry. Viridiplantae include the of division and form the phycoplast.
Chlorophyta and Streptophyta (of which a subset is land Within the ‘core’ Chlorophyta, the Chlorodentrales are
plants). The term ‘green algae’ includes all Viridiplantae the sister group to the remaining Chlorophyta lineages. The
with the exception of land plants and therefore does not con- Chlorodentrales comprise only a few scale-bearing unicellu-
stitute a monophyletic group. lar flagellates with four flagella per cell.
The Chlorophyta have both chlorophyll a and b, with The Trebouxiophyceae group is multifaceted, including
starch used as the storage polysaccharide within chloro- flagellated unicellular or non-flagellated and branched or
plasts. Their plastids have two membranes as a result of pri- unbranched filamentous forms. The Trebouxiophyceae colo-
mary endocytobiosis and the group also has mitochondria. nise freshwater and marine habitats, with some species also
Chlorophyta comprise the majority of green algae, including living on land in symbiosis with fungi to form lichens or even
more than 17,000 known species inhabiting both terrestrial as secondary endosymbionts (Zoochlorella, genus Chlorella)
and aquatic habitats. Most of the Chlorophyta, however, in metazoans and unicellular eukaryotes.
are adapted to freshwater habitats. Chlorophyta are diverse, Most representatives of the Ulvophyceae are marine, with
taking on a variety of forms, including both flagellated and a few colonising limnic and terrestrial habitats. They may
non-flagellated protozoa as well as colonies of differentiated be unicellular and filamentous or form tissue-like, sheet-like
cells, unbranched and branched filamentous algae and more thalli. Some cells can even reach macroscopic size and some
complex thalli. Some species within the Chlorophyceae have are multinucleated.
become secondarily colourless and heterophilic (Polytoma The Chlorophyceae include flagellated or non-flagellated
and Hyalogonium). unicellular organisms living in colonies or as filamentous
The ‘core’ Chlorophyta include the basal group of Chlo- forms. Most species of Chlorophyceae live in freshwater
rodentrales as well as the Ulvophyceae, the Chlorophyceae, habitats, but there are also marine and terrestrial forms.
and the Trebouxiophyceae. In these groups, a phycoplast
Some basal groups within Viridiplantae are known as the specifically, the genera Ostreococcus and Micromonas can make
Prasinophytina. Previously, scale-bearing flagellates with up a significant portion of marine plankton.
two, four, or eight flagella emerging from a single flagellar The Pyraminomonadales are marine and limnic and in-
depression were combined under this name. However, mo- clude large flagellates with four (rarely eight or sixteen) fla-
lecular data show that this is a polyphyletic group, including gella and complex scales. Some species have transitioned to
the Mesostigmatophytina (as basal Streptophyta), as well as a mixotrophic (phagotrophic) feeding habit.
deep-branching paraphyletic groups. Molecular data lead to The Pycnococcaceae are marine and include flagellates
the exclusion of the Chlorodendrales (now ‘core’ Chloro- with scales and without cell walls as well as flagellates with-
phyta) and of the Mesostigmatophytina (now Streptophyta). out scales and with thin cell walls.
The remaining groups are paraphyletic, but are still known The marine and limnic Neproselmidophyceae are char-
under the term Prasinophytina. acterised by large, asymmetric cells with two unequally long
The Picocystis-clade includes scale-less coccoid cells with flagella as well as scales.
a thin cell wall. These occur in saline lakes and in marine The Prasinococcales are small, marine, scaleless coccoid
environments. cells with a thick cell wall.
The Mamiellophyceae include unicellular organisms lack- The Palmophyllales form multicellular colonies, in which
ing a cell wall, sometimes forming scales. Most species have individual cells are embedded in a gelatinous matrix. The
two flagella, though in Monomastix the second flagellum is species occur mainly in deeper waters, where only low levels
reduced to only a basal body. Most species are planktonic; of light can penetrate.
capsoid (capsal): category of algae in which the flagella are ECM: extra cellular matrix
largely reduced; cells embedded in gelatine monad: flagellated, single-celled
coccoid (coccoidal): class of algae which are spherical in siphonal: polynuclear, single-celled
shape, without flagella and with a single cell wall
See also: Alternation of generations: 2.3.3.11, 2.3.3.12, 4.4.3.3; Primary endocytobiosis: 2.2.2.5; Scales: 4.7.2
Archaeplastida: Viridiplantae 313
Palmophyllales stida
Pyramimonas sp. ae
pla
Rh
iza
Viridiplant ta
ria
oa
h
Prasinococcales rc
Rh
z
G
Cerco
odo
la ria
Nephroselmidophyceae uc ta
op Re
ph
Chr
hy
ae
Pycnococcaceae
y
Disc ta
Excavata
Basal groups within Chlorophyta are paraphy- oba olata
oma
Alve
Pyramimonadales letic and are summarised as Prasinophyta. Stra
onada
lveolata
men
Mamiellophyceae They are mainly scale-bearing unicellular or- Metam
a Ha
opile
s
zo
oa nta
Picocystis ganisms bo pt
Cry
oe op
o
ok
Am hy
pto
is t
ta
‘core’- Chlorophyta: These organisms form a phycoplast
soz
h
phy
Op
Apu
ta
As a result of morphological similarities, the
Chlorodendrales Chlorodentales was previously grouped with
Eubacteria Archaea
Prasinophytina
Chlorophyta
V
i
Ulvophyceae
r
i
d Ulothrix carmichaeli Enteromorpha sp. Ulva lactuca
i
p
l
Chlorophyceae
a
n
t Asterococcus limneticus Volvox sp. Pediastrum sp.
a
e
Trebouxiophyceae
Tetrastrum heteracanthum Eremosphaera viridis Dictyosphaerium lacustre
As a result of morphological similarities, the Mesostigmatophytina

Mesostigmatophytina
were also previously grouped with Prasinophytina
Chlorokybophytina
Streptophyta
Klebsormidiophytina
‘Core’- Streptophyta: comprises the paraphyletic Charophytina and land plants
The emergence of multicellularity and cell dif- colony and the included somatic cells die off.
ferentiation was a crucial step in the evolution Gonidia of the daughter colonies subsequently
of life. It is well established that multicellularity mature and begin their cell division. When com-
evolved independently several times in the Vir- plete, the embryos begin an inversion process
idiplantae. The development from unicellular and then increase the diameter of the colony by
(Chlamydomonas) to multicellular (Volvox) life the synthesis of ECM until it once again breaks up
can be demonstrated from extant species of the and releases daughter colonies.
Chlorophyceae. This is evident not only in the dif-
ferential morphology but also in the progressive
differentiation into somatic and vegetative cells
in the species occurring in the evolutionary lin-
eage of Volvocales. Volvox carteri is a real mul-
ticellular organism with two different cell types
that mostly occupy different tasks: only a small
proportion of cells are capable of reproduction,
whereas the large majority of cells are somatic
cells, functioning for the synthesis of the extra-
cellular matrix (ECM) and for locomotion. After
the release of daughter colonies, the mother Volvox aureus
Multicellularity
314 Megasystematics
4.4.3.1
Streptophyta
The Streptophyta include all land plants (Embryophyta) the dryer environment led to further adaptations to cell archi-
as well as a diverse paraphyletic collection of freshwater tecture, metabolism, and physiology.
green algae, such as the Mesostigmatophytina, Chlorokybo- Many typical features and characteristics of Embryophy-
phytina, Klebsormidiophytina, Zygnematophytina, Coleo- ta had already developed in the ancestors of land plants. Im-
chaetophytina, and Charophytina. portant developments in streptophyte algae included a cell
The land plants developed from the precursors of extant wall of cellulose, multicellularity, the formation of a phrag-
streptophyte green algae. Land plants colonised terrestrial moplast during cell division, plasmodesmata, apical growth,
habitats around 450–470 mya, paving the way for the evolu- three-dimensional tissue, asymmetric cell division, and cell
tion of those groups of land plants which continue to domi- differentiation. In addition, terrestrial plants and the strepto-
nate Earth’s ecosystems (Embryophytes = Marchantiophyti- phyte algae also share physiological and biochemical similar-
na, Anthoceratophytina, Bryophytina, and Tracheophytes). ities, such as the type of photorespiration, the presence of a
Exposure to the atmosphere, increased solar radiation, and plastid, and thioredoxin-regulated GAPDH (glyceraldehyde-
3-phosphate-dehydrogenase).
Molecular data suggest a close relationship between the The phylogenetic relationship between land plants and
Mesostigmatophytina and Chlorokybophytina. The former streptophyte algae remains unknown. For a long time, the
include only genus Mesostigma, a group of asymmetric bi- complex multicellular Charophytina were regarded as the
flagellate freshwater algae. Mesostigma is the only single- closest relatives of land plants; however, molecular data sug-
celled, scale-bearing flagellate within the Streptophyta. The gest that Zygnematophytina and Coleochaetophytina are
Chlorokybophytina include only a single genus: Chlorokybus. more closely related to land plants than Charophytina.
These algae form small clusters comprising a few cells and Charophytina have multicellular, branched thalli and are
live in moist soil habitats for the most part. common in nutrient-poor, stagnant bodies of fresh water.
Klebsormidiophytina are the sister group of the ‘core’ They are characterised by the regular subdivision of their
Streptophyta, including some unbranched filamentous al- thalli, often several decimetres long, into nodes, stem ele-
gae. They are found in freshwater and soil habitats and are ments (inter-nodes), and rhizoids. Side branches arise from
spore-forming. the nodes, with the same structure as the main axis. Sexual
The above groups reproduce asexually and divide by sim- reproduction takes place by oogamy.
ple cleavage, whereas the ‘core’ Streptophyta form a phrag- The Coleochaetophytina include parenchymatous fresh-
moplast and reproduce sexually. They also have plasmodes- water algae.
mata, secondarily reduced in Zygnematophytina, which are The Zygnematophytina comprise unicellular and filamen-
designed for cell-to-cell communication. tous freshwater algae.
apical: (Lat.: apex = peak) pertaining to the apex phragmoplast: microtubuli assembled perpendicular to the cell
oogamy: fertilisation of the ovum; union of an egg cell (large, plate during cell division
immotile gamete) with a sperm cell (smaller, highly motile gam- plasmodesmata: channels between two plant cells enabling
ete) in sexual reproduction the transport of matter between them
photorespiration: (Grk.: phos = light, Lat.: respiratio = breath- thioredoxin: small proteins which function as cofactors in the
ing) a process in plant metabolism in which oxygen instead of transfer of electrons
carbon dioxide is added to RubisCO during which phosphogly-
colate is created
See also: Colonisation of terrestrial environments: 2.3.3.6; Cell to cell contact: 2.2.2.8; 4.2.3.1
The Streptophyta have an asymmetric flagellar root system featuring so-called stida Rh
pla iza
ae
Viridiplant ta
ria
‘multi-layered-structures’. The group is also supported by molecular similarities,
oa
h
rc
Rh
z
G
A
including the presence of glycolate, Gap-A/B-gene duplications and flagellar per-
Cerco
odo
la
uc ria
ta
oxidase op Re
ph
Chr
hy
ae
y
Disc ta
Excavata
oba olata
oma
Alve
The basal position of Mesostigmatophytina within Streptophyta Stra
onada
lveolata
men
Mesostigmophytina supports the assumption that the Streptophyta were derived Metam opile
a Ha s
zo
from unicellular freshwater algae
oa nta
bo pt
Cry
oe op
o
ok
Am hy
pto
is t
ta
soz
h
phy
Op
Apu
Chlorokybus atmosphericus, an alpine terrestrial algal species, is
ta
Chlorokybophytina the only species within Chlorokybophytina. The vegetative cells
are sessile Eubacteria Archaea
This group contains organisms with filamentous thalli and tRNA introns for alanine and isoleu-
cine. As in Chlorokybophytina, this group exhibits a sessile vegetative phase
S
non-branching filamen-
t tous algae; zooflagellates
r Klebsormidiophytina
with two flagella
e
p Klebsormidium sp.
t phragmoplasts, plasmodesmata, branching filaments, apical growth
o C
p O
h R Charophytina
y E
t Chara virgata Chara vulgaris Chara globularis
a S
t
r Coleochaetophytina
e
p Coleochaete soluta Coleochaete scutata
t flagella, plasmodesmata, apical growth, and secondarily reduced
tRNA for isoleucine
o
p
h Zygnematophytina
y
t Closterium Micrasterias Zygnema sp.
a striolatum apiculata
Embryophytes generational shift, parenchymatous tissue
Feeding pressure increased in the Neoproterozoic with the Morphological adaptations and structures which reduce
evolution of phagotrophic protists and, later, multicellular the ‘edibility’ of prey can be found across a number of
consumers. The mortality of prey organisms depends on organismal groups. Examples include the formation of ap-
how well they can escape grazing pressure, in principle by pendages as well as the production of gelatine.
one or several of the following three main strategies: However, even a simple increase in size can decrease the
susceptibility of a prey organism to predation. Thus, larger Merismopedia sp.
1) The growth rate of the prey population must be high individuals and multicellular colonies are often harder to
enough that the population is able to survive despite loss- predate upon compared to smaller individual cells. It is
es to predation. These organisms invest their energy into therefore thought that grazing pressure had a significant
high growth rates and, in turn, expend less energy on mor- impact on the evolution of multicellularity.
phological protection for each individual cell.
2) Prey organisms are able to flee from predators.
3) Prey organisms have evolved grazing defence mecha- Asterionellopsis glacialis
nisms (chemical and morphological) or unpalatability,
making them unpleasant for predators to handle.
Daphnia cucullata
Shape as protection against predation

316 Megasystematics
4.4.3.2
Basale embryophytes: bryophytes

The term ‘bryophyte’ denotes an organisational form Most bryophytes have developed simple adaptations to
rather than a monophyletic group. Bryophytes were among terrestrial life, including structures to regulate water and
the first land plants (Embryophyta) and currently inhabit al- gases (cuticula and stomata) as well as structures for water
most all terrestrial habitats. The oldest bryophyte fossils can absorption, conduction, and storage (rhizoids, hydroids).
be dated back to around 360 mya. They are thought to have These structures are, however, not found in all bryophyte
developed from the precursors of green algae, which explains species.
the presence of the photopigments chlorophyll a and b. In contrast to the tracheophytes (vascular plants), the ga-
Bryophytes do not have true roots or stable water vessels metophyte is the dominant generation within the bryophyte
(trachea). As a result, their size is limited since they are not development cycle. The diploid sporophytes are only short-
able to transport water across great distances within the or- lived and are usually dependent on the gametophyte. The
ganism. Their cell walls consist of cellulose but do not, how- sporophyte consists of a sporangium, which is connected to
ever, contain lignin. Bryophyte fertilisation and reproduction the gametophytes by a stem (seta), which also supplies nutri-
processes are heavily dependent on the presence of water. ents and metabolites. The seta (shaft) positions the sporan-
gium at a higher level, facilitating distribution.
The paraphyletic bryophytes are divided into three line- The phylloides of the foliose gametophytes are arranged spi-
ages. The liverworts (Marchantiophytina) are an early di- rally on the caulloids and have a distinct mid-vein and sto-
verging group, comprising around 10,000 species. They in- mata to facilitate water and gas exchange. Some very large
habit moist, warmer areas, especially tropical rainforests, but mosses also possess specialised cells, hydroids, which hold
also temperate habitats. Liverworts are characterised by the a particular function in water transport within the gameto-
presence of oil bodies, which are responsible for their typical phyte and sporophyte. The moss sporophyte can be either
smell. terminally (acrocarp) or laterally (pleurokarp) arranged.
Liverworts can be divided into two main morphological Mosses of the genus Sphagnum (peat mosses) differ from
types. The thallus type has a flat, dichotomously branched other moss species because the prothallus (protonema) does
gametophyte, with rhizoids on the bottom part of the organ- not consist of a network of cell filaments but is thallose and
ism. The foliose type, however, is structured into ‘leaves’ rhizoids are lacking.
(phyllodes), ‘stems’ (caulloids), and rhizoids. Phyllodes have The hornworts (Acanthoceratophytina) are found in tem-
no true mid-vein. Some species are able to hold water in spe- perate and tropical regions and are able to survive in soil or
cialised sacs, while a number of species are distinguished by on rock in damp conditions. Roughly 100 species have been
a further row of leaves (amphigastria) on the underside of described. As an adaptation to drier locations, the stomata
the caulloids. The sporophyte of liverworts is usually smaller are located on the underside of the thallus and the antheridia
than that of the mosses (Bryophytina) and hornworts (An- and archegonia are sunken into the thallus. In contrast with
thocerotophytina). Propagules (gemmae), which are located other bryophytes, the sporophytes of hornworts can feed
on the gametophyte, serve to enable vegetative proliferation, themselves and are also able to grow indefinitely, since their
during which the propagules fall and grow into a new thal- basal region is capable of many cell divisions. Hornwort
lus. One of the most well-known liverworts is the fountain sporophytes therefore continuously produce spore-bearing
liverwort (Marchantia). tissue.
Mosses (Bryophytina) are always foliose and colonise al-
most all terrestrial habitats. Over 15,000 species are known.
adaptation: the process of adapting protonema: earliest stage (haploid phase) in moss gameto-
antheridium: male reproductive organ in land plants phytes
archegonium: female reproductive organ in land plants rhizoids: similar to roots, serving primarily to anchor the plant
columella: central column in the spore-case of mosses to the ground, to a lesser extent they also serve to absorb nu-
elaters: spiral-shaped cells in plant spore capsules which serve trients and water as they possess no specialised vascular tissue
to disperse spores sporophyte: spore-producing diploid generation in the alterna-
foliose: a growth form with leaf-like structures tion of generations in land plants
gametophyte: the gamete-forming, haploid stage in the thallose: thalloid vegetative tissue with no distinct parts or
change of generations in land plants ‘leaves’
hydroids: non-woody cells in mosses for transporting water
See also: Gametophyte: 2.3.3.11; Colonisation of terrestrial environments: 2.3.3.6; 2.3.4.2; Sporophyte: 2.3.3.12
stida Rh
pla iza
Tracheophytes ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
Anthoceratophytina op Re
ph
Chr
hy
ae
y
Disc ta
Excavata
Gametophyte: thallose rosettes, stomata, unicellular rhizoids, no oil bodies, oba olata
oma
Alve
endogenously emerging gametangium Stra
onada
lveolata
men
Sporophyte: horn-shaped, long-lived, autotrophic, columella, pseudoelaters Metam
a Ha
opile
s
zo
oa nta
bo pt
Cry
oe op
o
ok
Am hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
Eubacteria Archaea
E Megaceros fuegiensis Folioceros fuciformis Anthoceros agrestis

m
b Bryophytina
r Gametophyte: foliose, no stomata, multicellular protonema, branched, filamentous, multicellular rhizoid, alternating leaflet
y structure, ribbed and pointed, no oil bodies, food conducting cells (leptoids, hydroids), endogenously emerging gametangium
o Sporophyte: long-lived, spore capsule differentiated by seta stretching, spore capsule with stomata, capsule with columella,
no elaters
p
h
y
t
e
s
Mnium spinosum: Mnium hornum: Plagiopus oederi Sphagnum cristatum
gametophyte sporophyte
Marchantiophytina
Gametophyte: foliose or thallose, lacking stomata, protonema comprised of only a few cells, non-ribbed leaflets and multi-
pointed, unicellular rhizoid, oil bodies, endogenously emerging gametangium
Sporophyte: short-lived, spore capsule differentiated by seta stretching, thin-walled seta, spore capsule lacking stomata,
capsule without columella, forms elaters
Metzgeria furcata: Diplophyllum obtusifolium: Lunularia cruciata: Lepidozia pendulina

thallose liverwort foliose liverwort incubation bodies
cuticula
Terrestrial organisms need to protect them- Animals do not possess a cell wall. How-
selves from dehydration and UV-radiation. ever, as in plants, the outer cell layers sup- vacuole
epidermis
As a result, several terrestrial groups have port against gravity and protect against
developed structures that restrict the loss evaporation in animals; evaporation is of-
of water through the organism’s surface. ten reduced in metazoa by dead skin lay-
tonoplast
In plants, fungi, algae, and various prokary- ers or other special skin growths (feathers,
plasmalemma
otes, the cell wall serves this protective fur etc.) or the presence of a cuticula. In
cell wall
function. In addition, the surface of the or- Ecdysozoa (molting animals), the cuticula
ganism is often coated with water-repellent serves as an outer skeleton. The develop-
substances (for example, a cuticula), which ment of such protective layers was a key
considerably reduces evaporation. These step in the evolutionary invasion of terres-
structures, as well as internal turgor pres- trial habitats.
sure, also contribute to giving individual
cells structure in an air-filled environment
lacking the buoyancy of aquatic habitats.
In plants, the main component of cell walls
is cellulose, whereas it is chitin in fungi and
murein in bacteria.
Cell wall and cuticula

318 Megasystematics
4.4.3.3
Rhyniophytina and Lycopodiophytina

Vascular plants (tracheophytes) are those that possess a sporangia are found on the upper side or the upper axes of
specialised vascular bundle. In contrast with bryophytes, the sporophytes and open through a longitudinal crack. The
sporophyte generation dominates in vascular plants, which gametophyte lives mostly underground and in a mycotrophic
comprise club mosses, seed plants, ferns, and the extinct manner. The Lycopodiophytina include some extinct groups,
Rhyniophytina. as well as the extant Lycopodiopsida, which includes club-
The Rhyniophytina represent the oldest known vascular mosses (Lycopodiales), Isoetopsida, which includes spike-
plant group in the fossil record and are widely recognised moss (Selaginellales), and the quillwort (Isoetales).
as the sister group of all living vascular plants (Eutracheo- Although the Lycopodiophytina appeared already in the
phytes). They lived from the mid-Silurian to the Middle Silurian, their diversity expanded only in the Carboniferous.
Devonian, forming dichotomous, equal, axis-shaped shoots In the late Palaeozoic, the club mosses, horsetails, and ‘real’
which were not divided into roots, stems, and leaves. They ferns dominated the flora. They reached the size of today’s
also had terminal sporangia, standing across either their side trees; for example, genera Lepidodendron and Sigillaria, which
or main axes. Their spores were monomorphic (isospores). belonged to Lepidodendrales (Isoetopsida), reached up to
Within the Eutracheophytes, the monophyletic Lycopodi- 50 m in height.
ophytina are the sister group of all remaining vascular plants The height of trees was limited at the time because of the
(Euphyllophytes). Around 10–15 genera comprising around size restrictions characteristic of in a flow system with only
1,200 species are known, mostly small herbaceous plants. a small secondary xylem and without a secondary phloem.
Both roots and shoots are dichotomously branched. Apical From the Mesozoic, the tree-like club mosses were increas-
growth is based on multi-layered meristems. Roots are shoot- ingly replaced by the emerging seed plants. Today‘s Lycopo-
born, so no single root can be identified as a major one, with diophytina are predominantly herbaceous.
mycorrhizal fungi often associated with the club mosses. The
The oldest Lycopodiophytina fossils originate in the Up- phyte. The development and maturation of antheridia and
per Silurian, with the oldest specimens (Baragwanathia sp.) archegonia only begins after 6–15 years.
having been discovered in Yea, in the state of Victoria, Aus- The Isoetopsida include Selaginellales as well as the ex-
tralia. Baragwanathia and the genus Asteroxylon, common tinct Lepidodentrales, and the Isoetales. Quillworts are the
throughout the Devonian, belong to the Drepanophycales only extant representatives of Isoetales, growing in water
and are presumably transitional forms to the basal extinct or on damp sediment beds. The sporophyte is a short fleshy
groups of Lycopodiophytina. Together, these basal groups stem, which penetrates the sediment, bearing several long
are known as Zosterophyllopsida, even though they are microphylls on its upper surface. The genus Isoetes is heter-
likely not monophyletic. Unlike in the Rhyniophytina, the osporous with a megasporangium at the base of the outer
sporangia of Zosterophyllopsida were positioned laterally on sheets and the microsporangia on the inner, younger leaves.
short stalks, with a centripetally developed xylem. Quillworts possess a cambium.
The sporophyte of Lycopodiopsida is a creeping or up- The Sealginellales comprise only a single recent genus (Se-
right shoot with dichotomous roots. The flow system is laginella, spike mosses or lesser club mosses) of around 750
plectostele; in other words, a central core of vascular tissue species. Most of these species live in moist habitats in the
where the xylem elements are arranged in usually paral- tropics, although a few prefer dry areas, such as Selaginella
lel plates surrounded by phloem elements. Microphylls are lepidophylla (the ‘false rose of Jericho’). The heterospore
mostly spirally arranged. Fertile microphylls of the sporo- Selaginella forms megasporangia to megasporophylls and
phyte feature kidney-shaped sporangia on their upper side. microsporangia to microsporophylls. Micro- and megaspo-
In Lycopodium and Diphasiastrum, the sporophylls are united rangia occur on the same strobilus. The stems and roots of
by spike-like strobili. The prothallium is a bisexual gameto- Selaginella form a protostele, distele, or siphonostele.
centripetal: from the outside to the centre ligule: part of the leaf at the junction of sheath and leaf
dichotomous: (Grk.: dichotomos = in two parts) splitting of a micropyle: canal between the integuments at the tip of the
shoot axis into two parts ovulum in seed plants
epilithic: (Grk.: epi = on, litho = stone) growing on the surface mycotroph: feeding on fungi or nutrition in a symbiotic asso-
of rocks ciation with fungi
epiphytic: (Grk.: epi = on, phyton = plant) growing on plants
See also: Gametophyte: 2.3.3.11; Devon: 2.3.3.7; Carbon: 2.3.3.8; Rhynia, Silurrian: 2.3.3.5; Sporophyte: 2.3.3.12
aa
idri
Rhyniophytina pRlahsitza Rh
izAar
Radiolaria
ae rciah
C
Vierid
Sporophyte: leafless isosporous land plants, unicellular sporangia most-
Rh ercozoa
h
rc a
Rhora
F
ta
rcip
G
hy
ep
ly emerging from main or side shoots. The oldest fossils (Cooksonia sp.)
odm
ozlaont
la ria
Eu uco ta tae
las
op
opinhif
† from Wales and Ireland (428 mya, Silurian). Fossils from Rhyniophytina Replan
a ae
od
C
ata
gle ph
tC
idharom
i
yetraa
no yt
D rid hytata
ExcEaxvcaatva
are found worldwide, predominantly on the former continent Laurasia Heistecoba oa a
rolob
z
Vi ulvceoopla
A
osea Gla
Gametophyte: star-shaped branches with arching ascending gametan-
alveolata
ada Stra Hapto
onlia
asa men phyta
gia bodies Merab
Pa tam opile
otaa HaCry s
oozn
StCrypAto
a
pt ptop
etobk
soozzo oant
ra
op hy
mhois
m
Zosterophyllopsida
zk
p hy ta
Ch
en
oa
A
to
O ta
eisb
op
lvpehoy
ro
Sporophyte: leafless isosporous land plants, sporangia
poh
ile
AOm
m
AAppuu
s
al
latata
mostly spiked, exarch xylem, so older cells found externally.
ve
† lat o
Paraphyletic group of extinct plants, which spread for the
a
most part during the Devonian Eubacteria

Eubacteria Archaea
Archaea
Gametophyte: same as Rhyniophytina
E
u Lycopodiopsida
Sporophyte: isosporous, dichotomous plants with micro-
t L phylla arranged in alternation with fertile microphylla on
r y their upper side, these are partly linked to the sporophyll
a c columns
c o Gametophyte: prothallia underground, heterotophic nod-
ules in symbiosis with a mycorrhizal fungus, monoecious,
h p sunken gametangia Sporophyte Sporophyll stand Gametophyte
e o (Lycopodium clavatum) with sporangia (Lycopodium sp.)
o d Selaginellales
p i Sporophyte: herbaceous, heterosporous plants with microphylla. Megasporangia to mega-
h o sporophylls. Microsporangia to microsporophylls, both united within a sporophyll stand
Gametophyte: dioecious prothallia, strongly reduced. Male gametophyte remains in the
y p
spore, whereas the female gametophyte develops in the spore and continues to grow exter-
t h nally. The embryo develops within the megaprothallium within the spore
e y Selaginella canaliculata
Isoetopsida
S t Lepidodendrales
Sporophyte: tree-shaped with secondary growth. Dichotomously branched, hetero-
i
sporous. Dominant in Carboniferous stone coal forest. Stems with characteristic leaf
n † scars (eg.: seal tree Sigillaria). Shallow buried xylem, stem for the most part made of
a periderm. Sporangia located on upper surface of sporophyll, inside the strobili
Gametophyte: prothallium develops in the spore as in Selaginellales Lepidodendron – bark
Isoetales
Sporophyte: immersed, almost stemless with microphylla arranged in a rosette-
formation. Heterosporous megasporophylls lie externally whereas microsporophylls
are internal. The Isoetales are aquatic or amphibious. Possess a cambium
Gametophyte: small prothallia, development in the spore as in Selaginellales
Isoetes melanospora
Euphyllophytes (ferns and seed plants)
Various forms of reproduction may alternate from generation to genera-

tion. If the gametes are formed directly through meiosis and a diploid or-
ganism resembling the parent arises directly from the zygote, no genera-
tional change occurs (top examples: vertebrates). However, land plants can Vertebrates: only one diploid
reproduce both through the zygote but also through haploid spores, which generation with no generational
are created through meiosis. These organisms, which change so drastically alternation
between generations, are known as heterophasic (alternate haploid and
diploid generations) and anisomorphic (differing phenotypes). Different
reproductive strategies may be differentially effective. For example, sexual
reproduction is vital for mixing the gene pool. However, asexual reproduc- meiose I meiose II syngamy
tion tends to favour strategies producing a large number of offspring. Al-
ternation of generations can be observed in many protists and land plants, zygote
but also in cnidarians and tunicates. Further distinct types of generational
alteration are homophasic generational alternation (no haploid/diploid Land plants: diploid and haploid
alternation), isomorphic generational alternation (identical phenotypes), generations – heterophasic gen-
metagenesis (alternating between two-sex, asexual, and sexual reproduc- erational alternation
tion), and heterogony (parthenogenetic and sexual reproduction).
Alternation of generations – meiosis

320 Megasystematics
4.4.3.4
Monilophyta (Ferns)
The Monilophyta (monilophytes or ferns) are sister to the with just one or no vascular bundle. Ferns have primary plas-
seed plants (Spermatophytina) within the Euphyllophyta. tids (chlorophyll a and b), as well as mitochondria.
The monilophytes include the extinct basal ferns Marattiop- In addition, their protoxylem is limited to certain lobes of
sida, Psilopsida (fork-leaved plants), Equisetopsida (horse- the xylem. To that end, the name monilophytes comes from
tails), and the Polypodiopsida (‘true’ ferns). the necklace-shaped xylem arrangement. On the molecular
There are around 300 extant monilophyte genera com- level, the group is characterised by the insertion of nine nu-
prising roughly 9,000 species. Ferns have a worldwide dis- cleotides in the plastid gene rpS4 (Small Ribosomal Protein).
tribution and can often be found in shady, moist forest areas The wall of fern sporangia was originally composed of sev-
or wall cracks, crevices, ravines, and stream banks. However, eral cell layers (eusporangiate). This architecture can still be
the bulk of fern diversity can be found in the tropics, includ- found in the Psilotopsida, Equisetopsida, and Marattiopsida.
ing tropical rainforests, home to the largest tree ferns. In what is currently the most diverse fern group, the Poly-
Most monilophytes have underground shoots often ar- podiopsida (true ferns), the sporangium comprises just one
ranged in rosettes and usually comprising multipennate cell layer (leptosporangiate). Most ferns are isospore with a
leaves in a wide variety of patterns. At one extreme, tree usually small prothallia (under 1 cm) and are bisexual (mo-
ferns can reach heights of over 20 m; at the same time, the noecious).
Psilotopsida and Equisetopsida feature mostly smaller leaves
The Marattiopsida are eusporangiate ferns. Their isospore The Equisetales (horsetails) are isospores and usually in-
sporangia are located on the underside of the leaves. The old- clude terrestrial and aquatic perennial ferns. The trunks of
est known Marattiopsida fossils date back to the Carbonifer- some fossil groups, such as the Calamites within coal forests,
ous; in the Lower/Middle Permian, the group was both spe- were lignified and reached up to 30 m in height and 1 m in
cies-rich and the dominant plant group with individuals up diameter. In extant groups, the sporophyte can reach heights
to 10 m tall. Extant Marattiopsida are significantly smaller of 8 m, although it is smaller in the majority of species. The
and less diverse, and limited to the tropics. Species are long- mostly distinctly ribbed stems arise from a rhizome, form-
living, autotrophic, and associated with mycorrhizal fungi. ing adventitious roots at the nodes. The microphylls are ar-
The prothallium, or gametophyte, is multi-layered. The an- ranged in whorls. The sporangia-bearing structures are usu-
theridia and archegonia are sunken into the underside of the ally arranged as cone-like strobili.
plant. The Polypodiopsida (Pteridopsida) are leptosporangiate.
The Psilotopsida include Psilotales (fork-leaved plants) The sporangia open along a predetermined breaking point,
and the Ophioglossales (adder’s tongues). Their relationship called the annulus. The majority of ferns are herbaceous
is mainly understood using molecular data. Their prothallia with a perennial rhizome. In eagle ferns (Pteridium aquili-
cannot photosynthesise and live underground in association num), which can live for 70 years, these can reach up to 40 m
with mycorrhizal fungi. The Psilotales have no root. In con- in length. Vascular bundles are concentric and include an in-
trast with the Lycopodiophyta, the dichotomous branching ner xylem. The usually pinnate leaves grow from a double-
of the sporophyte is secondary. The sporophyte forms rhi- edged apical cell and are often characteristically curled. The
zomes with rhizoids. Sporangia sit in or above the dichoto- sporangia sit in clusters (sori) on the underside of the leaves
mous sporophyte branches. Adder’s tongues feature reduced (sporotrophophyles). Most Polypodiopsida are isospore,
roots and usually just one leaf with a photosynthetic and forming monoecious prothallia, whereas the pepperworts
sterile lower part, and sporangia on the upper part. and floating ferns are heterosporous, forming dioecious pro-
thallia.
adventitious root: plant root developing from stem or leave isospory: having identical spores
tissue or as the result of a wound leptosporangiates: sporangia consisting of a single layer of
eusporangiate: wall of the mature sporangium arising from cells
several cell layers prothallium: haploid gametophyte in ferns
heterospore: possessing different spores strobili: cone-shaped sporangia-bearing structures
See also: Gametophyte: 2.3.3.11; Carbon: 2.3.3.8; Microphyll: 2.3.3.10; Perm: 2.3.3.9; Sporophyte: 2.3.3.12
aa
pRlhasiztaidri Rh
iAzra
Spermatophytina
Radiolaria
ae
Viridip
crhia
Cerc phfyetraa
a
h
rc a
Rhoram
Rh Cercozo
F
ta
G
hy
ep
odo in
ozlaoa
la ria
uc ta tae
las
op
Marattiopsida Eu
gle oph Ripelan
ntae
od
ta
tiCd
i
Sporophyte: significant fossil group with only a few extant species. Disc nozo yta
ExcEaxvcaatvaa
rid ophlayta ta
haroma olata C
Hete oba a
rolob Vi ulv c eo
Isosporic, eusporangiate. The sporangia are often laterally fused or osea GlaA
ada StraHapto
combined within sori
lve
Pa rab
e ta asa
m onlia men phyta
M opile
Gametophyte: above ground, photosynthetic prothallia, antheridia ota HCaryp s
oozn
St CrypA
a
teobk pt top
oa t
ra tlovpeho
ussooz kooan
op hy
and archegonia sunken on the leaf underside hiso
m
tooz
pm hy ta
en
a
O A
heisb
ta
hr
op
Opo
om
ile
Am
s
AAppu
al
ylatata
ve
lat o
a
Eubacteria
Eubacteria Archaea
Archaea
Psilotopsida
Sporophyte: terrestrial and herbaceous, most species live as epi-
phytes. The sporangium has several cell layers (eusporangiate). The
E root system is secondarily reduced and completely absent in the
u Psilotaceae. The leaves are also reduced in Psilotaceae, although
p M these are present in Ophioglossaceae
h o Gametophyte: underground prothallium, non-photosynthetically
y active and associated with mycorrhizal fungi Ophioglossum vulgatum Psilotum nudum
n (Ophioglossaceae) (Psilotaceae)
l i
l l
o o Equisetopsida
p p Sporophyte: isospore, eusporangiate. Small and arranged in whorls.
h h Leaves and stem are usually clearly divided by nodes and internodes.
y Sporophylls are plates with a central stalk and numerous sporangia
y
t at the underside. They are arranged in terminal spikes. Fossils over
t 30 m in height are known in Calamitaceae from the carboniferous
e e fossil forest
s s Gametophyte: richly branched and strongly lobed, photosynthetic Sporophyte of Gametophyte of
thallus. Monoecious or dioecious. Antheridia sunken, archegonia Equisetum fluviatile Equisetum hyemale
sticking out from the surface
Polypodiopsida
Sporophyte: herbaceous plants or tree ferns up to 20 m in height,
although with no secondary growth. The sporangium wall features a
single cell layer and annulus, at which the mature sporangium sub-
sequently breaks
Gametophyte: prothallium is usually short-lived, usually monoe-
cious. Antheridia and archegonia on the shaded side of the leaf, usu-
ally not sunken into the tissue Sporophyte of the fern Gametophyte of the fern
Dicksonia antarctica Dicksonia antarctica
concentric with an concentric with an radial closed collateral open collateral open bicollateral
inner xylem outer xylem
phloem phloem phloem
phloem xylem phloem
xylem
xylem phloem xylem
xylem xylem phloem
Ferns (rhizome and Monocot spermato- Spermatophytina Monocot spermato- Dycot spermatophyte Curcurbitatceae
leaves) phytes (rhizome) (roots) phyte (shoot) (shoot) Solanaceae
Vascular bundles
322 Megasystematics
4.4.3.5
Gymnosperms
The Spermatophytina (seed plants) are primarily woody are taken into account (Bennettitopsida, Glossopteridopsida,
plants with secondary growth in girth. Herbaceous plants, and basal seed ferns).
it follows, are considered to be derived. The gametophyte Within acrogymnosperm groups, only the Cycadopsida
generation of seed plants is largely reduced, shrinking, and and Ginkoopsida have flagellated male gametes (sperma-
corresponds to the germinating pollen grain and the embry- tozoids). In Coniferopsida – including Gnetales – these are
onic sac. non-flagellated. The embryonic sac (female gametophyte) re-
The extinct Progymnosperms were the ancestral seed mains in the maternal tissue and is surrounded within a spe-
plants. Extant seed plant lineages include the Magnoliopsida cial organ, known as the integument. The integument later
(angiosperms) and the paraphyletic gymnosperms. forms a seed coat. As a result, fertilisation is largely water-
Gymnosperms possess mitochondria and primary plas- independent.
tids with chlorophyll a and b. Another important gymno- The acrogymnosperms include three extant lineages,
sperm characteristic is that their ovule is not housed within comprising around 840 species as well as a number of ex-
a carpel (‘naked’). Their flowers are almost always unisexual tinct groups. The three extant lineages are the Cycadopsida,
and wind-pollinated. They comprise exclusively perennial the Ginkgoopsida, and the Coniferopsida (including Pinales,
woody plants with secondary growth in girth. Cupressaceae, Taxales, and Araucaria; the position of Gn-
Extant gymnosperms (acrogymnosperms) form a mono- etales is disputed).
phyletic group, although paraphyletic when extinct groups
The Cycadopsida originated in the Carboniferous and housed within a catkin or cone-like sleeve, whereas the fe-
reached their greatest distribution during the Mesozoic. At male gametes are housed within the axils of covering scales
present, the group comprises 11 genera with around 300 in cones. The plants are monoecious or dioecious.
species, living mainly in the subtropics and southern hemi- The Cupressales are evergreen trees or shrubs with most-
sphere. They have a palm-like appearance, including a trunk ly scale-like leaves. The group includes Cupressus (cypress),
of up to 20 m in height, and many large compound leaves at Thuja (arborvitae), and Chamaecyparis (false cypress). A few
its tip. Fertilisation is delayed by up to seven months after species also have needle-shaped leaves, including Juniperus
pollination. (juniper). Their leaves are arranged opposite or in whirls,
The Ginkoopsida are trees up to 30 m in height, and are their cones are small, woody, and berry-like.
distinctive because of their forked leaf venation. They origi- The Taxales include evergreen trees or shrubs. In particu-
nated in the Carboniferous and diversified in the Upper Trias- lar, the yew (Taxus baccata) is widespread in Central Europe.
sic becoming a widespread group in the Mesozoic. The only They feature spirally arranged, parted, and mucronate nee-
extant species, Ginko biloba, is deciduous and is thought to dles. A middle vein is visible on the surface of the needles.
originate in a set of mountain valleys in China; however, it is All parts of the plant, except the seed coat (the aril), are toxic
also planted in a number of cities to create shading. Fertilisa- as a result of taxane derivatives (taxin, taxol).
tion is delayed by up to four months after pollination. The Gnetales display features that would otherwise only
The Coniferopsida originated in the Carboniferous and be seen in Magnoliopsida, including the trachea and flower-
are today the dominant group of gymnosperms. Coniferop- like structures. The lineage only comprises Welwitschia (with
sida comprises the Pinales (approx. 200 species), the Cupres- the single species Welwitschia mirabilis, a desert plant), Gne-
sales (approx. 25 species), the Podocarpales (approx. 130 tum, and Ephedra. Molecular analyses place Gnetales in the
species), the Taxales (approx. 25 species), the Araukariales Coniferopsida as a sister group to Pinales.
(approx. 23 species), as well as the Scidaopitales (one spe- The systematic position of the extinct Glossopteridopsida
cies) and the Cephalotaxales (one species). Most likely, the and the Bennettitopsida is unclear, although they can likely
Gnetales also belong to the Coniferopsida. group basal to Magnoliopsida but possibly also close to the
The order Pinales is the most species-rich group of coni- seed ferns. The Glossopteridopsida were originally distrib-
fers (Pinus = pine; Abies = fir; Picea = sprice; Larix = larch). uted in temperate areas of the southern hemisphere during
The lineage is characterised by trees – rarely shrubs – with the Permian. The Bennettitospida were common and wide-
needle-shaped leaves, with either compressed, short shoots spread seed plants from the Triassic to the Cretaceous.
(larch) or long shoots (fir, spruce). The male flowers are
integument: (Lat.: integumentum = covering, shell) protective

layer covering the ovule
See also: Mesozoic: 2.3.4 to 2.3.4.6

stida Rh
Progymnosperms and basal seed ferns ae
pla iza
Viridiplant ta
ria
oa
h
The progymnosperms did not possess seeds and were therefore not seed plants. They are thought to rc
Rh
z
G
Cerco
odo
be the ancestors of seed plants and belong to the Spermatophytina lineage, even though they did not la
uc ria
ta
op Re
ph
possess the same organisational structure. The progymnosperms were the first to possess a dipleuric
Chr
hy
ae
y
Disc ta
Excavata
cambium (generates a secondary xylem and secondary phloem) oba olata
oma
Alve
Stra
onada
lveolata
men
Metam
Cycadopsida a Ha
opile
s
zo
oa nta
Palm ferns are dioecious and tree-shaped, palm-like gymnosperms bo pt
Cry
oe op
o
ok
with large pinnate leaves. They were a diverse and ecologically sig- Am hy
pto
is t
ta
soz
h
phy
nificant component of the Mesozoic flora. They currently generally
Op
Apu
ta
inhabit the tropics and semi-tropics of the southern hemisphere
A
c only round (circular) – no elongated (scalariform) worts Eubacteria Archaea
r
Ginkgoopsida
S o dioecious tree-like plants, flat leaves with dichotomous nervation. Ginko bal-
p g boa the only extant species
e y
r m Cordaitopsida
n shrubby or tree-shaped and up to 45 m height. Tree-shaped Cordaitopsida
m
possessed a monopodial stem with a distal crown made of large, spatulate
a o leaves. The Cordaitoposida were present across Europe, North America,
t s and China during the Palaeozoic.
o p
p e Coniferopsida
Characteristic features of the Coniferopsida, including Gnetales, are linear
h r
leaves, reduced sporophylls, and a protoxylem with round pits. Today, the
y m Coniferopsida, and especially the Pinales, dominate cold-temperate zones
t S (taiga) Pinales Cupressales
i Gnetales
n The position of Gnetales remains unresolved. Molecular data suggest the group is closely
a related to Pinales. Morphological data, on the other hand, groups it together with Glos-
sophilia within the broader lineage Anthophyta. It is also possible that Gnetales is a sister
lineage of the Cordaitopsida and Coniferopsida
Glossophytina
Glossopteridopsida (excluding Gnetales)
trees with seasonal growth (annual rings) spread within the temperate zones of the southern hemi-
sphere (Glossopteris-flora) during the Permian to Triassic
Bennettitopsida
reproductive organs within flower-shaped cones, globally distributed from the Triassic to the
Cretaceous
Magnoliopsida (angiosperms)
The formation of taxa or larger groups bivalve molluscs in epibenthic habitats

of species, their radiation and, finally, previously dominated by brachiopods.
their quantitative propagation, are
processes usually lasting across long Example 3: The diatoms likely emerged
geologic time periods. already in the Upper Permian or in
the Lower Triassic, yet the group only
Example 1: Gymnosperms originated became widespread in the Cenozoic.
in the Lower Carboniferous. However, Diatoms require silicate to build their
their dominance only began after the silica shell; as a result, it is thought that
formation of the supercontinent Pan- their distribution increased as a direct
gaea with the increasingly dry climate result of the weathering of silicate on
of the Upper Permian, as seed plants land due to the spread of grasses.
were better adapted to dry climate.
Example 2: Clams and brachiopods

originated in the Cambrian, yet only
the spread of the starfish in the Meso-
zoic promoted the quantitative expan-
sion of the at least partly endobenthic
Pecopteris sp. (Marattiaceae, Carboniferous)
Origin, radiation, and dominance of taxa

324 Megasystematics
4.4.3.6
Magnoliopsida I: Overview
The Magnoliopsida (angiosperms) comprise the mono- idioblasts with ethereal oils. These are absent in the Eud-
cots (monocotyledonous), eudicotyledons (dicotyledonous), icotyledons.
as well as a number of basal groups (the ANITA-clade and As the origins of the Magnoliopsida and their relation-
magnoliids). ships – especially to the Bennettitopsida and Gnetales – are
While some monophyletic groups, such as the monocots, controversial, their evolutionary development remains un-
are supported by many morphological synapomorphies, oth- clear. Varying hypotheses differ specifically with respect to
er groups display few or no such morphological similarities, interpretations of the homology of ovule structure within
yet they are supported by molecular data. Bennettitopsida and Gnetales. With certainty, the Magno-
Basal orders of Magnoliopsida as well as the monocots liopsida can be seen in fossils dating back to the transition
have pollen grains with a single opening (monocolpate); between the Jurassic and Cretaceous. Presumably, they were
Eudicotyledons, on the other hand, have pollen with three already present in the Lower Jurassic. Today, the group com-
apertures (tricolpate). Similarly, the basal orders also have prises approximately 230,000 extant species, making them
the most diverse group of land plants.
Magnoliopsida ovules are enclosed in one or several car- double-fertilised, subsequently forming a secondary triploid
pels, which enclose the seed at maturity. The group is char- endosperm.
acterised by its fruits, which are only formed in those plants The monocots differ from other Magnoliopsida due to a
possessing closed carpels or ovules. The fruit is the flower of number of characteristics: firstly, they have only one coty-
Magnoliopsida in the state of seed maturation. ledon. In addition, monocots have a secondary homorhizic
The carpel or the axis tissue or the perianth may be in- root system, their vascular bundle is closed collaterally and
volved in the formation of a fruit. Fruit types are distin- scattered across the shoot cross-section, the leaves are always
guished depending on whether the seeds are enclosed within alternating, the stipules are never formed, and the leaves are
the ripe fruit (dehiscent fruits) or set free (indehiscent fruits). either curved or parallel-veined.
Other distinctive features of the angiosperms include the The eudicotyledons have two cotyledons, tricolpate pol-
sieve tubes and companion cells of the phloem (developing len, their root system is allorhizic, their vascular bundle
from one common “mother cell”), stamens with two pairs of opens collaterally with an annular arrangement, and the
pollen sacks, and anthers with a hypodermal endothecium. leaves can be interchangeably arranged in alternate, oppo-
The male gametophyte consists of only three cells. Cells are site, or whorled form; they also possess a net-like nervation.
allorhizy: term given to plants with different primary and sec- hypodermal endothecium: fibrous layer under the epidermis
ondary roots of pollen sacs in Magnoliopsida
carpel: (Grk.: karpos = fruit) organs of a flower with one or idioblast: cells that differ in form and/or function from their
more ovules neighbours in surrounding tissue
companion cells: cells forming a complex with the sieve-tubes ovary: (Lat.: ovum = egg) female organ which holds the ovules
of the magnoliopsida secondary endosperm: nutritional tissue created by the fertili-
convergence (evolutionary): similar characteristics which sation of polar nuclei in the seeds of most Magnoliopsida
have developed independently in unrelated taxa sieve elements: the type of cell in the phloem in Magnoliopsida
homorhizy: phenomenon in plants where all of the roots stem in which organic metabolites are transported
from the shoot synapomorphy: an evolved characteristic common to a mono-
phyletic group
See also: Vascular bundles: 4.4.3.4; Homology, synapomorphy: 4.1.1.6

stida Rh
basal angiosperms (ANITA-clade) ae
pla iza
Viridiplant ta
ria
oa
h
flora organs in alternation or threefold spirally, mainly monosulcate rc
Rh
z
G
Cerco
odo
pollen, carpels usually not present la
uc ria
ta
op Re
ph
Chr
hy
ae
y
Disc ta
Excavata
oba olata
oma
Magnoliids Alve
many spirally arranged stamens dicotyledonous onada
Stra
lveolata
men
Metam opile
a Ha s
zo
oa nta
bo pt
Cry
oe op
o
ok
Am hy
pto
is t
ta
soz
Monocotyledons
phy
Op
monocolpate
Apu
one cotyledon (second cotyledon reduced), leaves with
ta
parallel venation, usually triple blossom rings
Eubacteria Archaea
monocotyledonous
M two cotyledons, tricolpate pollen, no essential oils in
a idioblasts
g mostly free petals, two circles of stamens or a second-
n arily increased androecium, with stipules, ovule with
two integuments
o R
l o
i E Eurosida I (Fabids)
u s lineage supported by molecular data
o i
p d
i d
s s
i C Eurosida II (Malvids)
lineage supported by molecular data. Gy-
d o 2 integuments
noeceum generally featuring a simple style,
a t seeds with small endosperm
y
dicotyledonous
l tricolpate
e mostly large petals, fewer stamens than petals, seed
d case with only one integument
A
o s Euasterida I (Lamiids)
n late sympetaly: petals grow separately as in-
t
dividual primordia by the shoot apex of the
s e flowers, developing at a later point in time
r
i primordia free
d Euasterida II (Campanulids)
s early sympetaly: a ring wall forms at the
1 integument
vegetative tip of the flower, the individual
primordia are connected to each other from
the beginning
primordia connected
This review is limited to the main lineages and is therefore not representative of all known groups
Earlier morphological studies of seed plants already showed that the Gn- However, since there are no extant links between Gnetales and Mag-
etales share many characteristics with the Magnoliopsida. For example, noliopsida, and the presumably closest relatives of Magnoliopsida are
Gnetales cones resemble some of the inflorescences of the Magnoliop- extinct, reconstructing accurate phylogenetic relationships remains dif-
sida. Similarly, tracheae are present in their xylem. In addition, Ephedra ficult.
has been observed to doubly-fertilise, which is a process that was previ-
ously considered unique to the Magnoliopsida. However, the second fer-
tilisation of Ephedra leads to further embryos whereas in Magnoliopsida
this leads to a secondary endosperm.
The extensive morphological similarities suggest a relationship between
Gnetales and the Magnoliopsida. However, molecular findings do not
support this view: genetic data indicate a closer relationship between
Gnetales and Pinales and, thus, a grouping of Gnetales within the Co-
niferopsida. Most likely, the common features of Gnetales and the Mag-
noliopsida are the product of parallel evolution rather than emergence
from a common ancestor.
With fossil plant groups taken into account, a relationship of Magnoliop-
sida to Bennettitopsida and Glossopteropsida is considered. Gnetum sp.: seeds Gnetum sp.: male inflorescence
Ancestry of the Magnoliopsida lineage

326 Megasystematics
4.4.3.7
Basal Magnoliopsida and Monocotyledons

The basal orders of Magnoliopsida include various dicot- and the Eudicotyledons (plus the Ceratophyllales) on the
yledonous, mainly woody plants. They feature pollen grains other.
with a single germ opening and were therefore formerly The Monocotyledons have a number of distinctive char-
grouped together as monosulcate dicots. Their idioblasts acteristics: they have only one cotyledon, a stunted primary
contain ethereal oils and their leaves are simple and have no root, and adventitious roots. The leaves are parallel-veined
stipules. The arrangement of the reproductive organs is usu- and have entire margins, and the closed vascular bundle in
ally spiral and the carpels are mostly not connate (not fused the shoot axis is arranged in a scattered formation (ataktost-
to each other). ele). In general, there is no secondary growth in girth. Only
The basal orders of Magnoliopsida comprise around 8,600 a few species display secondary growth (Dracaena), which
species. They possess primary plastids with chlorophyll a differs from the pattern of gymnosperms and dicotyledon-
and b as well as mitochondria. They do not, however, form a ous angiosperms and is known as atypical secondary growth.
monophyletic lineage. The ANITA-clade includes Amborel- The perianth usually appears in threes and is not separated
lales, Nymphaeales, and Austrobaileyales. These groups do into a calyx and corolla.
not have a benzylisoquinoline alkaloid and the organisation The phylogenetic position of the Ceratophyllales is dif-
of their embryo sac differs from that of other Magnoliop- ficult to assess. In aquatic plants, many features are highly
sida: in the Amborellales, the embryonic sac has four nuclei, derived. Morphologically, they possess a number features
as opposed to nine in the Nymphaeales and Austrobailey- in common with the monocots, but also with the Chloran-
ales. The embryo sac of all other Magnoliopsida contains thales. Similarly to the Eudicotyledons, the idioblasts con-
eight nuclei, including in the Chloranthales and Magnoliids. taining ethereal oils are missing. In addition, the pollen of
The latter two groups are united by the characteristic ses- Ceratophyllaceae has no aperture, and xylem tracheae are
quiterpene. All other angiosperms form a monophyletic line- missing. Molecular data indicate that Ceratophyllaceae is
age and can be divided into the monocots on the one hand sister to the Eudicotyledons; therefore, morphological simi-
larities are likely the product of convergent evolution.
The subset of groups covered here includes the Nym- by the presence of UV-fluorescent cell wall compounds of
phaeaceae (Nymphaeales, ANITA-clade), the Magnoliaceae ferulic and coumaric acid, as well as silicic acid in the leaves.
(Magnoliales, Magnoliids), and the Poaceae (Poales, Mono- Commelinids include palm trees and grasses, which are
cotyledons). mostly wind-pollinated (anemophily). As a result, flowers
The Nymphaeaceae (water lilies) include only about 75 are strongly reduced in these groups, although the number
species, most commonly found in freshwater habitats out- of flowers is high for the most part. The ovule fuses with
side the polar regions. They are usually perennial, rarely an- the carpel, forming a caryposis. The Poaceae (grasses) com-
nual, herbaceous plants with rhizomes, which are anchored prise about 10,000 species and are distributed in all climates
to the ground with adventitious roots. The rhizomes can be around the world. Notable members of this group are maize,
bulbous; they have no cambium and no secondary growth. wheat, rice, millet, rye, barley, and oats, making up the ma-
The seeds of many species can disperse by floating aided by jority of the humanity’s food supply.
air pockets in the aril and the seed wall. The Liliacea (lily family) comprise about 630 species and
The Magnoliaceae (magnolia family) comprise about 227 are distributed for the most part in the northern temperate
species and are mainly found in temperate to tropical areas zone and, in particular, in East Asia and North America.
of Southeast Asia and the Americas. They include woody They are mostly herbaceous plants, producing onions to en-
trees or shrubs with alternating or spirally arranged leaves able overwintering.
with large stipules. They form bellows or legumes, arranged The Iridaceae (iris family) comprise around 2,000 species
in a conical spiral, which is an arrangement that has already and are found worldwide in temperate to subtropical cli-
been found in early fossil Magnoliopsida. mates. They are usually perennial, herbaceous plants with a
Within the monocots, the Arecales, Poales, Commelina- short creeping rhizome and an often sword-shaped unifacial
les, and Zingiberales make up the Commelinids. This mono- leaves.
phyletic subgroup within Monocotyledonae is characterised
aperture: germination pore on the wall of a pollen grain sesquiterpines: subgroup of terpenes
arillus: seed coat (fleshy covering)
See also: Synapomorphy: 4.1.1.6; Savannah: 3.2.2.10; Temperate grasslands: 3.2.2.6

stida Rh
ANITA-clade: Amborellales, Nymphaeales, Austrobaileyales ae
pla iza
Viridiplant ta
ria
oa
h
rc
Rh
Nymphaeaceae (as an example of Nymphaeales)
z
G
Cerco
odo
la ria
hermaphrodite, spirally arranged flowers featuring uc ta
op Re
ph
usually four sepals and up to 50 petals. Ovaries most-
Chr
hy
ae
y
Disc ta
Excavata
oba olata
ly superior made of 5–35 partially fused carpels. The
oma
Alve
up to 750 carpels show morphological transitions to onada
Stra
lveolata
men
Metam opile
the petals (staminodes) zo
a Ha s
oa nta
bo pt
Cry
Nymphaea alba oe op
o
ok
Am hy
pto
is t
ta
soz
h
Chloranthales
phy
Op
Apu
ta
Magnolids: Canellales, Piperales, Laurales, Magnoliales
Eubacteria Archaea
Magnoliaceae (as an example of the Magnoliales)

M usually hermaphrodite flowers arranged in altera-
a tion. Perianth of up to 18 tepals, many stamens, car-
pels superior and not joined
g
n Magnolia sp.
Monocotyledons
o Acorales, Alismatales, Petrosalviales, Dioscoreales, Pandanales, Liliales, Asparagales, Arecales, Poales, Commelinales, Zingiberales
l
Liliaceae (as an example of the Liliales)
i hermaphrodite, radially symmetrical flowers. Peri-
anth composed of six usually free tepals, six stamens
o and three carpels present, superior ovaries of only
p three carpels
s Lilium sp. Lilium martagon
i Iridaceae (as an example of the Asparagales)
hermaphrodite, radially symmetrical flowers. Some
d species zygomorphous, tepals usually fused togeth-
a er, the three stamens partly fused with the tepals or
the superior part of the style, ovary inferior of three
carpels
Iris varietega Crocus sp.
Poaceae (as an example of the Poales)
greatly reduced and modified flowers, the palea is a
product of a merger between the two tepals of the
outer perigon ring, two tepals of the inner perigon
ring formed from the lodicules (swelling bodies),
mostly three stamens, superior ovary of three car-
pels Zea mays Lagurus ovatus
Ceratophyllales
Eudikotyledons
Carnivorous plants (animal-trapping plants) obtain specialised leaves, which close and imprison prey
their mineral nutrients mainly from nitrogen com- within seconds. Prey items are again digested us-
pounds, by digesting insects, other vertebrates, ing enzymes. The sundew forms sheets covered in
and protozoa. Roughly 500 species of carnivorous a glue-like substance, secreted to trap insect prey.
plants are known, including among others the sun- Carnivorous moss, including the genera Colura
dew (Drosera spp.), the pitcher plants (Nepenthes and Pleurozia, also possess distinctive capturing
spp.), or the Venus flytrap (Dionaea muscipula). mechanisms.
Carnivorous plants are mainly found in nutrient- Carnivorous plants are autotrophic, feeding them-
poor habitats, including peatlands, although they selves by photosynthesis. However, as a result of Drosera capensis Nepenthes sp.
may also be epiphytic, growing on other plants. their carnivorous habit, they are able to survive
In most carnivorous plants, the leaves are used and grow faster in more nutrient-poor and acidic
to entrap prey. For example, the pitcher plant habitats.
uses bright colours or odours to capture insect or Carnivorous fungi form sticky traps or snares from
small rodent prey with their tube-shaped leaves. the hyphae in which the prey is caught. The fungus
Once inside, prey organisms cannot escape, as subsequently grows into the prey item, digesting it
they are trapped by rigid, downwardly directed from the inside.
hairs which line the inside of the plant. The prey
is subsequently digested by enzymes and bacte-
ria. The Venus flytrap, on the other hand, has two Dionaea muscipula
Carnivory in plants and fungi

328 Megasystematics
4.4.3.8
Eudicotyledons I: Rosids
Like the basal angiosperms, the Eudicotyledons possess mens arranged either in two circles or centripetally/centrifu-
two cotyledons. Pollen grains display three germinal furrows gally increased in number. The nucellus is strongly developed
(tricolpate). Flowering organs are arranged in whorls. within the ovules (crassinucellate ovule), surrounded by two
Some basal Eudicotyledons have a variable flower mor- integuments. In the formation of endosperms, the nucleus
phology, also differing in a number of other features from the of the large central cell of the embryo sac initially divides
core-eudicots. Flowers are partly helically arranged, as in Ra- without the cell wall being retracted (nuclear endosperm for-
nunculales. For groups with whorled leaves, the number of mation), with membranes and cell walls subsequently being
leaves per leaf circle often differs from the pentacyclic form formed.
of the core Eudicotyledons. In many groups, the carpels are Molecular data support a further subdivision of the Euro-
not fused. Moreover, ellagic acid is not found in the basal sida, with the combined group eurosids-I (fabids) only sup-
Eudicotyledons, with the exception of Gunnerales, the clos- ported by molecular data. Morphological synapomorphies
est sister group to the core Eudicotyledons. for this group are not yet known. The eurosids-II (malvids)
Most core Eudicotyledons have a fivefold perianth and are for the most part supported by molecular data. Common
contain ellagic acid. These include two large lineages, the morphological characteristics for this group include the gy-
asterids and the rosids, as well as a number of basal groups. noecium with simple pistils as well as seeds with a usually
The rosids usually have flowers with free petals, with sta- smaller endosperm.
Here, we use the Ranunculaceae as representatives of for the northern hemisphere. Roses are herbaceous plants,
basal Eudicotyledons, with the Fabaceae and Rosaceae as shrubs, or trees.
examples of eurosids-I (fabids) and the Brassicaceae as ex- The Brassicaceae (mustard family) comprise around 4,000
amples of eurosids-II (malvids). Finally, we discuss the Car- species, spread globally in all climates but with a preference
yophyllaceae as representatives of the basal asterids. to the Mediterranean region as well as Central and South-
The Ranunculaceae (buttercup family) comprise about west Asia. They are usually annual or perennial herbaceous
2,500 species and are distributed worldwide, although pref- plants, with only a few woody species. The Brassicaceae are
erentially in temperate zones in the northern hemisphere. important as crops (cabbage, rape), and the group also in-
Buttercups are mostly herbaceous and perennial. Stipules are cludes thale cress (Arabidopsis thaliana), the most well-studied
mostly lacking, with some species featuring only one cotyle- plant in botanical research.
don. The Caryophyllaceae (the pink or carnation family) com-
The Fabaceae (legume family) are one of the most spe- prise around 2,200 species and are distributed worldwide,
cies-rich plant families, comprising around 20,000 species although this is centred on the temperate latitudes of the
worldwide. Legumes include both herbaceous and woody northern hemisphere. There are usually annual or perennial
plants. herbaceous plants, and occasionally woody plants. Mycor-
The Rosaceae (rose family) comprise approximately 3,000 rhizae have never been observed in the Caryophyllaceae or
species and are found worldwide, although with a preference in other families within the Caryophyllales.
achene: fruit of the Asteraceae synapomorphy: an evolved characteristic common to a mono-

annual plants: yearlings, annuals phyletic group
gynoecium: (Grk.: gyne = woman, oikos = house) collective whorl: arrangement of leaves in which two or more leaves arise
term for the parts of a flower that produce ovules from a single node
pentacyclic: flowers with five whorls
See also: Centripetal: 4.4.3.3

stida Rh
basal Eudikotyledons: Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales ae
pla iza
Viridiplant ta
ria
oa
h
Ranunculaceae (as an example of the Ranunculales) rc
Rh
z
G
Cerco
odo
flowers mostly bisexual and radially symmetrical,
la
uc ria
ta
op Re
ph
some zygomorphic (for example, columbine or
Chr
hy
ae
y
Disc ta
Excavata
monkshood), perianth made of a leaf circle of four oba olata
oma
Alve
to several leaves, attracting apparatus often made of onada
Stra
lveolata
men
Metam opile
nectar leaves, stamens and carpels not joined Ranunculus sp. a Ha s
zo
oa nta
bo pt
Cry
Gunnerales oe op
o
ok
Am hy
pto
is t
ta
soz
h
phy
Op
basal sister groups of the rosids: Dilleniales, Saxifragales, Vitales
Apu
ta
Eurosids I (fabids):
Zygophyllales, Celastrales, Oxalidales, Malpighiales, Fabales, Rosales, Cucurbitales, Fagales Eubacteria Archaea
Fabaceae (as an example of the Fabales)

c flowers usually hermaphrodite and zygomorphic,
sepals often fused, upper petal enlarged (barb), the
o E lower two fused together into a vessel, nine to ten
r u stamens fused. Superior ovary made of one carpel
e r
Ononis spinosa Trifolium medium
o
e s Rosaceae (as an example of the Rosales)
flowers usually hermaphrodite and radially symmetri-
u i
cal, flower cups (hypanthium) always present, free se-
d d pals and petals, stamens usually ten to many and not
i s fused, one to many mostly unfused carpels
k
Prunus padus Rubus fruticosus
o
Eurosids II (Malvids): Geraniales, Myrtales, Crossosomatales, Picramniales, Sapindales, Huerteales, Malvales, Brassicales
t
y Brassicaceae (as an example of the Brassicales)
l flowers usually hermaphrodite and mostly radially
e symmetrical, sepals and petals not fused, stamens in
d two circlets with a total of six stamens, the outer cir-
clet featuring only two stamens
o
n Brassica napus Raphanus sativus
s basal sister groups of asterids: Santalales, Berberidopsidales, Caryophyllales
Caryophyllaceae (as an example of the Caryophyllales)
flowers usually hermaphrodite and radially symmetri-
cal, sepals free or fused, petals always free and with a
long ´needle´, often bilobed, stamens usually free and
sometimes fused with the crown or the calyx, ovary
superior comprising five or three carpels
Silene sp. Silene uniflora
Asterids: Cornales, Ericales, Euasterids I, Euasterids II
Many species spread their distribution units (seeds, cysts etc.) by either len grains have a significantly increased surface area. Wind-pollinated
the wind or upon other animals. Units distributed by animals often have plants include grasses, rushes, fagaceae, and the birch family. Zoophil-
a sticky or rough surface (pollen) or feature other adhesive structures, ous plants attract pollinators using brightly coloured flowers or fragranc-
such as hook hair (burdock). Wind distribution units, however, possess es. They generally produce less pollen than the anemophilous flowers,
features enabling them to float in the air for as long as possible, includ- although they also produce nectar. The unpleasant smell of carrion is
ing the air sacs in pollen grains or the floating extensions of the dande- mimicked by plants pollinated by flies.
lion achenes. Accordingly, the dispersal of seeds by wind (anemochory) and by ani-
The spread of pollen by the wind is known as anemophily, whereas on mals (zoochory) differs: the number of seeds is higher in anemochory
animals it is known as zoophilia and in water it is called hydrophilicity. and the seeds possess more appendages, facilitating air dispersal.
Anemophilous flowers are inconspicuous and do not produce nectar or
fragrances, possessing pollen attached to long, flexible filaments. Pol-
Left: Bee with pollen and pollen grain of Carbaea scandens; middle: pine blossom and pine pollen; right: burr in dog fur and dandelion
Distribution mechanisms (wind and animal)

330 Megasystematics
4.4.3.9
Eudicotyledons II: Asterids

The asterids are a sister group of the Caryophyllales, char- The Lamiids usually have alternate, entire leaves. During
acterised by flowers with mostly fused petals and often only flower development, individual flower primordia initially
one stamen circle and a weakly developed nucellus (tenuinu- grow apart from each other and fuse later (late sympetaly).
cellate ovule). The ovule is enclosed by a single integument. Subsequently, corolla lobes are formed by increased cell di-
During endosperm formation, membranes and cell walls are vision. The ovary is often superior, featuring capsule fruits.
built directly after nuclear division (cellular endosperm). The Campanulids usually have alternate, dentated or ser-
The asterids comprise the two basal orders Cornales and rated leaves. In the development of the individual flower, pri-
Ericales as well as the Euasterids I (Lamiids) and the Eu- mordia are fused to each other from the beginning forming a
asterids II (Campanulids). Apart from the two basal orders, ring (early sympetaly). The ovary is often inferior, featuring
asterids generally do not contain ellagic acid. indehiscent fruits.
As examples of Euasterids I, we present the Boraginaceae ception of some woody species. Some genera that were pre-
(Boraginales), the Lamiaceae (Lamiales), the Plantaginaceae viously affiliated with the Scrophulariaceae have now been
(Lamiales), and the Scrophulariaceae (Lamiales). As case assigned to other families. Speedwell (Veronica), snapdragons
studies from Euasterids II, we present the Asteraceae (Aster- (Antirrhinum), foxglove (Digitalis) and other genera are now
ales) and Apiaceae (Apiales). known to belong to the Plantaginaceae. The semi-parasites
The Boraginaceae (borage family) comprise about 2,800 cow-wheat (Melampyrum), tooth trost (Odontitis), and louse-
species distributed across the planet from temperate to wort (Pedicularis) and the full-parasite toothwort (Lathraea)
tropical regions. These are annual to perennial herbaceous are now known to belong to the Orobanchaceae (broomrape
or woody plants. Their leaves and stems are usually hairy. family).
Some members of the group are important crop or medici- The Asteraceae comprise about 24,000 species and are
nal plants, for example borage (Borago officinalis) and comfrey found worldwide in all continents and climates, with the
(Symphytum officinalis). Among the well-known ornamental exception of Antarctica. These herbaceous, rarely woody,
plants is the forget-me-not (Myosotis spp.). plants make up the most species-rich plant families in Europe.
The Lamiaceae (Lamiaceae) comprise about 7,000 species They are annual, biennial, or perennial. The Asteraceae are
and are represented in all climates worldwide. The Lamiace- characterised by basket-shaped flowers, each representing a
ae include both herbaceous and woody plants. Many species pollination unit (flower). Each flower head is surrounded by
contain essential oils and are often aromatically scented (for bracts (involucrum).
example, mints (Mentha), basil (Ocimum basilicum), lavender The Apiaceae (Umbelliferae) comprise about 3,800 spe-
(Lavandula), or sage (Salvia)). The shoot axis is often square. cies and are widespread in temperate zones worldwide. They
The Plantaginaceae (Plantain family) comprise around are mostly herbaceous plants with multipennate leaves and
2,000 species, which are found worldwide in all climatic compound umbels as inflorescence. Many species, such as
zones. They are mostly annual or perennial herbaceous the carrot (Daucus), form a taproot. Some species, such as
plants, although some species are shrubs. dog parsley (Aesthusa cynapium) and hogweed (Heracleum)
The Scrophulariaceae (figwort family) comprise around contain toxins which are poisonous to animals that consume
1,700 species and are mostly herbaceous plants with the ex- them.
dentate leaf: leaf possessing rounded notches between the involucre: protective structure made of bracts in certain flower-
teeth on its fringes ing plants
ellagic acid: a polyphenol phyllotaxis: the alternate arrangement of leaves on a plant
hemiparasite: parasitic plants which obtain water and nutri- stem
ents from their host but which are still capable of photosynthesis primordium: (Lat.: primordium = the beginning, origin) an or-
themselves gan or tissue at its earliest developmental stage
holoparasite: parasitic plant which is completely dependent on serrated leaf: leaf possessing sharp sub-teeth between the
its host and is incapable of photosynthesis teeth on its margin
indehiscent fruit: fruit which does not open at maturity sympetalae: having fused petals in flowering plants
See also: Sympetaly: 4.4.3.6

stida
Euasterids I (Lamiids): Garryales, Gentianales, Lamiales, Solanales, Boraginales ae
pla
Rh
iza
Viridiplant ta
ria
oa
h
rc
Rh
Boraginaceae (as an example of the Boraginales)
z
G
Cerco
odo
flowers hermaphrodite and usually radially sym-
la
uc ria
ta
op Re
ph
metrical, basal sepals, petals completely fused into
Chr
hy
ae
y
Disc ta
Excavata
tubes or into a plate-shaped flower stalk, stamens oba olata
oma
Alve
and petals merged, superior ovaries with false sep- onada
Stra
lveolata
men
Metam opile
ta (four schizocarps) zo
a Ha s
oa nta
bo pt
Cry
Anchusa officinalis oe op
o
ok
Am hy
pto
is t
ta
Lamiaceae (as an example of the Lamiales)
soz
h
phy
Op
flowers usually hermaphrodite, zygomorphic,
Apu
ta
tubed fused sepals, connate petals, usually four
stamens fused with the corolla, superior ovaries of Eubacteria Archaea
two carpels with false septa (four schizocarps)
Lamium maculatum
Plantaginaceae (as an example of the Lamiales)
flowers mostly hermaphrodite, zygomorphic and
highly variable, five (four) sepals free or fused,
fused petals, mostly four stamens (rarely two or
A one) adherent to the corolla tube, superior ovary
S of two (one) carpels.
T Digitalis purpurea Linaria alpina
E Scrophulariaceae (as an example of the Lamiales)
R flowers usually hermaphrodite and zygomorphic,
I five or four sepals and petals, sepals and petals are
fused, the stamens are fused with the petals, supe-
D rior ovaries of two carpels
S
Verbascum nigrum Buddleja davidii
Euasterids II (Campanulides): Aquifoliales, Asterales, Escalloniales, Bruniales, Apiales, Paracryphiales, Dipsacales
Asteraceae (as an example of the Asterales)
radially symmetrical tubular flowers or zygomor-
phic florets, sepals usually reduced to a fringe of
hair (pappus), petals and stamens fused into a
tube, inferior ovaries of two carpels
Carduus platypus Echinacea sp.
Apiaceae (as an example of the Apiales)

flowers usually radially symmetrical, sepals often
stunted or missing, petals and stamens free, infe-
rior ovaries of two carpels
Daucus carota Angelica sylvestris

The coevolution within pollination biology has been driven

by strong specialisations by pollinators and flowers. In part,
interdependent relationships have developed between
species. For instance, fig wasps have a very close relation-
ship with fig trees, laying their eggs only in the flowers of
certain fig species and pollinating only these. The larvae
develop in the inflorescences and use parts of the fruc-
tification as food. This symbiotic relationship appears to
have developed 34 mya. All of the present-day anatomical
specialisations can also be observed in fig wasp fossils, in-
cluding adjustments for easier penetration of the flower or
pollen bags. As a result, we can assume that the anatomy
of the fig has barely changed during the same time period.
Coevolution within pollination biology

332 Megasystematics
4.5
Rhizaria
The Rhizaria is one of the major groups of the SAR clade, dia, reticulopodia, or axopodia. The rhizarian fossil record
along with the Alveolata and the Stramenopiles. is dominated by Retaria, since they possess skeletal elements
Rhizaria comprise a diverse range of protists divided into of chalk or silicate.
two groups: Cercozoa and Retaria. The phylogenetic posi- Very few Cercozoa can be seen in the fossil record, even
tion of Gymnosphaerida remains unresolved, but they likely though they are an important component of aquatic (ben-
belong to the class Granofilosea and, therefore, to the Cer- thic) and terrestrial food webs and presumably also have
cozoa. been so in the past.
The Rhizaria are rich in morphological diversity, with
most taxa displaying pseudopodia, usually either as filopo-
The Cercozoa are a morphologically diverse group and are often grouped as Radiolaria, even though this group is
their internal systematic relationships are still unresolved. polyphyletic. The main component of their skeletons (tests)
They are roughly divided into taxa with predominantly filose is mostly lime (Foraminifera), silicate (Polycystinea), or
pseudopodia (especially Monadofilosa) and those with pre- strontium sulfate (Acantharia). The skeletons of Foraminif-
dominantly reticulose pseudopodia (especially Granofilosea era and Polycystinea are frequently observed within the
and Chlorachniophyta). fossil record. Since lime is almost entirely dissolved below
The locomotion of Cercozoa is mostly by gliding on the the compensation depth, sediments at such depths consist
substratum. In benthic marine and freshwater habitats, Cer- largely of the skeletons of Polycystinea (‘radiolarian ooze’).
cozoa are one of the most common eukaryotic groups and The hardening of these sediments results in radiolarite, a si-
among the most important bacterivorous protists. liceous, homogeneous sedimentary rock.
The Retaria, which are mostly marine, include the Fo-
raminifera, the Acantharia and the Polycystinea. The latter
SAR-clade: clade including Stramenophiles, Alveolates and

Rhizaria
See also: Amoebozoa: 4.2.3, 4.2.3.1; Axopodia, Filopodia, Reticulopodia: 4.2.3

Rhizaria 333
Retaria: marine, heterotroph, reticulopodia or axopodia, various types of skeleton

Polycystinea: basal ‘Radiolaria’, axopodia, often with silica skeleton
Foraminifera: reticulopodia, mostly with test (organic, mineralised or agglutinated)
Acantharia: ‘Radiolaria’, axopodia, skeleton of 10 or 20 spicules of strontium sulphate
Cercozoa: diverse clade with different, heterogeneous morphological characters
Filosa
Monadofilosa: mostly filose pseudopodia, naked, or with a theca or scales
Granofilosea: fine branching granuloreticulopodia
Chlorarachniophyta: amoeboid, plastids of secondary origin (four membranes, nucleomorph, chl a,b)
Metromonadea: gliding, nonpseudopodial flagellates
Endomyxa
The Foraminifera (left: living foraminiferan) are an important group of marine protists. They have a mostly calcareous case, known as a test (middle left
to right), which is found in the fossil record and plays an important role as indicators in petroleum exploration
The Radiolaria are polyphyletic. The Polycystinea form skeletons of silicate (middle-left to right), which make up a large proportion of the shallow
sediment in marine habitats. These sediments and the skeletons of Polycystinea they contain solidify to form radiolarite (left)
The Cercozoa comprise various organisms, most of which are amoeboid. Some build siliceous tests or scales
Plastids originally arose through endocytobiosis by containing 464 protein-coding and housekeeping nucleus plastid
an ancestor of the Archaeplastida. In other organis- genes, especially genes involved in transcription and
mal groups, plastids came from the endocytobiosis translation. As in other reduced genomes, the A+T
of a heterotrophic algae. These plastids have charac- content of the nucleomorph is relatively high (75 %).
teristics that indicate their eukaryotic origin. Plastids The nucleomorph of Bigelowiella natans (Chlorar-
within cryptophytes and the amoeboid Chlorarachni- achniophyta) has a significantly smaller genome of
ophyta contain a nucleomorph, a rudimentary nucle- 373 kbp; however, it is striking that its chromosome
us, which sits between the two outer and two inner structure and genomic architecture is similar to that
plastid membranes. Studies indicate that the crypto- of the cryptophyte nucleomorph which consists of
phyte nucleomorph originates from the nucleus of 284 protein-encoding, predominantly housekeep-
red algae (Rhodophyta) whereas the nucleomorph ing genes. The nucleomorph is probably the most nucleomorph
of chlorarachniophytes originates from the nucleus compelling evidence for the existence of secondary
of green algae (Chlorophyta). In both groups, the endosymbiosis and is considered as the ‘missing link’
nucleomorph contains only three chromosomes. In for the evolution of secondary plastids. outer plastid
general, the genomes of Chlorarachniophyte nucleo- membrane inner plastid
morphs are smaller (330–610 kilo base pairs (kbp)) membrane
than those of the cryptophytes (550–845 kpb). The
first complete sequenced nucleomorph genome is Diagram of a cell featuring secondary
that of Guillardia theta (a cryptophyte), with 551 kbp, plastids and a nucleomorph
Nucleomorph
334 Megasystematics
4.5.1
Cercozoa
The Cercozoa and Retaria (Foraminifera, Acantharia and sess chloroplasts, obtained by secondary endocytobiosis of
Polycystinea) jointly make up the Rhizaria. a green algae.
The monophyletic Cercozoa comprise both flagellated Paulinella chromatophora, within the class Imbricatea, has
and amoeboid organisms, some of which were earlier clas- chromatophores (cyanelles — plastids in a wider sense) of
sified as Rhizopoda. Several clades that were previously cyanobacterial origin. This is the only known example of a
thought to belong to Stramenopiles are also members of photosynthetic organelle originating through uptake of a cy-
Cercozoa. anobacterium, apart from the origin of plastids.
Most Cercozoa are heterotrophic and inhabit both aquatic Cercozoa also have mitochondria and dictyosomes. Lo-
and terrestrial habitats. Only the Chlorarachniophyta pos- comotion is driven by two anisokont flagella or by pseudo-
podia.
The Cercozoa are subdivided into the Filosa and En- The Imbricatea are unicellular organisms whose cell sur-
domyxa (including Phytomyxea and Vampyrellida). The face is covered with overlapping silicate scales. Filopodia
Filosa comprise the Monadofilosa (gliding, weakly- or non- protrude through two openings between the scales. Their
amoeboid organisms), the Granofilosea (with fine granulore- mitochondria have tubular cristae. The Silicofilosea, part of
ticulopodia), Chlorarachniophyta (amoebae with secondary the Imbricatea clade, is divided into two groups: Thaumato-
plastids), and the Metromonadea (gliding, non-amoeboid monadida and Euglyphida (which includes Paulinella).
flagellates). Chlorarachniophyta are naked amoebae that use their
The Thecofilosea, Cercomonadida, and the Imbricatea filopodia to capture prey. Food is taken up by phagotrophy
are examples of the Monadofilosa. (phagocytosis) of bacteria, flagellates and algae. Chlorarach-
The Thecofilosea, at least the basal taxa, have an extracel- niophyta plastids contain chlorophyll a and b and are sur-
lular organic theca. The Phaeodarea, which were formerly rounded by four membranes (secondary endocytobiosis with
placed in Radiolaria, also belong to this group, characterised green algae). They contain a nucleomorph in an indentation
by a central capsule with three openings: a large one, the on the surface of the pyrenoid. Thylakoids are arranged in
astrophylum, through which extend pseudopodia used for twos and threes and form lamellae. Chlorarachniophyta are
feeding; and two smaller ones, the parapylae, through which known to form cysts and flagellated zoospores. The group
microtubules extend to the axopodia. In the centre of the cell contains four genera (Bigelowiella, Chlorarachnion, Chryp-
is the phaedium, a dense mass of darkly pigmented, granular tochlora, Lotharella) comprising roughly 100 known species.
cytoplasm. However, the capsule of the Phaeodarea is not The Endomyxa contain a number of taxa with unknown
homologous to the central capsule of Polycystinea. phylogenetic relationships. For example, Phytomyxea are
The Cercomonadida are free-living amoeboflagellates obligate intercellular parasites in the roots of plants, form-
without a cell wall that are found in aquatic and terrestrial ing multinucleate plasmodia within the host. Invasion of the
habitats across the planet. They have two asynchronously host uses a unique set of organelles derived from differen-
beating flagella without mastigonemes. Food is acquired us- tiation of the endoplasmic reticulum. After the plant host
ing pseudopodia. disintegrates, fruiting bodies and spores are released. Sexual
reproduction has also been observed.
anisokont: flagella of differing length carboxylase/oxygenase); act as centres of carbon dioxide enrich-
cyst: resting stages in single-celled organisms, plants and ani- ment
mals, which develops during unfavourable environmental condi- rhizopodal: organisms with no fixed cell wall or flagella which
tions (also used for reproduction or dispersion) have an amoeboid form of movement using pseudopods; the
incertae sedis: (Lat.: incerta sedes = uncertain placement) un- obsolete name for amoeboid organisms (‘rhizopoda’) stems from
certain systematic taxonomy this term
pyrenoid: structure in the plastids in several algae and horn-
worts largely consisting of RubisCO (ribulose-1,5-bisphosphate
See also: Pseudopodia: 4.2.3; Secondary endocytobiosis: 4.1.2.3, 2.2.2.5

Rhizaria: Cercozoa 335
stida Rh
Cercozoa ae
pla iza
Viridiplant ta
h ria
ozoa
rc
Rh
Filosa G
odo
la ria
Cerc
uc ta
op Re
phy
Monadofilosa
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Thecofilosea: ancestrally with organic extracellular theca Alve
Stra
onada
lveolata
men
Metam
Imbricatea: ancestrally with silica scales on upper cell surface a Ha
opile
s
zo
oa nta
bo pt
Cry
oe op
o
Paulinella: with primary chromatophores, emerged independently of plastids
ok
Am hy
pto
is t
ta
soz
h
phy
Op
Cercomonadida: amoeboflagellates, kinetosomes connected to the nucleus
Apu
ta
Glissomonadida: only slightly amoeboid, mostly gliding on longer posterior cilium
Eubacteria Archaea
Pansomonadida
Granofilosea: fine branching granuloreticulopodia
Chlorarachniophyta: amoeboid, plastids of secondary origin (four membranes, nucleomorph, chl a, b)
Metromonadea: gliding, nonpseudopodial flagellates
Endomyxa
Ascetosporea: complex spore structure
Gromia: multinucleate amoebae with filopodia, with organic test
Filoreta: multinucleate reticulose amoebae
Phytomyxea: amoeboid or plasmodial stages alternating with flagellated stages
Vampyrellida: amoeboid stages alternating with digestive cyst; several taxa form plasmodia
Filosa: Imbricatea (top-left: Euglypha sp.), Cercomonadida (top-centre: Eocercomonas sp.), Granulofilosea (top- Endomyxa: Vampyrellida (top:
right: Reticuloamoeba sp.), Glissomonadida (bottom-left: Orciraptor agilis), Metopiida (related to Metromonadea, Vampyrella lateritia) and Filoreta
bottom-centre: Metopus sp.), Chlorarachniophyta (bottom-right: Chlorarachnion sp.) (bottom)
The ability to photosynthesise, the process by as a chromatophore. Although these chroma-

which light is converted into chemical energy, tophores have lost two-thirds of their original
is considered to be one of the most important genes, they are, in contrast to plastids, still able
evolutionary developments since the origin of to autonomously photosynthesise. In contrast,
life. The emergence of chloroplasts in eukary- in chloroplasts, some of the photosynthetic
otic cells was a prerequisite for the radiation of genes have been transferred to the nucleus of
eukaryotes and the establishment of eukaryotic the host cell. It is believed that plastids were
food webs. Plastids emerged from primary en- developed in two stages: initially, by establishing
docytobiosis, whereby a eukaryotic cell took in of dependency based on an exchange of sub-
a photosynthetic prokaryote (cyanobacterium) stances (chromatophores), and later, by way of
which eventually developed into an organelle. a transfer of genes into the nucleus of the host
Many details of the conversion of a free-living cell, thus transferring the regulatory control of
cyanobacterium into an organelle remain un- the organelle to the host cell (chloroplast).
known, though new insights have been provided
by Paulinella chromatophora, an algal species
which is the only known example of primary
endocytobiosis of a cyanobacterium apart from
the origin of plastids. The endocytobiont (i.e. the
cyanobacterium) is not that strongly reduced as
in the case of plastids and is therefore known Paulinella chromatophora
Paulinella: a model for the emergence of plastids

336 Megasystematics
4.5.2
Retaria
The Retaria are a monophyletic group within the After the death of individual polycystine cells, their skel-
Rhizaria. They include the Foraminifera (forams), as well eton is deposited on the ocean floor and forms a radiolarian
as the Acantharia and Polycystinea (polycystines), both for- ooze before solidifying into radiolarite. Radiolarian ooze can
merly grouped with Phaeodarea (Cercozoa) as ‘Radiolaria’. reach a thickness of several hundred metres. Below the cal-
Retaria are amoeboid, marine, heterotrophic organisms cium carbonate compensation depth, pure radiolarite depos-
with reticulopodia or axopodia. Most have skeletons, which its can be found. The oldest ‘Radiolaria’ fossil (thought to be
are made of a range of substances depending on the group: Polycystinea) is from the Neoproterozoic, whereas the oldest
calcium carbonate in forams, strontium sulfate in Acantha- radiolarite rock strata are from the Upper Cambrian.
ria, and silicon dioxide in Polycystinea.
The Acantharia are spherical or elongated and reach a sellaria have a conical central capsule, with pores concen-
size of between 50 µm and 5 mm. Their skeleton is made trated at one pole. Spumellaria, however, are characterised
of 10–20 spines converging in the centre and composed of by a generally spherical central capsule with uniformly dis-
strontium sulfate. Acantharian cells are surrounded by a cap- tributed pores.
sule from which axopodia, spines, and pseudopodia extend Most of the fossil ‘Radiolaria’ belong to Polycystinea. Ac-
outward. The network of outer pseudopodia forms a hyaline cording to the fossil record, Spumellaria became important
ectoplasm whereas the inner endoplasm is granular and con- in the Triassic in terms of biomass, with Nassellaria emerg-
tains the organelles and often also endosymbiotic algae (but ing as the dominant group in the Jurassic and Cretaceous
no plastids). Since strontium sulfate is soluble in seawater, periods. After the Cretaceous–Palaeogene boundary mass
the skeletons of fossil Acantharia do not become fossilised. extinction, Spumellaria once again emerged to represent
The Polycystinea are 30 µm to 2 mm in size and usually the most successful group of polycystines, and continues
have a central capsule and skeletal elements of silicon diox- to dominate the marine environment. Because they lack a
ide, though some do not have any skeletal parts at all. The skeleton, collodarian remains cannot be found in the fossil
group includes the Collodaria, Nassellaria and Spumellaria. record.
With a few exceptions, Colladaria usually have no skeletal The Foraminifera usually have skeletons made of calcium
parts. Many colladarian species are colonial and, together, carbonate. They are a sister group to Acantharia, thus ‘Ra-
make up a significant proportion of marine plankton. Nas- diolaria’ are polyphyletic.
biogenic: (Grk.: bios = life) of biological or organic origin

hyaline: with a glassy or translucent appearance
See also: Axopodia, Reticulopodia: 4.2.3; Stratigraphy of the Mesozoic: 2.3.4

Rhizaria: Retaria 337
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la ia
uc t ar
op
phy
Re
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
Acantharia: symmetrically built strontium Stra
onada
lveolata
sulfate skeleton with 10 or 20 spines Metam
men
opile
a Ha s
zo
oa nta
bo pt
Cry
oe op
o
ok
Am hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
Foraminifera Eubacteria Archaea
Polycystinea: axopodia, mostly with a silicium skeleton
The Collodaria comprise some skeleton-

R forming organisms as well as non-skeletal
e and colonial species, including the genus Col-
lozoum (here)
t
a
r
i
a
The Nassellaria possess conical skeletons,
though some taxa have no skeletons at all.
Shown here are an extant (left) and fossilised
(right) species
The Spumellaria have spherically built skel-

etons, though some taxa have no skeletons at
all. Shown here are an extant (left) and fos-
silised (right) species
Biogenic minerals are a components within the

skeletal elements of a variety of organisms. Skel- mineral chemical formula organisms functions
etal elements protect individuals, but also serve as calcium carbonate CaCO3 Foraminifera exoskeleton
an anchorage for the locomotor system. Most bio- (aragonite, calcite) trilobite cell skeleton
genic minerals consist of only one substance. Some Coccolithophoridae gravitational sensor
of these biogenic minerals are interspersed with shells, corals
organic matter, including soluble and insoluble pro- gastropod
teins and polysaccharides, usually containing several fishes
carboxylate, phosphate and sulfate groups.
calcium Ca5(PO4)3(OH) vertebrate endoskeleton
Biogenic materials can form the basis of rock-build-
phosphate fishes teeth
ing processes and build sediments of hundreds of
(apatite) scales
metres in depth. Reef limestones, chalk deposits and
radiolarite sediments are all made from biogenic ma- silicon dioxide SiO2 x H2O bacillariophyceae exoskeleton
terials. (opal) Radiolaria cell skeleton
plants
iron oxide Fe3O4 bacteria orientation
chitons teeth
Biogenic minerals
338 Megasystematics
4.5.2.1
Foraminifera
Along with Acantharia and Polycystinea, Foraminifera ral, helical, and concentric tests are also known. Forams
(forams) belong to Retaria. Together with Cercozoa, these have mitochondria but not plastids. However, they are often
form the Rhizaria. associated with symbiotic algae and probably have a range
Forams are amoeboid testate protists. The foram test is of host-specific symbionts. Among others, Dinophyta, Chlo-
generally composed of calcium carbonate, but may also be rophyta, Rhodophyta, and Bacillariophyceae live within the
composed of agglutinated particles. The test is riddled with tests and can occupy up to 75 % of their volume.
pores (Lat.: foramen = small hole; ferre = to carry). Reticulo- Although most forams are benthic, the Globigerinida
podia emerge from the pores, creating a net for catching prey, are planktonic. Forams are capable of surviving at extreme
such as Bacillariophyceae or bacteria. However, the reticulo- depths in the marine environment. Live forams have been
podia also serve for locomotion and collecting mineral par- found in the deepest known oceanic point, at 10,896 m depth
ticles for the construction of the shell. The early-stage foram at the Challenger Deep within the Western Pacific’s Mariana
test is made of glycoproteins. Forams grow through the ad- Trench. Very few (around 50) foram species live in freshwa-
dition of new chambers. Calcium carbonate or other con- ter environments.
densed organic materials can become embedded within the Although they are unicellular, forams can reach a size
test. It is likely that multi-chambered testate forams evolved of several centimetres (Cycloclyperus carpenteri can reach up
from single-chambered lineages. Foram tests have a broad to 12 cm; Acervulina species are known to reach 20 cm in
morphological diversity: chambers may be straight and may length). They live for several months to years.
be positioned in one or two rows one behind the other. Spi-
Around 40,000 fossil species of forams have been de- as a result of this economic importance, fossil forams are
scribed. The oldest known foram fossils date from the Cam- relatively well studied.
brian period. Foraminifera undergo a heterophasic generation between
Foraminifera play an integral role in the formation of sexual haploid and asexual diploid generations. The genera-
sediment in marine areas, as a result of their calcareous tions are heteromorphic.
test. Nummulitic limestone, for example, which was used Most species of forams build tests with multiple chambers
for the construction of the Egyptian pyramids, is made pri- (multilocular), but some species may build tests with just one
marily of foram remains. Both the planktonic Globigerina chamber (unilocular). These chambers can be arranged uni-
and benthic Foraminifera formed an essential part of Mio- serially (in one row), bi-serially (in two staggered rows), tri-
cene sediments. Forams are important index fossils, making serially (three staggered rows), or in a flat spiral (spiral and
it possible to date sedimentary rocks from different regions aligned in a plane). The ordering of the chambers and the
(for example, Fusulinida in the Carboniferous and Permian materials used in the test are the basis of foram systematics,
periods or the nummulites in the Palaeogene period). They as their molecular systematics remain unclear.
are also important index fossils for petroleum exploration;
glycoproteins: macromolecules consisting of a protein and car-

bohydrate groups
See also: Fossil Foraminifera: 2.3.2.1; Index fossils 2.3.1.4; Reticulopodia: 4.2.3; Stratigraphy of the Phanerozoic: 2.3.3, 2.3.4, 2.3.5
Rhizaria: Retaria 339
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la ia
uc t ar
op
phy
Re
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
Stra
onada
lveolata
men
Metam opile
a Ha s
zo
oa nta
bo pt
Cry
oe op
o
ok
Am hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
Eubacteria Archaea
Foram tests are composed of a range of materials that are specific to each species or taxonomic lineage. In
many species, the test is made of calcium carbonate (left). In the Milionida, the calcium carbonate crystals
are so small (microcrystals) that the smooth surface forms a porcelain-like effect (middle-left). Other tests
can be made from agglutinated particles, such as sediment grains or diatom shells (middle-right). The plank-
tonic Globigerina (right) are characterised by large, inflated chambers
Foram cytoplasm is found both within and just outside the test as a network of reticulopodia (finely branched pseudopodia, left). The largest (single-
celled) foram may be several centimetres in size, such as this member of genus Amphisorus (right)
Biomineralisation refers to the formation of inorganic solids (biominerals). Most

of these serve to protect and support the organism’s softer materials, but they
can also be used for defence, locomotion, and as a tool. Biomineralisation likely
evolved as a result of metabolic pathways for detoxification, the targeted elimi-
nation of certain ions.
Many organisms, including bacteria, vertebrates and plants, are able to form bi-
ominerals. They are often the only structures of organisms which survive within
the fossil record and they are therefore vital in the reconstruction of evolution-
ary pathways. The number of biogenic structures found within the fossil re-
cord increased greatly in the upper Proterozoic (Ediacaran) and lower Cambrian
strata. This change appeared both as a result of alterations in ocean chemistry
and because of increased grazing pressure from the emerging multicellular or-
ganisms as exoskeletons provide protection from grazing.
The most common biogenic substances are calcium phosphate (apatite) and
calcium carbonate (calcite and aragonite), and sometimes, but rarely, amor-
phous silica.
Top-left: teeth; top-right: mineralised collagen fibres; bottom-left and bottom-

right: stony corals
Biomineralisation
340 Megasystematics
4.6
Alveolata and Stramenopiles

The Alveolata and Stramenopiles are closely related to menopiles is the heterokont flagellum, which features special
each other and, together with Rhizaria, make up what is hairs on the long, anteriorly facing flagellum. The hairs are
known as the SAR-clade. tubular and can be divided into three parts (tripartite): the
The Alveolata include Dinophyta (dinoflagellates), Cili- base, shaft, and thinner terminal end. The second flagellum
ophora, and the parasitic Apicomplexa. They are charac- is usually hairless and shorter. In some species, such as dia-
terised by alveoli, an endomembrane system made of small toms, the flagella are secondarily reduced.
membrane-enclosed spaces found just beneath the cell mem- Molecular data suggest that Alveolata and Stramenopiles
brane. Stramenopiles include several major groups of algae, are closely related; in addition, the plastid in phototrophic
including the Phaeophyceae, Bacillariophyceae, and Chrys- representatives of both groups, appears to have a common
ophyceae, as well as various heterotrophic groups and the origin.
parasitic oomycetes. A common characteristic of the Stra-
The ‘Chromalveolate Hypothesis’ describes the common Haptophyta is probably the sister group of SAR. To what
origin of plastids in all organisms with secondary plastids extent the cryptophytes are related to haptophytes or to Ar-
as coming from red algae. The hypothesis is based on the chaeplastida for that matter remains unclear. Since the re-
assumption that secondary endocytobiosis is a very complex lationship between haptophytes and cryptophytes remains
process involving a number of different genes and metabolic unclear, we treat it within a separate chapter (Hacrobia).
pathways. Molecular phylogenies of plastids show the rela- The term ‘Chromalveolata’ is used here to describe the core
tionship of all plastids dating back to their red algal origins. groups, i.e. alveolate and stramenopile groups.
However, host cell relationships (Alveolata, stramenopiles, Many groups within Rhizaria, the stramenopiles, and al-
haptophytes, and cryptophytes) are difficult to reconcile with veolata have no plastids. For many taxa, there is no convinc-
those of their plastids. ing evidence that their ancestors had plastids. Therefore, the
Regarding the host cells, the monophyly of alveolates is assumption that a common ancestor of all of these groups
supported by both molecular and morphological data. Simi- obtained a plastid through secondary endocytobiosis and
larly, the monophyly of stramenopiles is well-supported. The that this was subsequently lost in some groups remains un-
relationship between alveolates and stramenopiles is mainly likely. It is more likely that either secondary endocytobio-
supported through molecular data. It is thought that the sis occurred on multiple occasions or that an ancestor of a
group comprising alveolates and stramenopiles is the sister subset of lineages obtained a plastid from red algae through
group of Rhizaria. Together, the three groups are called the secondary endocytobiosis and that this organelle reached the
SAR-clade (Stramenopiles, Alveolata, Rhizaria). Moreover, other lineages through tertiary endocytobiosis.
alveoli: (Lat.: alveus = cavity) hollow cavities (e.g. alveolar sacs endocommensalism: (Grk.: endon = inside, skeletos = frame:
in lungs) com = together, mensa = table) commensal relationship inside
carotinoid: a type of terpene, the liposoluble accessory pig- the body of the host; for one partner the commensal relationship
ments in photosynthesis is beneficial, for the other it is neutral
chromalveolata: a supergroup including all organisms contain- mastigonemes: (Grk.: mastigo = thread, whip) hairs which
ing plastids with chlorophyll c (Alveolata, Stramenopiles, Hap- cover flagella
tophyta, Cryptophyta); strictly speaking, only the Alveolata and pusules: tubular system of membranes in dinoflagellates
Stramenopiles, because the taxonomic status of the Haptophyta
and Cryptophyta have not been clarified
See also: Heterokonts: 4.3.2.2; Monophyly: 4.1.1.6; Endocytobiosis: 2.2.2.5

Alveolata and Stramenopiles 341
Alveolata: characterised by alveoli located under the cell membrane
Ciliophora
Apicomplexa
Chromerida
Dinophyta
Stramenopiles: characterised by tripartite hairs on the anterior, longer

flagellum
Bigyra: Labyrinthulida, Bicosoecida
Clade I: Phaeophyceae, Xantophyceae, Chrysomerophyceae, Raphidophyceae, Phaeothamniophyceae

Clade II: Chrysophyceae, Synchromophyceae, Eustigmatophyceae, Pinguiophyceae
Ochrophyta
Clade III: Bacillariophyceae, Dictyochophyceae, Pelagophyceae, Bolidophyceae
Pseudofungi: Peronosporomycetes, Hyphochytridiomycetes
Representation of the molecular findings pertaining to the relation- Gene pool of dinoflagellate plastids
ship of plastids within Alveolata and Stramenopiles (each bar rep- (Peridinium species)
resents one gene): Both dinoflagellates and Apicomplexa (also be-
longing to alveolates) possess plastids. In both groups, however, the
plastid genome is greatly reduced. Since Apicomplexa are parasitic, Gene pool of apicomplexan
the plastid (apicoplast) only contains genes for heterotrophic meta- plastids (apicoplast)
bolic pathways. In the dinoflagellates, the plastids mainly contain
genes for photosynthesis. Only two genes are shared by both line-
ages. For a long time, it was unclear whether the plastids of Alveo- Gene pool of plastids from
lata could be traced back to a common origin, a question which was Chromera
resolved by the discovery of Chromera. Plastids in Chromera, which
is related to Apicomplexa, have a larger genome and possess more
genes than both dinoflagellate and apicomplexan plastids. The rela-
tionship of all three organismal groups can be understood through
their shared plastid genes.
The plastid genomes of Stramenopiles are significantly larger and in- Gene pool of strameno-
clude genes occurring in alveolate plastids. As a result, their plastids pile plastids
can likely be traced back to a common origin.
Membrane-bound compartments within cells are though mitochondria are capable of autonomous
referred to as cell organelles (small organs). These reproduction (even doubling) via their own genetic
include the nucleus, mitochondria, Golgi appara- apparatus, they are no longer independently viable.
tus, endoplasmic reticulum, lysosomes, vacuoles, Due to their double membrane envelope (outer en-
and chloroplasts. Each organelle performs a specific velope membrane of the host and inner endosymbi-
function. For example, the nucleus contains genetic ont membrane), mitochondria are completely sepa-
information, the Golgi apparatus and endoplasmic rated from the cytoplasm of the host. Furthermore,
reticulum are involved in the packaging of many of mitochondria have their own ribosomes within the
the proteins synthesised in the ribosomes, and cel- mitoplasma. During the course of evolution, the sym-
lular digestion takes place within food vacuoles and biont or organelle lost parts of its genetic material
lysosomes, whereas photosynthesis occurs in chloro- and some parts became integrated into the genome
plasts. The mitochondria are the energy powerhouse of the host. Phylogenetic studies have shown that
of the cell, where ATP energy is generated from the the emergence of mitochondria can be traced back
oxidation of carbohydrates and fatty acids. to a single endosymbiosis. All eukaryotes (with mito-
Mitochondria originate from the phagocytosis of an chondria) can therefore be traced back to a common
aerobic bacterium related to Rickettsia by an aquatic ancestor.
primordial cell. The host cell and the endosymbiont
underwent a common coevolution, which developed
into a mutual dependence in the course of time. Al-
Mitochondria from lung tissue
Organelles
342 Megasystematics
4.6.1
Alveolata
The Alveolata (alveolates) include Dinophyta, Chromeri- cavity system, which opens a narrow channel to the outside;
da, Ciliophora, and the Apicomplexa. As a group, alveolates the parasomal sack in Ciliophora, an infolding of the plas-
are well-supported by both morphological and molecular malemma in the immediate vicinity of the cilia between the
data. alveoli; and the micropores of the Apicomplexa, also located
Alveolates are characterised by the presence of alveoli, between the alveoli invaginations of the plasmalemma. The
flattened vesicles packed into a continuous layer supporting hypothetical ancestor of alveolates had heterokont flagella
the membrane, typically forming a flexible pellicle. The os- with mastigonemes, a morphological structure found in pre-
moregulatory structures of alveolata are also probably ho- sent-day dinoflagellates.
mologous: pusules in dinoglagellates, a membrane-bound
The Chromerida are alveolates providing a ‘missing link’ Until the discovery of Chromera it was unclear whether
between their close relatives, Apicomplex, and the photosyn- the plastids of apicomplexans were to be traced back to a red
thetic Dinophyta. So far, only two genera are known within or green algal origin. In addition, it was difficult to establish
the group: Chromera and Vitrella, distinguishable by the com- a relationship between the plastids of Apicomplexa and Di-
position of their accessory photopigments, though both con- nophyta.
tain chlorophyll a. Most of the latter have a plastid with chlorophyll a and
Apicomplexa comprise Plasmodium spp., the vector of c, which emerged from an endocytobiosis with red algae.
malaria, and other endoparasites. Apicomplexa have no Although Chromera lacks chlorophyll c, their plastid genome
functional plastids, although they carry a reduced plastid shares many genes both with Apicomplexa and Dinophyta.
known as an apicoplast. Although photosynthesis genes are On the basis of these common genes, researchers were able
lost, the apicoplast plays a role in fatty acid synthesis. to establish a shared descent of plastids from both groups as
well as the red algal origins of plastids.
apicoplast: a derived plastid found in Apicomplexa polar ring: thickening of the membrane complex at the anterior
apikal complex: an organ complex of the Apicomplexa on the and posterior ends of the cells in Apicomplexa
tapered end of the cell containing: polar rings, rhoptries and co- rhoptries: club-shaped secretory organelles in the apical com-
noids plex in Apicomplexa containing lytic enzymes
conoid: structure consisting of spirally-arranged microtubuli in
the apical complex of the Apicomplexa
See also: Algal blooms: 4.7.1; Babesiosis: 4.2.2.1

Alveolata and Stramenopiles: Alveolata 343
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
Ciliophora: Nuclear dimorphism with somatic macronucleus oba olata
oma
Alve
and generative micronucleus a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa nta
o pt
eb
Cry
op
o
mo
ok
A hy
pto
is t
ta
soz
h
phy
Kerona polyporum
Op
Apu
ta
Apicomplexa: parasitic, plastids reduced to apico-
plasts, apical complex of polar rings, rhoptries and Eubacteria Archaea
conoids
Plasmodium falciparum
Chromerida: secondary plastids surrounded by

four membranes, chlorophyll a, violaxanthin and
beta-carotene present
Vitrella brassicaformis Autospore (lower part of the pic-

ture) and autosporangium with
encapsulated spore tetrad of
Chromera velia
Dinophyta: characterised by a longitudinal and

transverse flagellum as well as chromosomes con-
densed during interphase
Gymnodinium sp.
Model organisms are species that have been selected for study as repre- in Tetrahymena. Algae are also of great importance as model organisms,
sentatives of larger groups of organisms. In general, they feature several for example Chlamydomonas reinhardtii, Volvox carteri and Phaeodac-
criteria: they are relatively easy to culture and cultivate, they usually tylum tricornutum. In general, the operation of photosynthesis and the
have short generation times and many offspring, they usually have a organism’s response to light can be more easily studied in these species.
relatively small genome, which has often already been sequenced, and In addition, Chlamydomonas was the first green alga whose genome
they have most often already been studied using a variety of means. was completely sequenced. The simple multicellular Volvox is consid-
Which model organisms are chosen for a particular study, however, ered a model organism for the study of the evolution of multicellularity.
depends on the question being asked. For instance, cell biological pro- Moreover, among the land plants, thale cress (Arabidopsis thaliana) was
cesses are often studied in unicellular organisms, whereas developmen- established in 1940 as a model organism in genetics and, in 1999, was
tal processes are more commonly studied in multicellular organisms. A the first plant to have its genome entirely sequenced. Similarly, the fruit
few examples of model organisms: The bacterium Escherichia coli is one fly Drosophila melanogaster was originally used as a model organism
of the most well-known prokaryotes. It is used in microbiology, medi- as far back as 1901 in zoology and inheritance. It has only four chromo-
cine, and molecular biology, but also plays an important role as a host somes and can be very easily grown and maintained in larger quantities.
organism in molecular studies. Ciliates of the genus Tetrahymena are Many vital findings within zoology, such as the mutagenic action of x-
also important among unicellular model organisms, especially in studies rays on genetic material or the linkage groups of genes and crossover,
focusing on the eukaryotic cell structure. This organism was vital in the were originally discovered in D. melanogaster.
discovery of catalytic RNA (ribozymes) by Thomas Cech, which led to
him winning the Nobel Prize in 1989. Elizabeth H. Blackburn also won
the Nobel Prize (2009) for research on the Telomere and on Telomerase
Model organisms
344 Megasystematics
4.6.1.1
Ciliophora
The Ciliophora (ciliates) belong within Alveolata which, Ciliates are between 10 µm and 3 mm long, inhabiting
together with Stramenopiles and Rhizaria, form the SAR- both aquatic (freshwater and marine) and terrestrial habitats.
clade. Some species live commensally, whereas others are symbi-
Ciliates are unicellular, heterotrophic protists featuring a otic or parasitic. Their distribution is cosmopolitan.
number of special features, including the presence of many Most species are motile, but some may also live in colo-
cilia. These have the same structure as the flagella of other nies or are sessile. Ciliates possess mitochondria. The exist-
protist groups, but they are usually shorter and have different ence of plastids has until now not been detected in ciliates;
locomotory patterns. however, it is assumed that their ancestors possessed plastids
Under their cell surface, ciliates possess both alveoli, char- and that these were secondarily reduced. Ciliates feed via a
acteristic of alveolates, but also trichocysts. When stimu- cystostome, with food (bacteria, algae, fungi, or other pro-
lated, these are able to project forwards a protein filament. tists) being digested in food vacuoles. Non-digestible residues
Ciliates possess two nuclei: a small generative diploid micro- are discharged through an anal orifice known as a cytoproct.
nucleus and a large polyploid somatic macronucleus. Within In addition to the food vacuoles, free-living ciliates also have
the macronucleus, genes lie in a high number of copies; these contractile vacuoles, which have an osmoregulatory func-
are vital for somatic processes. The macronucleus can be re- tion.
generated from the micronucleus, whereas after removal of The oldest known fossil ciliates are tintinnids from the
the micronucleus, ciliates are still viable but can no longer Ediacaran (around 580 mya).
reproduce.
Asexual reproduction usually occurs by transverse nucleus remains in each respective individual (stationary
division, although peritrichous ciliates perform this nucleus), whereas the other (floating nucleus) passes into the
function using longitudinal division. The genus Colpoda second individual along the plasma bridge and merges with
forms division cysts, in which several daughter cells grow. the stationary nucleus to form a diploid nucleus. This diploid
Sexual reproduction occurs by conjugation, where DNA nucleus then undergoes mitosis and a macronucleus, formed
is exchanged between two different individuals through by polyploidisation, emerges from one of its daughter nuclei.
a plasma bridge. During conjugation, the macronucleus Sexual recombination in ciliates is thus not associated with
degenerates and micronuclei from both conjugation partners an increase in numbers of individuals, a task accomplished
undergo meiosis. Three of the resulting four nuclei dissolve through asexual reproduction.
and the remaining nucleus undergoes further mitosis. One
contraktile vakuole: a type of vacuole which uses a process of motility: (Lat.: motio = movement) ability to move freely and
contraction to expel excess water from the cell actively
cytoplasm: cell contents excluding cell nucleus and organelles polyploidisation: multiplication of the number of sets of
food vacuole: vacuole which has formed by phagocytosis chromosomes in a cell
within which food particles are digested by lysosomal enzymes trichocyst: filamentous rods filled with secretions which
explode; they are used for defence or to capture food
See also: Flagellum: 4.2; Nuclear dimorphism: 4.2.2.4; Phagocytosis: 4.3; Stratigraphy of the Phanerozoic: 2.2.2
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
zo
oa nta
o pt
eb
Cry
op
o
mo
ok
A hy
pto
Spirotrichea: Heterotrichea: Prostomatea: Scuticociliatea: Peritrichia:
is t
ta
soz
h
phy
Op
Kerona sp. Blepharisma sp. Coleps sp. Cyclidium sp. Vorticella sp.
Apu
ta
Eubacteria Archaea
The contractile vacuole is responsible for water excretion. It takes liquid from
the cytoplasm and excretes it outside the cell. This is particularly necessary in
freshwater, where water is continuously flowing into the cell by osmosis since
the intracellular salinity is above that of the environment
Ciliates usually have two nuclei (nuclear dimor-

phism): a large polyploid macronucleus (white
arrow) and a small diploid micronucleus (black
cytosome arrow). The macronucleus controls the non-re-
(cell mouth) productive vegetative cell functions whereas the
micronucleus influences the generative process.
After conjugation, the macronucleus is formed Paramecium:
anew macro- and micronucleus
Several features of the ciliate cell surface are no-

table:
Their cilia have an identical structure to other eu-
karyotic flagella, although they are shorter.
Alveoli are flat vesicles sitting in a continuous
layer under the membrane and contributing to its
stability.
Trichocysts are thread-like rods, filled with pro- Pelagothrix: alveoli, cilia
tein that is explosively secreted for defence or
predation purposes. It is subsequently replaced
by other trichocysts
Food vacuoles (ingested diatoms in Loxodes magnus) Paramecium: Trichocysts
Some protists live inside other organisms as endo- als and dinoflagellates likely began already in the
symbionts. These include zoochlorellae (unicellular Triassic.
green algae of the genus Chlorella) living in ciliates, Many Retaria also host endosymbionts, which can
amoebae, and in several Metazoa, providing the appear green or golden.
host with assimilates from photosynthesis. In re- Kleptoplasty or kleptoplastidy occurs when plastids
turn, zoochlorellae receive protection from preda- (notably chloroplasts) from algae are sequestered
tors and obtain metabolic products produced by by host organisms. During periods of food shortage,
the host. Dinoflagellates, which live in symbiosis these plastids can be digested and absorbed again
with Foraminifera, Radiolaria, ciliates, Cnidaria, tu- later on, when nutrient conditions improve.
nicates, and molluscs, are colloquially referred to as
‘zooxanthellae’. Again, zooxanthellae supply their
host with the products of photosynthesis. Of par-
ticular importance is the symbiotic relationship of
the dinoflagellates with reef-building corals. If the
zooxanthellae die, or if they are expelled from the
corals, for example due to changes in environmental
conditions, the reef loses its ability to supply itself
with enough nutrients and eventually dies (coral
bleaching). The symbiotic relationship between cor- Ciliate Paramecium bursaria with
zoochlorellae
Endosymbiotic algae
346 Megasystematics
4.6.1.2
Dinophyta
The Dinophyta (dinoflagellates) are grouped within Al- epitheca. Unarmoured (‘naked’) taxa also possess alveoli,
veolata alongside Ciliophora (ciliates), Apicomplexa, and but they do not contain cellulose plates. During asexual re-
Chromerida. Along with the Stramenopiles and Rhizaria, production, the cell divides, with each new cell retaining a
Alveolata form the SAR-clade. flagellum and a part of the theca, and forming all missing
Dinoflagellates comprise species with both types of sec- parts anew. Dinoflagellates do not possess histones in their
ondary plastids (with three membranes and chlorophyll a nucleus; as a result, their DNA is not bound to such histones
and c) as well as with tertiary plastid types (four membranes as it is during interphase in other eukaryotes. The chromo-
and either chlorophyll a and c, or chlorophyll a and b). All somes are also condensed during interphase.
of the approximately 2,500 known both phototrophic and The oldest fossil dinoflagellates date back to the Cambrian
heterotrophic species possess mitochondria. Dinoflagellates and Silurian. In total, around 4,000 fossil species have been
have a global distribution and can be found in aquatic and described. Along with the Bacillariophyceae, dinoflagellates
benthic habitats, although most species belong to marine make up the largest component of marine phytoplankton
plankton. Some species, however, are also able to live as sym- (primary producers). In nutrient-rich coastal waters, they
bionts or parasites. can occur in masses and lead to characteristic, often red-
Dinoflagellates have two heterokont flagella with differ- dish algal blooms known as red tides. As some of the most
ing movement dynamics. These were originally inserted api- frequently bloom-forming species also produce toxins, these
cally, but the flagella are inserted ventrally in more developed algal blooms have significant economic impacts. In addition,
forms. One flagellum runs along a longitudinal groove of the the toxic Pfiesteria piscicida feeds heterotrophically on animal
cortex (sulcus) in the direction of the longitudinal axis of the prey, releasing chemicals to attract more individuals to prey
cell, extending beyond the rear end of the cell and is either items. Infected fish eventually die as a result of the toxins
naked or surrounded by two rows of stiff cilia. The second and wounds. Dinoflagellates are also found as intracellu-
flagellum beats transversely within the equatorial groove lar symbionts of radiolarians, foraminifera, molluscs, and
(cingulum), carrying a number of fine cilia. This flagellar ar- cnidarians, as well as some ciliates. These so-called zooxan-
rangement causes the dinoflagellate cell to swim in an alter- thellae provide phototrophic nutrition to the host cells, thus
nating motion. Some dinoflagellates are immobile, but these enabling them to survive in nutrient-poor environments. This
form reproductive cells (swarmers) with the typical flagellar symbiosis is significant in coral reefs, where the death of cor-
arrangement. Many taxa are armoured, with cellulose plates als is mainly due to zooxanthellae injury. Finally, some dino-
within the alveoli sitting just below the plasmalemma. The flagellates are able to produce flashes of light (marine phos-
shells formed below the cingulum are known as the hypoth- phorescence) using a luciferin-luciferase chemical system.
eca, whereas those formed above the cingulum are called the
Phototrophic taxa contain a wide variety of plastids of or from secondary serial endocytobiosis, i.e. when one of
differing origin. The original plastid type, the Peridinium-type, the secondarily lost plastids is renewed following secondary
can be traced back to secondary endocytobiosis with red al- endocytobiosis. The genus Lepidodinium possesses plastids
gae. This plastid is closely related to the apicoplast of Api- which arose by serial secondary endocytobiosis, where the
complexa and the plastids of Stramenopiles, Cryoptophyta plastid can be traced back to the ingestion of a green algae, is
and Haptophyta, whose plastids also can be traced back to surrounded by four membranes and has, notwithstanding all
the ingestion of red algae. This plastid type is surrounded other plastids of chromalveolates, chlorophyll a and b. Plas-
by three membranes. The outer membrane is, unlike in Stra- tids which arose by way of tertiary endocytobiosis can be
menopiles, Cryptophyta, and Haptophyta, not connected to found in the genera Kryptoperidinium (ingestion of a diatom),
the endoplasmic reticulum. The plastids have thylakoids in Karenia (ingestion of algae from the group Haptophyta), and
stacks of three, chlorophyll a and c, as well as the accessory Dinophysis (ingestion of an algae from the group of crypto-
pigments beta-carotene and xanthophylls (peridinin). phytes).
The plastids of several taxa stem from tertiary endocy-
tobiosis, i.e. the ingestion of algae with secondary plastids,
histones: basic proteins forming part of the structure of longitudinal: relating to length or longitude
nucleosomes luciferin: compounds which generate light (bioluminescence)
See also: Algal blooms, Mass proliferation 4.7.1; Heterotrophy, Mixotrophy, Phototrophy: 4.6.2.3; Secondary endocytobiosis: 4.1.2.3, 4.1.2.4
plastid cellulose plates pla

stida Rh
iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
thylakoid
z
G
Cerco
odo
la
uc ria
ta
mitochondrion op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
epitheca
oma
Alve
Golgi apparatus Stra
a
lveolata
Meta monad men
opile
a Ha s
zo
oa nta
o pt
eb
Cry
pyrenoid op
o
mo
ok
A hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
cingulum
Eubacteria Archaea
dinokaryon
alveoli with
hypotheca
cellulose plates
sulcus
Marine algal blooms are often

caused by dinoflagellates. Above:
algal bloom caused by dinoflag-
ellates on the Spanish Mediter-
ranean coast (Costa Brava); left:
Akashiwa sanguinea is a bloom-
forming dinoflagellate species
Ceratium hirundinella Dinophysis tripos: Light microscopic Protoperidinium Cyst of Spiniferites

micrograph (left) and electron microscopic pellucidum ristingensis
micrograph (right)
Some organisms have evolved the ability to bioluminesce, or emit light.

Bioluminescence is generated by a biochemical reaction, producing visible
light. The light-imaging substrate luciferin reacts with the enzyme luciferase
and energy is released as light. Various variations of luciferase and luciferin
produce light in different colours. Bioluminescence, which can be primary (self-
fish luminous) or secondary (symbiotic), can be used by predators to attract prey fungi
or by individuals to attract partners, or it may serve in order to communicate
a warning. Various organisms are able to produce bioluminescence. These
include dinoflagellates (Noctilula, Pyrocystis), fungi (such as Armillaria), beetles,
bacteria, coral and most deep-water fish. Only higher vertebrates and plants
have not developed luminescence.
dinoflagellate glowworm
sea anemone ctenophore
Bioluminescence
348 Megasystematics
4.6.1.3
Apicomplexa
The Apicomplexa, along with Ciliophora, Chromerida, apparatus. The alveoli of the endomembrane surround the
and Dinoflagellata, are summarised as Alveolata and form entire cell body with the exception of the front and rear end
one of the major groups within the SAR-clade. as well as the micropore openings.
Apicomplexans are obligate endoparasites of animals. Apicomplexans are named after their distinctive apical
They usually have a two or three-phase generation with ge- complex, though they are also characterised by an apico-
nus-specific infection, growth, propagation, and sexual stag- plast, an organelle usually surrounded by four membranes
es. A generational change is often connected with a change sitting in close proximity to the nucleus and mitochondria.
in the host. The infection occurs mostly through long, spin- As in plastids of dinoflagellates, the presence of the apico-
dle-shaped sporozoites, either directly or protected within a plast dates back to a secondary endocytobiosis with red al-
sporocyst and oocyst, transferred to a new host through the gae. The apicoplast has a greatly reduced genome and has
sucking action of a blood-sucking insect. lost its photosynthetic function, although it is involved in the
Apicomplexa are characterised by a number of distinc- biosynthesis of fatty acids and isoprenoids. Since the host
tive structures located at the apical, pointed end of the cell, organisms (vertebrates) do not have plastids, this is a poten-
known as the apical complex: pole rings are thickenings of tial target for the pharmacological control of apicomplexan
the inner pellicular membrane complex and can be found at parasites.
the front and rear of the cell; conoids, a set of spirally ar- Among the most important apicomplexan taxa are Plas-
ranged microtubules, enable the cell to penetrate hosts; rhop- modium, the trigger of malaria, and Toxoplasma, the causative
tries, specialised bottle-shaped secretory organelles; and, agent of toxoplasmosis.
finally, micronemes, enzyme-filled derivatives of the Golgi
The different species of Plasmodium (as the causative Schizonts form many smaller merozoites, which return to
agent of malaria) usually infect primates, but rarely other the bloodstream and infect red blood cells there. In eryth-
mammals. Some species also infect birds (avian malaria) or rocytes, further multiplication takes place via schizogony.
reptiles. All Plasmodium have a complex life cycle featuring Since the developmental cycle runs synchronously, it occurs
an obligate change of host between insects, in which there is almost simultaneously with the release of the parasites. This
sexual reproduction, and vertebrates, in which asexual repro- process is synchronised mostly for one to four days alongside
duction occurs. the release of new merozoites, causing the characteristic pe-
Sporozoites are transmitted into the body of a vertebrate riodic fever in malaria sufferers.
through the saliva of infected mosquitoes. In mammals, the Some Plasmodium develop in erythrocytes to gametocytes.
sporozoites enter the blood vessels before infecting liver cells, Having been taken up by a mosquito, the microgametocytes
in which they multiply by schizogony; other Plasmodium cells divide into microgametes (exflagellation) inside its gut, form-
can also infect different organs and tissue in birds and rep- ing a zygote through merging with a macrogamete. In the gut
tiles. In some species, dormant stages can occur, making the wall of the mosquito, the zygote forms an oocyst, which in
parasites more difficult to target by way of drugs and subse- turn forms sporozoites that migrate to the insect’s salivary
quently leading to a relapse of the illness. glands.
apicoplast: a derived plastid found in Apicomplexa oocyst: (Grk.: oo = egg, kystis = bladder) developmental stage
erythrocytes: (Grk.: erythros = red, kytos = container) red of the apicomplexa containing sporocysts
blood cells schizogony: asexual reproduction in which daughter cells are
gametocyte: sex type developing from merozoites formed by mitosis in the mother cell; these are then freed when
microgametocyte: male gametocyte the mother cell disintegrates
obligate endoparasite: (Lat.: obligare = to bind, to tie) para- sporozoite: infectious stage in parasitic Apicomplexa
sites living inside their host and are totally dependent on their
host, i.e. they cannot survive independently
See also: Parasites: 4.2.2.1, 4.3.1, 4.3.2

stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
conoid G
Cerco
odo
la
uc ria
ta
op Re
phy
apical polar rings
Chr
inner membrane complex hy
ae
conoid Disc ta
Excavata
oba olata
oma
(alveoli) Alve
a Stra
lveolata
Meta monad men
opile
a Ha s
micronemes zo
oa nta
o pt
eb
Cry
op
o
mo
ok
A hy
pto
micronemes
is t
ta
soz
h
phy
Op
Apu
ta
rhoptries Eubacteria Archaea
microtubules Golgi apparatus
nucleus
apicoplast
mitochondrion
nucleus
Golgi apparatus
Stained blood smear of Plasmodium falciparum, the causative

agent of Malaria tropica. The sickle-shape of trophozoites (thick
arrow) and the free gametocyte (thin arrow) are visible
The emergence of organelles was an important step in the evolution Cytosol: pH ~ 7.2, relatively
of the eukaryotic cell including towards establishing cell specialisa- reductive redox conditions
tion and forming tissues in multicellular organisms. In contrast to
prokaryotic cells, eukaryotic cells have membrane-enclosed compart-
ments, the interior of which is separated from the cytoplasm. This
compartmentalisation allows simultaneously different reactions in Mitochondrial intermembrane space:
separate reaction chambers under differing conditions (for example, pH ~ 7.0, comparatively strongly oxi-
pH or ionic strength). The membrane itself is also directly involved in dising redox conditions
the metabolism of the cell; for example, many enzymes are incorpo-
rated in the membrane. An example of an interaction between sever-
al compartments of the cell is the biosynthesis of fatty acids and their
processing into storage fats (triacylglycerol) as well as the conversion
of phosphoenolpyruvate to pyruvate.
Mitochondrial matrix: pH ~ 8.0,
comparatively oxidising redox
conditions
Membranes limit contact between different intracellular reaction

chambers with differing pH and redox conditions, here exemplified by
the mitochondrion
Compartmentalisation
350 Megasystematics
4.6.2
Stramenopiles
Stramenopiles are a sister group to Alveolata. They form Individual groups of stramenopiles are well characterised
a very diverse, heterogeneous lineage, so much so that their and their respective monophyletic lineage is well supported.
diversity by far exceeds that of Metazoa (animals) and Em- The relationship of the groups to each other is more diffi-
bryophyta (plants). This group is also important from an eco- cult to reconstruct. Stramenopiles include many groups of
logical and economic perspective. organisms that possess plastids (algae), but also many groups
All stramenopiles feature hollow tripartite Mastigonema, without them. Even within the groups of plastid-bearing
which sit in longitudinal rows on their longer, anterior flagel- stramenopiles, many lineages feed heterotrophically and
lum. This characteristic is responsible for the group’s name bear greatly reduced plastids.
(Lat.: stramen = straw, hollow stems, pilus = hair, bristle).
The plastid-bearing stramenopiles are considered to be gyra, which includes Opalinata, the Labyrinthulomycetes,
monophyletic and are known as Ochrophyta. Based on mo- and Bicosoecida. Bigyra may form the sister group of all of
lecular data, the Ochrophyta comprise three large groups, the remaining stramenopiles, although this has not yet been
each consisting of several important lineages. In addition to confirmed.
their genetic differences, the dominant synthetic pathways of The Opalinata comprises four genera and a total of
carotenoids between these groups are different: around 400 species. They were formerly classified within the
The Raphidophyceae, Phaeothamniophyceae, Phaeophy- ciliates because their flagella are arranged in oblique rows.
ceae, and Xantophyceae form a lineage based on this charac- However, they do not display other typically ciliate char-
teristic; in this group, carotenoids are synthesised in a variety acteristics, such as a nuclear dualism or alveoli. Opalinata
of different pathways. are non-pathogenic endo-commensals of a number of ver-
The second group mainly consists of Pinguiophyceae, the tebrates.
Chrysophyceae, Synchromophyceae, and Eustigmatales; this Labyrinthulea mostly colonise marine habitats but are
group primarily relies on the violaxanthin-antheraxanthin- sometimes found on rotting plant material in freshwater hab-
cycle to synthesise carotenoids. itats as well. Very few species are known within this lineage.
The third group comprises the Dictyochophyceae, the Pel- Some species live as parasites on marine plants and algae.
agophyceae, and the Bacillariophyceae; the diatoxanthin-di- Labyrinthula macrocystis is the causative agent of eelgrass dis-
adinoxanthin cycle dominates in this group. In addition, the ease.
flagella are largely reduced, specifically in the derived taxa. The Bicosoecida are important consumers of pelagic bac-
In addition to the Ochrophyta, the Stramenopiles com- teria and form a vital part of the heterotrophic nanoplankton
prise groups that do not contain plastids. These groups are community. All of the approximately 40 known species are
likely paraphyletic, although they seem to belong to at least either unicellular or colony-forming. They are found on a
two kinship groups: number of different substrates or free-floating in marine and
Pseudofungi, which includes Peronosporomycetes freshwater habitats. Some species have a lorica.
(Oomycetes) and the Hyphochytridiomycetes; as well as Bi-
bothrosomes: organelles of the Labyrinthulomycetes, which conoid: structure consisting of spirally-arranged microtubuli in
secrete the exoplasmic polysaccharide filaments surrounding the the apical complex of the Apicomplexa
cells infraciliature: the entire root structure of cilia in ciliates
capsoid (capsal): category of algae in which the flagella are monad: flagellated, single-celled
largely reduced; cells embedded in gelatine palmelloid: colony of algae in which the cells are embedded
coenobium: a colony containing a fixed number of cells often in a gelatinous matrix; in contrast to coenobia, there is no fixed
embedded in mucilage number of cells
See also: Heterotrophy: 4.6.2.3; Nuclear dimorphism: 4.2.2.4

Alveolata and Stramenopiles: Stramenopiles 351
stida Rh
Bigyra pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
A
many flagella, double-stranded connecting helices
Cerco
H
odo
la ria
Opalinata uc ta
op Re
phy
between the kinetosome and flagella E
Chr
hy
ae
Disc ta
Excavata
cells connected by polysaccharide-containing mu- T oba olata
oma
Labyrinthulomycetes Alve
cus fibers, with bothrosomes E a Stra
lveolata
monad men
two flagella, no connecting helix, often with at- R Meta opil
Bicosoecida zo
a Ha es
O
oa nta
tached posterior flagellum, some with lorica eb
o pt
Cry
op
o
mo
ok
T A hy
pto
is t
ta
Pseudofungi
soz
h
R
phy
Op
Apu
O
ta
Hyphochytridiomycetes one anterior flagellum P
forms a hyphal network and possesses a cell wall of H Eubacteria Archaea
Peronosporomycetes
glucan and cellulose
Ochrophyta: plastids
Carotenoid synthesis: different cycles
Raphidophyceae naked cells with an anterior-facing and a posterior-facing flagellum, no cell wall
Phaeothamniophyceae filiform, capsoid, palmelloid or coccoid, with a eye spot
Phaeophyceae filamentous to tissue-forming, tissue-forming algae differentiated as either phylloid, cauloid,

or rhiyoid, some species with an eye spot; cell wall made of cellulose and alginates
Xanthophyceae coccoid or tissue-forming, cellulose cell wall
P
Carotenoid synthesis: violaxanthin-antheraxanthin-cycle mainly H
O
T
Pinguiophyceae coccoid, cells naked or with a lorica, no eye spot
O
unicellular, capsoid, coccoid, or tissue-forming, forms resting stages (cysts) made of sil- T
Chrysophyceae
icate, upper cell surface sometimes features silicate scales, lorica sometimes present R
O
Synchromophyceae amoeboid, multiple plastids fused together into a complex P
H
Eustigmatales coccoid single cell-cells or colony-forming, cell wall of cellulose
Carotenoid synthesis: violaxanthin-antheraxanthin cycle mainly; flagella and flagella basis reduced in most
lineages except for some basal taxa
unicellular flagellates, colony-forming or amoeboid, no eye spot, kinetosomes
Dictyochophyceae pressed to the nucleus
flagellated, capsoid, coccoid, or tissue-forming, kinetosomes pressed to the nucleus,
Pelagophyceae
no eye spot
Bacillariophyceae usually not flagella, silicate cell wall
Most marine invertebrates are osmoconformers, water- and salt-levels. Using these vacuoles, these
meaning that they exist in an osmotic equilibrium species are able to continuously excrete water
with their environment. They are not capable of seeping into the cell. The vacuole absorbs water
regulating the osmotic pressure of their body flu- from the cytoplasm, moves it to the cell mem-
ids and are therefore required to live in stable en- brane, and releases it by fusing with the mem-
vironments, in particular regarding salinity. brane or through a porus to the outside.
Organisms in coastal areas or estuaries, on the The excretion of water via contractile vacuoles is
other hand, may have to encounter abrupt envi- driven by a proton pump: the cells pump protons
ronmental changes. These species are therefore into the contractile vacuole causing ions to enter.
capable of osmoregulation in order to regulate As a result of the increasing salt concentration,
the salinity of their body fluids. water also diffuses into the vacuole.
Freshwater fish, for instance, are able to take up
electrolytes through their gills and excrete them
via their urine. Marine organisms, which have a ‘Selectively permeable’ membranes are
lower osmotic pressure than their environment, permeable to water whilst blocking dis-
maintain their osmotic pressure by excreting salts solved ions. The osmoregulation of single-
over their gills. celled and multicellular organisms hinges
For example, some organisms, like the single- upon in the active exchange of ions across
celled Paramecium or Euglena, comprise con- membranes and the osmotic balance of
tractile vacuoles, with which they can regulate currents
Osmoregulation
352 Megasystematics
4.6.2.1
Peronosporomycetes (Oomycetes)
The Peronosporomycetes belong to the stramenopiles, secreted enzymes break down organic macromolecules,
making up a sister group to Alveolata. Together with which may then be absorbed into the cell. Most taxa live
Rhizaria, these groups form the SAR-clade. parasitically and can cause significant plant disease like, for
Lineages within Peronosporomycetes (‘egg fungi’, algal example, Phytophthora infestans, the causative agent of potato
fungi, or cellulose fungi) are heterotrophic organisms, in- blight, which infects the lenticels of potato tubers. As a re-
cluding some 400 species. They have mitochondria but no sult, P. infestans can infect stored potatoes, but it also affects
plastids. Most Peronosporomycetes are single-celled, but other solanaceous plants, including the tomato as well as
may also feature highly branched, multinucleate filaments representatives of certain other plant families.
without cross walls. These species were previously regarded P. infestans spreads very quickly, firstly by the transport of
as fungi as a result of their morphology and diet. However, infested fruits and plants and also by wind dispersal of its
molecular data and the cell wall structure, which is predomi- spores. The first documented outbreak of the disease was in
nantly made up of cellulose and hemicellulose, as well as the the eastern United States (New York and Philadelphia) in
fact that most lack chitin in their cell walls, supported their 1843. Two years later, the disease had already spread across
subsequent exclusion from fungi. The zoospores form during the last parts of the eastern US and, through the transporta-
the course of asexual reproduction of two flagella, as typical tion of seeds, carried over to Ireland, causing the Great Po-
for stramenopiles. tato Famine from 1845 to 1853, which killed over a million
The Peronosporomycetes feed osmotrophically and in- people and caused one of the most severe waves of emigra-
habit both aquatic and terrestrial habitats. Their outwardly tion from Europe.
Most species of Peronosporomycetes undergo both Similarly, Peronosporales are saprophytic or parasites of
asexual and sexual reproduction. In asexual reproduction, plants and form branched non-septated mycelia. This group
zoospores or sporangia (conidia on conidiophores, an ad- includes many agricultural crop pests, including Phytophtora
aptation to life on land) are spread whereas during sexual infestans, the blue tobacco mould genus Peronospora, and the
reproduction, male and female reproductive organs are fused downy mildew-causing genus Plasmopara.
(gametangiogamy). From the fertilised egg, a thick-walled The genus Pythium also infects plants and can cause a so-
oospore develops, a structure that is able to survive unfavour- called damping off disease. The species Pythium insidiosum
able conditions until it germinates again. can also infect mammals. Rhipidiales is a group of aquatic
The internal classification of Peronosporomycetes re- oomycetes, which is commonly found in polluted waters
mains unresolved. Lagenidiales are probably the ancestral and forms rhizoids for attachment of the organism to the
members of the group. The most widely dispersed group is substrate. Leptomitales have thickened sections of their cell
Saprolegniales, comprising saprophytes as well as parasites. wall; cell walls in this group also contain chitin.
oospore: (Grk.: oo = egg, spora = seed) fertilised oogonia, zy- secretory enzymes: enzymes secreted by excretory glands
gotes (etc) in Peronosporomycetes
See also: Blight: 3.2.1.7; Alien and invasive species: 3.2.1.7; Fungi: 4.2.2
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opil
a Ha es
zo
oa nta
o pt
eb
Cry
op
o
mo
ok
A hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
The oomycete Peronospora sparsa Potato infected with Fish infected with Saprolegnia (‘fish
causes downy mildew. Phytophtora infestans mold’)
Eubacteria Archaea
Asexual reproduction: the hyphal tip is separated from the

rest of the hyphae, becoming the sporangium. The spo-
rangium may remain on the hyphae or is distributed as a
conidium. Through mitosis, the sporangium is filled with
multiple nuclei. Together with a portion of the plasma each
The reproductive cells take a spherical shape and lose their
nucleus is subsequently surrounded by cell membrane. The
flagella. The spherical cell is referred to as a cyst
resulting mononuclear cells form the typical two flagella
before leaving the sporangium
swarmer
cyst
sporangium
oogonia
antheridia
Sexual reproduction: Mostly large, round female gametan-
gia (oogonia) and smaller male gametangia (antheridia)
arise at the top of hypha. Meiosis occurs in gametangia,
which are separated from the hyptha by a septum. Fertili-
sation takes place when nuclei migrate from the antheridia
to the oogonia through plasma tubes, i.e. the gametangia
merge (gametangiogamy)
hyphae
All known living things are made of car- as the lower reactivity levels of silicon and H H
bon compounds. This is no coincidence, silicon compounds, also reaffirms existing
R C C R
because not many elements have the hypotheses. Finally, silicon is far less flex-
necessary characteristics to sustain life. ible than carbon: double bonds in silicon H H
Biodiversity requires molecules made of are less stable and the formation of silane
a specific element that is able to take up chains is limited to a maximum of 15 Si-Si H
single and multiple bonds and stable long compounds. Several million organic com-
R C C R
chains, as well as making ring-shaped mol- pounds, i.e. based on carbon, are known,
ecules. These properties are characteristic but there are only around 100,000 inor- H
of the carbon group and, specifically, only ganic compounds. Further, evolution driv-
of carbon and silicon. Silicon is therefore en by silicon-based compounds over con- R C C R
a possible alternative to carbon as a basal ceivable time periods is hardly possible.
component of all life. Although the pos-
sibilities of alternative biochemical prop-
erties – including silicon-based and other
solvents, such as ammonia – are not quite
excluded, they remain unlikely. In addition,
the relatively high frequency of carbon Carbon atoms can form long chains, interlinked by means
compared to silicon in the cosmos, as well of single, double, or triple bonds
The chemical basis for life

354 Megasystematics
4.6.2.2
Phaeophyceae
Along with the Raphidiophyceae, Phaeothamniophyceae, regions of their colloid and phyllodes, whereas the inner sec-
Xanthophyceae, and some other groups, the Phaeophyceae tions are made up of strands of tubular cells serving a role
form a lineage within Ochrophyta. The Ochrophyta in turn, in transport.
along with Pseudofungi and Bigyra, form the stramenopiles, The main constituents within brown algae cell walls are
which, together with Alveolata and Rhizaria, makes up the cellulose and the salts of 1,4-glycosidically linked mannu-
SAR-clade. ronic and galuronic acids, making up alginic acid (alginate).
The Phaeophyceae (brown algae) are multicellular and The cellulose fibrils are embedded in an amorphous alginate
some species, such as the giant kelp of genus Macrocystis, gel, ensuring that the organism is strong and flexible enough
can grow up to 60 m in length. The group comprises around to survive conditions in the wave-rich intertidal zone. Algi-
1,800 known almost exclusively marine species, growing nates are also commercially used as emulsifiers in ice cream
mostly in shallow marine coastal areas up to the splash zone or cosmetics.
on rocky terrain. Some species (Sargassum spp.) can also be Flagella are found only in the brown algae’s reproductive
found drifting in the open sea. The brown algae are the only cells. These have two laterally inserting flagella, one an ante-
stramenopiles forming differentiated tissues: the thallus of riorly-facing flagella with two rows of tripartite hairs and the
brown algae is differentiated into various tissues and sec- other a smooth, whip-shaped flagellum facing the posterior.
tions. Species that are fixed to one location form a root-like The brown algae most often have one plastid per cell. This
attachment organ called a rhizoid, sprouting colloids (stem organelle is secondary, surrounded by four membranes and
swelling or tubercle), and leaf-like phyllodes (part laminar comprising chlorophyll a, c1 and c2, as well as the accessory
branched stem). Several species are characterised by gas- pigments ß-carotene, fucoxanthin, and to a lesser extent dia-
filled sacks (aerocysts), which help with buoyancy. Most dinoxanthin and diatoxanthin. Chrysolaminarin is formed
brown algae are only photosynthetically active in the outer as a storage polysaccharide.
Brown algae undergo a heterophasic generational change Alginates consist of alginic acid and calcium ions. In the
between haploid and diploid generations. In some taxa, the food industry, they are used as emulsifiers and thickening
two generations are alike (isomorphic), whereas in others, agents in, among other things, baked goods, frozen foods, ice
the gametophyte is reduced compared to the sporophytes cream, and preserves.
(heteromorphic). In the Fucales, the haploid generation is al- In medicine, they are used for cleaning wounds, as they
most completely reduced. Brown algal taxa with identically are able to absorb over twenty times their own weight in se-
designed, flagellated gametes (isogamy) can also be found, cretions. Alginates also have a haemostatic effect, in other
as well as those with differently sized, flagellated gametes words they are able to stop bleeding, as a result of their cal-
(anisogamy) and those with non-flagellated female ova (oo- cium component. They can also be used as a biomaterial
gamy). for the encapsulation of human tissue, so that exogenous
Alginates can be extracted from brown algae using spe- materials may go undetected by the immune system after a
cial harvesting equipment (trawler) or by collecting seaweed transplant.
on the beach, followed by extraction in alkaline solutions. Finally, since the 17th century, potash (potassium car-
The most common genera from which alginates are obtained bonate), calcium sulphates, and natrium carbonates for the
commercially include: Laminaria, Ecklonia, Macrocystis, Les- glass- and soap-making industry have been extracted from
sonia, Ascophyllum, and Durvillea. the ashes of brown algae.
chrysolaminarin: a storage polysaccharide found in strameno- heterophasic: generational change between the haploid and
philes; β 1-3- and β 1-6-glycosidic bonds the diploid generations
cuttlebone: brittle gas-filled structure used for buoyancy in thallus: multicellular undifferentiated vegetative tissue in plants,
Sepiida (e.g. cuttlefish) algae and fungi without the organisation of a cormus (sections
emulsifier (emulgent): an agent which enables two normally incl. stem, root, leaf)
unmixable materials to be mixed together and stabilised
See also: Alternation of generations: 4.4.3.3; Compartimentalisation: 4.6.1.3

stida Rh
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Viridiplant ta
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Cerco
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Chr
hy
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Disc ta
Excavata
oba olata
oma
Alve
a Stra
lveolata
Meta monad men
opil
a Ha es
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oa nta
o pt
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Cry
op
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A hy
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Op
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Eubacteria Archaea
Oogonia Antheridia
top: Laminaria sp. Entire thallus of Saccorhiza polyschides top: tissue from Fucus vesiculosus
middle: Laminaria hyperborea middle: aerocysts of a bubble tange
bottom: Sargassum sp. bottom: rhizoid
Organisms that live in water must be able to regulate their

buoyancy. Many species have air chambers (top-left: cuttlefish;
bottom-left: Nautilus). Most bony fish have a swim bladder with
which they regulate swimming depth and are able to stabilise
themselves into an upright position. Their swim bladder is formed
by a protrusion of the foregut (top-right: goldfish with damaged
swim bladder). Fish without a swim bladder regulate their depth
by constantly swimming. Cyanobacteria and some other bacteria
have gas vesicles, which help them to maintain buoyancy and reg-
ulate their depth in order to gain exposure time in nutrient- and Sepia officinalis Goldfish with a swim bladder disease
oxygen-rich waters. Gas vesicle membranes are often imperme-
able to water and solutes, but not to gases. Another form of buoy-
ancy comes from gas bubbles (aerocysts). Both aquatic brown
algae (Laminariales and Fucales) form aerocysts, which help them
float in water. Similarly, wind-dispersing plant pollen is encapsu-
lated in air bags, increasing their dispersal range once released
into the air (bottom-right).
Nautilus sp. Pine pollen with airbags
Buoyancy
356 Megasystematics
4.6.2.3
Chrysophyceae
Along with the Synchromophyceae, Pinguiophyceae, Eu- one of the most important constituents in algal communities,
stigmatophyceae, and a number of other groups, the Chryso- especially in nutrient-poor habitats. The Synurales are all
phyceae (golden algae or chrysophytes) form a lineage with- phototrophic. Other groups of chrysophytes are mixotrophic
in Ochrophyta. Along with the Pseudofungi and Bigyra, the or heterotrophic, feeding phagotrophically on bacteria and
Ochrophyta make up the Stramenopiles which, with Alveo- other small particles. Mixotrophic chrysophyte groups com-
lata and Rhizaria, form the SAR-clade. prise all gradations of predominantly photogrophic to het-
Chrysophytes possess two flagella, although the short erotrophic taxa. Mixotrophic nutrition allows organisms to
flagellum may be greatly reduced in some species. Chryso- take up nutrients in food and thus circumvent the nutrient
phytes are morphologically diverse, including both unicellu- limitations of photosynthesis in nutrient-poor waters.
lar species and colony-forming moulds. At least five lineages have independently lost the ability to
Many chrysophytes produce resting stages (stomato- perform photosynthesis, and the plastid is greatly reduced in
cysts), which are made of silicate. These resting stages have these. However, the plastid is also important in these hetero-
a variety of ultrastructural surface patterns, and have a porus trophic species, playing a role in various metabolic pathways,
through which the organism can hatch. such as the synthesis of fatty acids. Heterotrophic chryso-
Some groups (Synurales, Paraphysomonadales) have sili- phytes are some of the most commonly observed eukaryotes
cate scales on their cell surface. in aquatic and terrestrial habitats. In contrast with photo-
In many lineages, the ability to photosynthesise is second- trophic chrysophytes, heterotrophic species are also found
ary reduced, although even these colourless species possess in marine environments, in lakes with high pH values and
rudimentary plastids. in soil. They are therefore able to colonise a wider range of
Photosynthetic chrysophytes mostly inhabit freshwater habitats than the phototrophs.
habitats at neutral or slightly acidic pH values. They make up
The photosynthetic golden algae (genera Synura, Mall- On the one hand, the most important heterotrophic chrys-
monas, Tesselaria) have been proposed as a separate family ophytes are the scale-bearing Paraphysomonadales and, on
(Synurophyceae) sister group of the chrysophytes. Recent the other, a polyphyletic group of colourless and scaleless
molecular studies, however, show that these organisms rep- taxa.
resent an order (Synurales) within the chrysophytes them- These ecologically significant and widespread, colourless,
selves. The Synurales possess silicate scales and are primarily non-scale-bearing taxa were formally known under the col-
found in humic material-rich and slightly acidic (pH 5–6.5) lective name Spumella-like flagellates, or Spumella spp. Recent
lakes. studies show, however, that a number of heterotrophic col-
Among the most important and widespread representa- ourless flagellates have developed within the chrysophytes.
tives of the mixotrophic chrysophytes is the genus Dinobryon, These are almost indistinguishable morphologically and
which makes up a significant proportion of algal biomass, have so far only been assigned to the correct genera and line-
particularly in spring plankton. Dinobryon spp. forms tree- ages based on molecular data.
like colonies, in which individual cells sit within a funnel-
shaped or tubular housing (a lorica).
autotrophy: (Grk.: autos = self, trophe = nourishing) the ability mixotrophy: (Grk.: mixis = mixture, trophe = nutrients) ability
of organisms to produce and store organic nutrients exclusively of some organisms to absorb both carbon dioxide and to survive
from anorganic substances on organic sources of energy
heterotrophy: (Grk.: heteros = different, trophe = nutrition)
ability of organisms to use existing organic carbon to form nutri-
ents and store energy
See also: Scales: 4.7.2

stida Rh
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Viridiplant ta
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Cerco
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uc ria
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Chr
hy
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Disc ta
Excavata
oba olata
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Alve
a Stra
lveolata
Meta monad men
opil
a Ha es
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Cry
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A hy
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Dinobryon divergens Synura sp. (Synurales; phototro- Mallomonas annulata (Synurales;
(Chrysophyceae; mixo- phic) phototrophic) Eubacteria Archaea
trophic)
longer flagellum with

tripartite hairs
Golgi apparatus
mitochondrion shorter
flagellum
without hairs Silicate scales of Mallomonas sp. (left) and stomatocysts from the
sediment of a mountain lake (right)
plastid
thylakoid
TEM image of heterotrophic (colourless) golden algae Acrispumella

chloroplast-endoplasmic msimbaziensis (left) and Pedospumella encystans (right). The masti-
reticulum (CER) gonemes on the long flagellum are clearly visible
The basic dietary habit (phototrophy, mixotrophy, heterotrophy) may Mixotrophic nutrition is selected for from an autotrophic starting point,
vary greatly between closely related groups of organisms. Generic terms especially in nutrient-limited environments, as phagotrophic nutrition
such as ‘algae’ or ‘heterotrophic nanoflagellates’ therefore only denote can supplement nutrients for photosynthesis. In the permanent absence
the functional groups listed in ecological studies. However, in the phylo- of light, mixotrophic organisms may lose their ability to photosynthesise.
genetic context, these groupings do not always make sense. The reverse, i.e. the change from heterotrophic to phototrophic/mixo-
Transitions between diets can be seen in various groups of organisms, trophic nutrition, has been observed far less often, as this generally re-
including within higher-level plants, where parasitic lineages evolved quires the inclusion of a phototrophic endosymbiont and its subsequent
separately at least twelve times. In addition, various lineages, although conversion to a plastid. This is a much more complicated process than
also feeding autotrophically, are able to capture and digest animal food the gradual loss of the ability to perform photosynthesis.
as carnivores.
Conversely, many metazoans live in close symbiosis with algae or use the
plastids of algae as kleptoplastids to supplement their heterotrophic nu-
trition by autotrophy. In protists, this image is still more diverse: within
the golden algae, heterotrophic lineages have emerged independently
five to ten times. In addition, many mixotrophs display a number of
dietary modes of differing importance. Similarly, nearly all other algal
groups feature lineages or species with reduced photosynthetic capabili-
ties or at least mixotrophic capabilities in addition to their autotrophy.
Phototrophy, mixotrophy, heterotrophy

358 Megasystematics
4.6.2.4
Bacillariophyceae
The Bacillariophyceae (diatoms) form, along with the them together. During cell division, the cell halves are di-
Pelagophyceae and Dictyochophyceae, a lineage within vided amongst the daughter cells, becoming their epitheca,
Ochrophyta. Ochrophyta belong to the Stramenopiles which whereas the hypotheca is formed anew. Shell components
are part of the SAR-clade (together with Alveolata and are formed within the vesicles of the Golgi apparatus (silica
Rhizaria). deposition vesicles – SDVs). Since the smaller shell half is
Bacillariophyceae are a diverse group of primarily unicel- always newly formed, asexual reproduction always leads to
lular algae, although in some groups, these may form simple a reduction in size of the cells in a population. This makes
cell clusters. Diatoms live in marine, freshwater, and terres- regular sexual reproduction cycles necessary for the popula-
trial habitats, and can be observed in samples dating back to tion to survive. During sexual reproduction, a zygote with-
the Jurassic. However, their diversity and distribution grew out a cell wall (auxospore) is produced, which is capable
to what it is today during the Cretaceous. In the sea, diatoms of growing in size. Diatoms have no flagella and even their
form an important component of phytoplankton, and these flagellar basal bodies are greatly reduced. Only the gametes
are responsible for roughly a quarter of global primary proof some centric diatoms form the flagellum, with tripartite
duction. Diatoms have mitochondria and secondary plastids, mastigonemes, characteristic of Stramenopiles. In all other
which are surrounded by four membranes. Their plastids are taxa, flagella are completely reduced.
coloured brown due to the presence of fucoxanthin, and Diatom deposits may be rock-forming and are mined as
these also contain chlorophyll a and c. Diatoms use chrys- diatomaceous soil. Diatoms are commercially important, for
olaminarin as a nutrient storage material. example as abrasives in toothpaste, as a reflector material in
Diatoms are characterised by their silicate casing, known road markings, as support material for nitroglycerin in dy-
as a frustule. The frustule is composed almost purely of sil- namite, and also used in polishing agents, filter media, or
ica, and is coated with a organic layer. The frustule struc- in insecticides (shells clog the tracheae of insects). They are
ture is usually composed of two overlapping sections, known an important group of indicators for water quality and are
as thecae (epitheca and hypotheca). The join between the therefore routinely included in environmental water analy-
two thecae is supported by bands of silica, which hold ses.
Morphologically, diatoms can be grouped as either round, Diatoms are the only diploid group within the algae,
radially symmetrical taxa (centric – Centrales) or longitudi- meaning that they have a double set of chromosomes in all
nally stretched, bilaterally symmetrical taxa (pennate – Pen- but their reproductive cells, which are formed by meiosis
nales). Many pennate diatoms are able to move using spe- (gametes).
cialised structures known as raphes, which centric diatoms Due to their double gene pool, diatoms are not often di-
do not possess. Many species also form floating extensions rectly affected by mutations, which may explain their rela-
or vacuoles and oil droplets, in order to increase buoyancy. tively high evolutionary rate of and, thus, their broad diver-
sity.
chrysolaminarin: a storage polysaccharide found in strameno-

philes; β 1-3- and β 1-6-glycosidic bonds
See also: Biomineralisation: 4.5.2; 4.5.2.1

stida Rh
pla iza
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Viridiplant ta
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Cerco
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Chr
hy
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Disc ta
Excavata
oba olata
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Alve
a Stra
lveolata
Meta monad men
opil
a Ha es
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Cry
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A hy
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Pinnularia viridis, a pennate diatom Thalassiosira punctigera, a centric diatom
Eubacteria Archaea
central nodule raphe end mode
epitheca
Diatom shells are used as abrasives in

epivalva toothpaste
epipleura
hypotheca
hypopleura Diatom shells are used to make reflec-

tive road markings
hypovalva
Successively smaller shell sizes as a

result of rebuilding of the hypotheca
during asexual reproduction
Although pennate diatoms do not have flagella, these can move using contractions of the body. For example, snails use their flattened base
a raphe. Raphes are slit-shaped apertures in the silica shells, which are (foot) to move either in a wavy motion or in a two-part walking gait.
located on one or both shell halves. Pennate diatoms can, using their Here, they secrete a mucus carpet over which they can crawl or slide.
raphe, crawl at a rate of 20 µm/s in two directions. Using their raphes, This mucus also protects against dehydration and predators.
the cells excrete polymers onto the substrate before pulling on them
as an anchor point. Raphes are usually located in the longitudinal axis
of the shell, but may also be arranged eccentrically or on the edge of
the shell. A corresponding ‘crawling’ locomotion can also be observed
in other taxa. For example, the Zygnematophyceae have neither flagella
nor any other specialised structures for locomotion, yet they are still
capable of slowly creeping along the substrate by adhering firmly with
one cell pole and subsequently secreting mucus through large pores, on
which they move around.
The cyanobacteria, both unicellular and filamentous, may also move
by creeping on mucus secretions. In the genus Oscillatoria, the entire
filament rotates around its longitudinal axis. Some representatives also
use a creeping locomotion to reproduce, discharging short filament frag-
ments out of a jelly-like substance. Even multicellular organisms may
move around by mucus secretion, often in combination with wavelike Arion rufus (mollusc) and Oscillatoria sp. (Cyanobacteria)
Locomotion by gliding
360 Megasystematics
4.7
Hacrobia and eukaryotes of uncertain placement (incertae sedis)

Together, Haptophyta and Cryptophyta make up Hacro- The relationship of Haptophyta and Cryptophyta with
bia. this SAR-clade and with the ‘core Chromalveolates’ is still
In line with the ‘chromalveolate hypothesis’, these groups uncertain; however, it is likely that Haptophyta is a sister
have conventionally been grouped with Alveolata and Stra- group of the SAR-clade. The Cryptophyta, in contrast, may
menopiles as Chromalveolata, as a result of their chloro- be more closely related to Archaeplastida.
phyll c-containing plastids. However, the relationship of Since the relationships of these groups are not clear, they
these groups to each other remains unclear. Alveolata and are listed as incertae sedis eukaryotes; those without a known
stramenopiles can be summarised as ‘core Chromalveolates’ phylogenetic position.
which, along with the sister group Rhizaria, is known as the
SAR-clade.
The Haptophyta include algae-carrying plastids contain- arctica has alveoli beneath the cell membrane and tripartite
ing chlorophyll c. Studies indicate that Haptophyta and the hair on its longer flagellum.
SAR-clade are related. The Picozoa are a phylum of tiny flagellates that are only
Also, the Centrohelida as well as the flagellate group Tel- a few micrometres in size. They are among the smallest
onema are probably related to Haptophyta. known eukaryotes and are mostly found in the oligotrophic,
The Centrohelida comprise part of the organisms previ- cold coastal seas where they make up a significant part of the
ously known as Heliozoa (heliozoans). These spherical cellls biomass. They possess two flagella and their cells are divided
of roughly 30-80 µm in size are characterised by their radial into two hemispheres. The phylogenetic position of Picozoa
axopods, supported by microtubules placed in a triangular- is controversial.
hexagonal arrangement. These microtubules emerge from The Cryptophyta, also of controversial taxonomic af-
central tripartite granules (centroplasts). filiation, include the phototrophic Cryptophyceae and the
The genus Telonema is a deep-branching lineage of uncer- heterotrophic Kathablepharidaceae. They are thought to be
tain taxonomic affiliation. Telonema are bi-flagellated with related to Haptophyta, but some studies group them with Ar-
a proboscis-like structure and a complex skeleton made of chaeplastida instead.
microtubules and microfilaments. The species Telonema ant-
exudation: (Lat.: exsudatio = sweating out) process of emitting incertae sedis: (Lat.: incerta sedes = uncertain placement) un-
or losing organic molecules through a cell membrane certain systematic taxonomy
See also: Mycorrhizae: 4.2.2.2

Hacrobia 361
Haptophyta, Telonema, and Centrohelida lineage
Haptophyta
flagellates with two flagella, usually possessing a haptonema, mitochondria with tubular cristae,
plastids present
Pavlovophyceae
cell surface without scales
Prymnesiophyceae
cell surface with scales
Telonema
flagellates with two flagella, the longer of which has tripartite tubular hairs, possessing mitochondria with tubular cristae,
chloroplasts absent
Centrohelida
unicellular, spherical, possessing radial axopods (‘heliozoa’, ‘sun-animalcules’), axopods supported by a triangular or hexagonal
structure of microtubuli emerging from the central centroplast, flat mitochondrial cristae
Picozoa
picoflagellates (smaller than 3 µm) with two flagella, heterotrophic, marine, tubular mitochondrial cristae, chloroplasts absent
Cryptophyta
Cryptophyceae
flagellates with two flagella, cell wall of proteins (periplast), tubular mitochondrial cristae, plastids present
Cryptomonadales
plastids present and containing a nucleomorph
Goniomonadales
plastids absent
Kathablepharidaceae
flagellates with two flagella, marine and limnic, apical cytostome supported by longitudinal microtubules, cell membrane
thickened by lamellar casing, tubular mitochondrial cristae, chloroplasts absent
Much of primary production is released as dissolved organic carbon large part of primary production is released via the root system of plants
(DOC) as a result of exudation and cell lysis. This carbon is used by bac- and mycorrhizal fungi. Dissolved carbon and dead biomass is absorbed
teria, which are subsequently eaten by flagellates. In this way, only a by fungi and bacteria. Bacteria are consumed by gliding flagellates, such
small fraction of primary production is directly consumed by metazoans, as cercomonads, kinetoplastids, chrysophytes, and euglenoids, as well
whereas the majority is available indirectly via the microbial food web as amoebae (including Amoebozoa and Heterolobosea). The micro-
(‘the microbial loop’), which undergoes respiration during feeding rela- bial food web is vital for all soil ecosystems and a large part of primary
tionships within microbial communities of bacteria, flagellates, and cili- production is directly absorbed by microbial components. Water-filled
ates. Mesotrophic waters contain around a few hundred to a few thou- pores in soil are populated by around ten million bacterial and 10,000
sand algae per ml, one to three million bacteria per ml, approximately flagellate and amoebae cells, as well as several hundred nematodes per
1,000 flagellates per ml, and 100 ciliates per ml. In contrast, each ml con- gram of soil. Fungi in soil ecosystems provide a large part of the biomass,
tains only a few metazoans (usually fewer than ten rotifers per ml and though microbial components are of similar importance. In addition to
one or fewer – on average – small planktonic crustaceans [Cladoceran or these, apart from plant roots, only earthworms are quantitatively as im-
Copepods]). In ultraoligotrophic oceans, the abundance of these organ- portant in the soil environment.
isms is lower by one to two orders of magnitude, whereas in eutrophic
ponds, abundances are higher. Among the most important primary pro-
ducers are diatoms, dinoflagellates, and green algae, whereas the con-
sumer population is dominated by choanoflagellates, dinoflagellates,
bicosoecids, heterotrophic Chrysophyceae, and ciliates. In terrestrial
ecosystems, the most important primary producers are land plants. A
Eukaryotic biocenosis and the ‘microbial loop’

362 Megasystematics
4.7.1
Haptophyta
The Haptophyta make up a significant portion of marine The haptophytes possess secondary plastids surrounded
photosynthetic plankton. They colonise all of the oceans on by four membranes and containing chlorophyll a and c, as
Earth and, due to their large volume, play an important role well as the accessory pigments fucoxanthin or diatoxanthin.
as primary producers in the sea, although only a few can be The outer membrane of each plastid (one or two per cell)
found in freshwater environments. Around 500 haptophyte merges with the endoplasmic reticulum (the chloroplast-
species have been described. ER). Most haptophyte species are unicellular and phototro-
Haptophytes are characterised by cellulose plates, which phic, although some are colourless and phagotrophic.
cover the surface of their cells. These scales are formed by the They also feature a thread-like organelle (haptonema) in-
Golgi apparatus. In some haptophytes, known as the Cocco- serted between the two flagella of usually equal length. The
lithales (Coccolithophoridae), these scales are calcified and haptonema differs in structure and function to all other fla-
called coccoliths; these hardened plates can be traced back gella, consisting of six or seven microtubules and helping the
to the Carboniferous in the fossil record and dominate large cell attach to surfaces, move by gliding, and forage.
chalk deposits of the Cretaceous. However, the broad mor- Energy reserves are maintained in the form of chrysolam-
phological diversity witnessed in haptophytes grew out of inarin, oil, and sometimes paramylon (same in Euglenida).
the Mesozoic and Jurassic. These are formed outside plastids in vacuoles. Some species
also possess eye-spots (stigma).
Haptophytes are divided into the scale-bearing Prymne- na can also cause toxic blooms contributing to the mass mor-
siophyceae and the scale-free Pavlovophyceae. Some species tality of fish and other marine organisms.
are of global importance, particularly representatives of the Individual cells of the genus Phaeocystis (Phaeocystales;
Prymnesiophyceae: ‘foam algae’) can clump into gelatinous colonies, held to-
Emiliania huxleyi (Isochrysidales) is an important produc- gether by coiled chitin filaments protruding from the cell.
er of biogenic calcium carbonate, which is significant for the During a bloom, these cells release a conspicuous foam
fixation of global carbon reserves. The only 3–5 µm wide al- which depletes oxygen reserves in local waters. Phaeocystis
gae can multiply explosively under nutrient-rich conditions, also releases large quantities of dimethyl sulphide, a com-
forming algal blooms stretching for hundreds of square kilo- pound which aids in cloud formation and thereby the altera-
metres. Haptophytes can therefore have important economic tion of the climate.
consequences. Representatives of Coccolithales form calcified scales,
Prymnesium parvum (Prymnesiales) is known to attach it- sometimes making up a significant portion of economically
self to fish gills using the haptonema, secreting toxins that important materials, such as chalk.
can kill fish populations. Likewise, the genus Chrysochromuli-
acid rain: precipitation possessing a lower pH level than pure nanoplankton: (Grk.: planktos = errant) organisms between
rainwater (approx. pH 5.5) 4–40 µm which float/swim in water
ER: endoplasmatic reticulum toxins: (Lat.: toxicum = poison) poisonous substance produced
greenhouse gases: gaseous matter which absorbs infrared by living organisms
radiation emitted from the Earth, thereby contributing to the
warming of the atmosphere
See also: Biomineralisation: 4.5.2, 4.5.2.1; Cretaceous: 2.3.4.5

Hacrobia 363
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
Stra
onada
lveolata
men
Metam opile
a Ha s
zo
oa nta
bo pt
Cry
oe op
o
ok
Am hy
pto
is t
ta
soz
h
phy
Op
Apu
ta
Emiliania huxleyi Prymnesium parvum with hap- Pleurochrysis sp. Eubacteria Archaea
tonema
haptonema flagella
Golgi apparatus
plastids
cellulose scales
(when calcareous: coccoliths)
Haptophyceae algal bloom (top), coc-

mitochondrion coliths (middle), chalk cliffs (bottom)
Mass proliferation (blooming) is a common phe- months and may stretch from a few metres to
nomenon across different groups of organisms. It several hundred square kilometres in size. Vari-
occurs in insects (e.g. bark beetles, locusts), mam- ous species of cyanobacteria, chlorophytes, dino-
mals (e.g. lemmings, voles), and also in microor- phytes, and haptophytes are able to bloom mas-
ganisms (algal blooms). Blooms take place when sively and multiply. Some of these species produce
environmental conditions are favourable, leading toxic substances which, at high concentrations,
to a population explosion within a short period of may be harmful to other organisms. Blooms may
time. They may also be anthropogenically induced also reduce the light permeability of the water col-
as a result of environmental change. For exam- umn, changing the photosynthetic dynamics of the
ple, human impacts on the environment, which water body. Algal blooms also strongly influence
cause changes in the nutrient balance, introduce oxygenation of the oceans. They produce large
alien species, influence food chains (overfishing), amounts of oxygen during photosynthesis, leading
or change water system flows, may all contribute to supersaturated levels of dissolved oxygen in the
to creating blooms. Blooms may also be naturally water column. Conversely, during respiration, algal
induced primarily through climatic influences, blooms remove oxygen from the water column,
such as changes to ocean currents, water column leaving little behind for other organisms.
stratification, solar radiation, water temperature,
and the input of nutrients from land or rivers. Al-
gal blooms may persist for days or even several Algal blooms: cyanobacteria (top) and
dinoflagellates (bottom: Noctiluca)
Algal blooms
364 Megasystematics
4.7.2
Cryptophyta
Cryptophyta (cryptophytes) include the heterotrophic nucleus from the red algal symbiont), are visible between
Kathablepharidaceae, the genus Goniomonas, as well as the the second and third membranes. The nucleomorph itself
Cryptophyceae discussed here. As with the haptophytes, contains only three chromosomes. The outermost plastid
the taxonomic position of cryptophytes remains unknown, membrane is connected to the nuclear membrane and the
though they are thought to be related to Archaeplastida. endoplasmic reticulum.
Cryptophyte species are unicellular protists which colo- Unlike in cyanobacteria and red algae, the water-soluble
nise marine and freshwater. They can reach high abundance phycobilins of cryptophytes are not organised in phycobili-
levels and therefore make up a high relative biomass despite somes. The one or two chloroplasts per cell are, depending
their small size of under 50 µm. Sixteen genera with around on their accessory pigments, coloured differently (blue, blue-
200 species of cryptophytes have been described. green, reddish, red-brown, olive-brown, brown, or yellow-
Many of these are specialists in low-light conditions, sur- brown).
viving as a result of the particular photopigments targetin the Colourless, phagotrophic cryptophytes also exist, which
‘green gap’ of chlorophylls. They are therefore able to form still contain reduced secondary plastids with a nucleomorph
denser populations at relatively greater depths within the wa- and plastid. Three lineages of such cryptophytes are known
ter column, near the chemocline. They can also survive and to exist; these lineages were formerly combined in the genus
multiply under ice during winter. Chilomonas.
Cryptophyceae obtained plastids with chlorophyll a and A number of species from other groups, including the cili-
c2 with four membranes through secondary endocytobiosis ate Mesodinium and various dinoflagellates, use cryptophytes
of a red algae. Starch grains and a nucleomorph, a reduced or their plastids as endosymbionts or as kleptoplastids.
Cryptophytes have a periplast instead of a cell wall. The The main furrow system is inwardly densely lined with
periplast is a three-layered structure consisting of inner and large ejectosomes (explosive organelles). Further more, ejec-
outer protein layers (or protein plates) with a protein mem- tosomes, invisable by way of conventional microscopy, of
brane embedded in between the two. the same type are scattered underneath the periplast. Ejec-
In addition, cryptophytes are characterised by two dis- tosomes consist of two spirally wound bands which, when
tinctly different flagella, emerging from an invagination in chemically or mechanically stressed, sling the ejectosomes
the cell. The longer flagellum has stiff bipartite hairs (com- projectile. The specific function of ejectosomes is still un-
prised of a shaft and terminal filaments) on both sides and clear, although they may possibly serve as a defence mecha-
beats back and forth for locomotion to pull the flagellum (lo- nism against predators.
comotive flagellum). In contrast, the shorter flagellum only Cryptophyte cells are asymmetrical, causing them to ro-
has one row of hair; the genus Goniomonas has hairs on only tate around their longitudinal axis and rock back and forth
one flagellum. as they swim.
chemocline: the sudden point of division between bodies of periplast: intracellular layer made of protein plates which form
water differing in chemistry within the water column a strong cell membrane
kleptoplastidy: process in which plastids are sequestered by phytoplankton: (Grk.: phyton = plant, planktos = drifting)
an organism but are not passed on to the next generation (not phototrophic organisms which float in water (plankton)
endosymbiosis)
See also: Nucleomorph: 4.5; Secondary endocytobiosis: 2.2.2.5, 4.1.2.3; Tripartite hair: 4.6
Hacrobia 365
stida Rh
pla iza
ae
Viridiplant ta
ria
oa
h
rc
Rh
z
G
Cerco
odo
la
uc ria
ta
op Re
phy
Chr
hy
ae
Disc ta
Excavata
oba olata
oma
Alve
Stra
onada
lveolata
men
Metam opile
a Ha s
zo
oa nta
bo pt
Cry
oe op
o
ok
Am hy
p
is t
ta
top
soz
h
Op
h
Apu
yta
Eubacteria Archaea
Cryptomonads: Chroomonas sp. (left) Periplast (cell envelope) from Cryptomonas sp.
and Goniomonas sp. (right)
Golgi apparatus
nucleus
70S ribosomes
chloroplast-endoplasmic thylakoid
reticulum (CER)
nucleomorph
80S ribosomes
pyrenoid
Cryptomonas ovata
mitochondrion
Many protists have scales or other surface structures. The cryptophytes have relatively
small scales, which sit on their cell surface as well as on the flagella. Haptophytes
are covered in scales, which sit on the outside of the cell and are made of polysac-
charides. These are formed in the Golgi apparatus and transported to the cell surface
before being deposited there. In the order Coccolithophorales (Haptophyta), these
scales are encrusted with lime. These calcified scales (coccoliths) account for a signifi-
cant proportion of the material making up calcareous sediments, such as chalk. The
Prasinophyceae (Chlorophyta) have organic scales on their cell surface as well, and
are also formed within the Golgi apparatus (left: electron microscopic section through
the cell membrane of Mesostigma viride (Streptophyta) with sectioned surface scales.
The Baccillariophyceae (diatoms) have scales made of silicate. Some chrysophytes also
possess scales made of organic material or silicates (top right: individual silicate scale;
below: arrangement of scales around a cyst). These are formed in special vesicles
(SDVs: silica deposition vesicles) and emerge from the Golgi apparatus. The Dinophyta
are usually also surrounded by cellulose scales; however, these do not sit on the cell
surface but are found within the alveoli (alveolar plates).
Surface scales
Glossary 367
Glossary
16S: the small subunit of prokaryotic ribosomes, as well as plastids alveoli: (Lat.: alveus = cavity) hollow cavities (e.g. alveolar sacs in
and mitochondria with a sedimentation coefficient of 16 Sved- lungs)
berg (S) units ambulacral grooves: grooves running along the radial arm of an
18S: the small subunit of eukaryotic ribosomes with a sedimentati- ambulacral system
on coefficient of 18 Svedberg (S) units ambulacral system: system for channeling coelom fluid in echi-
70S-ribosome: prokaryotic ribosome with a sedimentation coef- noderms
ficient (S) of 70S; mitochondrial and plastid ribosomes also be- amniotes: vertebrates in which the embryo is surrounded by an
long to the 70S type due to their origin additional covering called the amnion – including reptiles, birds
abiotic: (Grk.: a = not, bios = life) not living and mammals
accessory pigments: antenna pigments which capture light and amorphous: unformed, shapeless
generate the energy necessary for photosynthesis anaerobe: (Grk.: an = not, aer = air, bios = life) processes or orga-
achene: fruit of the Asteraceae nisms which can survive without molecular oxygen
acid rain: precipitation possessing a lower pH level than pure rain- anapsids: monophyletic group of amniotes with skulls which have
water (approx. pH 5.5) no temporal fenestrae; extinct group of reptiles
acidophile: preferring low pH conditions anatexis: partial melting of rocks in the continental crust during
acoelomate: not possessing a coelom (a fluid-filled, sealed secon- high-grade regional metamorphism
dary body cavity) anisokont: flagella of differing length
Acrisol: extensively eroded, red-coloured acid soil with accumu- annual plants: yearlings, annuals
lated subsurface layers of clay, this soil group is produced by anoxia: the total depletion of oxygen
extensive leaching anoxygenic: producing no molecular oxygen
acrodont: dentition in which the teeth have no roots and are antheridium: male reproductive organ in land plants
fused to the jaw bone at their base anthropogenic: (Grk.: anthropos = man, gen = cause) caused,
adaptation: the process of adapting influenced, brought about by human beings
adaptive mutation: mutation resulting in improved adaptation aperture: germination pore on the wall of a pollen grain
adaptive radiation: the emergence of a multitude of new life aphotic zone: the deep water layers which sunlight fails to pe-
forms from a single ancestor as the result of adaptation to diffe- netrate
rent ecological environments apical: (Lat.: apex = peak) pertaining to the apex
adaptive zone: the combination of environmental conditions or apical complex: an organ complex of the Apicomplexa on the
ecological niches respectively, which are occupied by species tapered end of the cell containing: polar rings, rhoptries and
that exploit the same resources in a similar way conoids
adhesion: (Lat.: adhaesio = adhere) the way in which two cells, apicoplast: a derived plastid found in Apicomplexa
substances or particles cling to one another apomorphy: a trait that is newly derived in the phylogenesis of
adventitious root: plant root developing from stem or leave tis- taxa which was not present in their ancestors
sue or as the result of a wound aragonite: an orthorhombic crystal made of calcium carbonate
aerobe: (Grk.: aer = air, bios = life) processes or organisms requi- (CaCO3)
ring an oxygenated environment archegonium: female reproductive organ in land plants
agglutinated: consisting of clumps of particles arid: dry
aggregation: (Lat.: aggregatio = accumulation) accumulation, arillus: seed coat (fleshy covering)
clustering articulated: possessing a joint permitting angular movement
air embolism: embolism (blockage in a vessel) caused by an air ascocarp ( = ascoma): fruiting body of the ascomycete
bubble in the vascular system assimilation: conversion of matter from the environment into the
aldehyde: organic compound containing an aldehyde group body's own materials
(-COH- group) ATP: adenosine triphosphate – transporter of energy within cells
algae: photoautotrophic, eukaryotic organisms not belonging to autapomorphy: describes an apomorphic feature unique to one
land plants; ecology usually classifies cyanobacteria as algae as species or one terminal monophyletic taxon
well autospores: daughter cells are formed within the mother cell wall;
Alisol: acidic soil caused by leaching with accumulated subsurface autospores resemble the mother cell
layers of clay, less eroded than Acrisols autotrophy: (Grk.: autos = self, trophe = nourishing) the ability
alkaliphile: preferring high pH conditions of organisms to produce and store organic nutrients exclusively
allantois: embryonic urinary bladder from anorganic substances
allorhizy: term given to plants with different primary and secon- axostyle: a sheet of microtubules forming a thin rod behind the
dary roots main body
Baltica: continental plate covering northern and eastern Europe

J. Boenigk et al., Biodiversity and Earth History, DOI 10.1007/978-3-662-46394-9
368 Glossary
banded iron: (mainly Precambrian) marine sedimentary rock con- capsoid (capsal): category of algae in which the flagella are large-
taining iron-rich layers ly reduced; cells embedded in gelatin
basal body: centriole at the base of the eukaryotic cilium or fla- carbonisation: formation of organic fossil materials releasing wa-
gellum ter, CO2 and hydrocarbons and leaving almost only pure carbon
basalt: volcanic, finely crystalline rock of mafic composition carnivorous: (Lat.: carnivorus = meat eating) consuming meat
base triplet: a series of three bases (nucleotides) in DNA or RNA carotenoid: a type of terpene, the liposoluble accessory pigments
which code for a specific, single amino acid in photosynthesis
benthic: benthic organisms live on or in the sediment at the bot- carpel: (Grk.: karpos = fruit) organs of a flower with one or more
tom of a body of water ovules
binary (binomial) nomenclature: in taxonomy, the system of carposporophyte: formed by the fusion of haploid gametes in
giving species a name composed of two parts identifying both the three-stage lifecycle of red algae
the genus and the epithet catalysis: (Grk.: katalysis = dissolution) bringing about, accelera-
biodiversity: (definition given by the UN Convention on Biological ting or decelerating a chemical reaction using a catalyst
Diversity) the variability among living organisms from all sources cell adhesion: state of binding between cells
including, inter alia, terrestrial, marine and other aquatic eco- Cenozoic Era: most recent era in Earth’s history (covering the last
systems and the ecological complexes of which they are a part; 66 million years)
this includes diversity within species (genetic diversity), between centrioles: cell structures involved in forming the spindle appa-
species (diversity of species) and of ecosystems (and the interac- ratus
tions contained within them). centripetal: from the outside to the centre
biogenic: (Grk.: bios = life) of biological or organic origin chelicerae: mouth parts of the chelicerata
biostratigraphy: a branch of stratigraphy assigning relative ages chemical weathering: processes leading to the chemical alterati-
of rock strata using fossils on or dissolution of minerals
biotic: (Grk.: bios = life) living chemocline: the sudden point of division between bodies of wa-
bipedal: locomotion by means of two legs ter differing in chemistry within the water column
bitumen: (Lat.: bitumen = earth pitch) organic mixture formed chemoorganotroph: organisms that obtain their energy from
from petroleum oxidising organic electron donors
bituminous slate: oil slate, a soft form of clay slate impregnated chorda dorsalis: notochord; internal axial skeleton of all chor-
with bitumen dates
blastopore: embryonic mouth chorion: outer membrane around the amniotic sac surrounding an
bothrosomes: organelles of the labyrinthulomycetes, which se- embryo in vertebrates
crete the exoplasmic polysaccharide filaments surrounding the Chromalveolata: a supergroup including all organisms contai-
cells ning plastids with chlorophyll c (Alveolata, Stramenopiles, Hap-
branchial gut: part of the foregut containing gill slits. The gill slits tophyta, Cryptophyta); strictly speaking, only the Alveolata and
enable the animal to breathe as well as extract particles of food Stramenopiles, because the taxonomic status of the Haptophyta
from water through a process of filter-feeding and Cryptophyta have not been clarified
browning: process of soil formation in which iron compounds chronostratigraphy: the geological discipline that classifies the
form, thus influencing the colour of the soil age of rocks according to time and in relation to their absolute
bryozoa: moss animals, classified among the protostomes age; subdiscipline of stratigraphy
buccal pumping: (Lat.: bucca = cheek) a form of breathing using chrysolaminarin: a storage polysaccharide found in stramenophi-
the cheeks only (in amphibians) in which the animal raises and les; β 1-3- and β 1-6-glycosidic bonds
lowers the floor of its oral cavity and contracts its trunk muscu- circumpolar: surrounding one of the Earth’s poles
lature in order to pump air between the lungs and oral cavity cisterna: an individual membrane-enclosed disc in a dictyosome in
while its mouth is closed the Golgi apparatus
bundle sheath cells: cells surrounding the vascular tissue of clastic sediments: rock fragments consisting of other rocks and
plants minerals which have been subject to mechanical destruction
burial metamorphism: metamorphism caused when rocks are clayification: process of soil formation yielding smaller clasts as
buried at great depth in the ground the result of silicate weathering and the new formation of clay
buttress root: large, rib-like roots arranged in a star formation minerals
around a tree to increase stability coccoid (coccoidal): class of algae which are spherical in shape,
C5-sugar: sugar molecule with five carbon atoms without flagella and with a single cell wall
Calcisol: soil that possess a strong secondary calcic horizon coelom: (Grk.: koiloma = cavity) secondary body cavity completely
calcite: trigonal crystal made of calcium carbonate (CaCO3); cons- lined with mesodermal cells
tituent of numerous biogenic sediments coenobium: a colony containing a fixed number of cells often em-
Calvin Cycle: a series of reactions during photosynthesis in which bedded in mucilage
carbon dioxide is converted into carbohydrates coiled: flat, spiral shape
CAM: (Crassulacean Acid Metabolism) temporal division between Coleoptera: order of beetles
carbon fixation and the Calvin cycle columella: central column in the spore-case of mosses
Glossary 369
commensalism: symbiotic relationship between two organisms cytosol: (Grk.: kytos = cell, kinisis = dissolve) liquid portion of the
from different species in which one partner benefits and the cytoplasm of a cell
other neither benefits nor suffers any disadvantage cytostome: cell mouth in protists
compaction: the process in which increased stress levels cause decomposers: organisms that live on dead or decaying organisms
sediment to densify and consolidate and which are involved in the process of decomposition
companion cells: cells forming a complex with the sieve-tubes of dentate leaf: leaf possessing rounded notches between the teeth
the magnoliopsida on its fringes
compartmentalisation: (Lat.: compartere = to divide) division desilification: part of the process of silicate leaching which pro-
into separate, closed spaces duces orthosilicic acid
conglomerate: hardened clastic sediment with clasts >2 mm, desmin: homopolymer, constituent of a cytoskeleton
fragments usually rounded detoxification: process of detoxifying
conidia: type of spore in fungi (Ascomycota and Basidiomycota) detritivore: feeding on organic detritus and decomposing plant
and in prokaryotes of genus Streptomyces; characteristic of the and animal matter
biological dispersal of fungi; the spores are formed outside the detritus particles: (Lat.: detritus = rubbing away) small particles
sporangium after developing specialised hyphae, or on conidio- of organic origin
mata diagenesis: compression of sediments by lithification; chemical,
conjugation: transfer of DNA to another cell by means of a plas- physical or biological change at relatively low temperatures
ma bridge diapsids: amniotes that have developed two fenestra in the cheek
conodonts: toothlike structures made of apatite and layers of or- and temple regions; includes most recent reptiles as well as di-
ganic material, probably from basal chordates nosaurs and birds
conoid: structure consisting of spirally-arranged microtubuli in the dichotomous: (Grk.: dichotomos = in two parts) splitting of a
apical complex of the Apicomplexa shoot axis into two parts
consumers: (Lat.: consumere = to consume) heterotrophic orga- dictyosome: stack of cisterna enclosed in a sac – the totality of
nisms which feed on other organisms dictyosomes constitutes the Golgi apparatus
contact metamorphism: metamorphism caused by temperature differential interference contrast: technique used in optical
increases due to hot magma microscopy in which differences in the optical path length are
continental shelf: underwater landmass extending out from the changed into levels of enhanced illumination
edge of a continent (up to a depth of 200 m) diplobiontic: organisms with two generations (a haploid and di-
contractile vacuole: a type of vacuole which uses a process of ploid generation)
contraction to expel excess water from the cell diploid: (Grk.: di = two) double set of chromosomes
convection: circular movement within fluids due to differences Diptera: order of two-winged insects (flies and mosquitoes)
in density dissociation: separation of salts into ions, or of a molecule into its
converge: (Lat.: convergere = incline towards) to move together, constituent elements
to herd, to rally α-diversity: punctual diversity, diversity in a habitat
convergence (evolutionary): similar characteristics which have β-diversity: difference between α- and γ-diversity, that part of
developed independently in unrelated taxa γ-diversity (i.e. the diversity in a region) which is not part of
cormus: (Grk.: kormus = stump) plant body divided into root, lea- α-diversity (i.e. the diversity of a certain habitat)
ves and shoot axis γ-diversity: regional diversity; diversity of a landscape
cosmopolitan: found all over the world DNA bank: institution in which DNA samples extracted from orga-
costa: rod-like structure consisting of proteins at the base of the nisms can be stored for future testing
undulating membrane, movable in some species DOC: dissolved organic carbon
craton: continental shield; central region of a continent which was domain: the highest classification of an organism: eukarya, bac-
formed in the early Precambrian and which has suffered no tec- teria and archaea
tonic deformation since the Precambrian dominance structure: frequency distribution (dominance) of the
cristae: (Lat.: crista = comb, crest) numerous folds on the inner various species in a habitat
membrane of mitochondria Doushantuo-Formation: a fossil Lagerstätte of the Ediacarium
cuttlebone: brittle gas-filled structure used for buoyancy in Sepi- geological period in Guizhou Province, China
ida (e.g. cuttlefish) drifting: passive distribution of organisms in their different mor-
cyst: resting stages in single-celled organisms, plants and animals, phological phases
which develops during unfavourable environmental conditions dynein: one of the motor proteins in eukaryotic cells which enab-
(also used for reproduction or dispersion) les movement of the flagella and other functions
cytokinesis: (Grk.: cytos = cell, kinesis = movement) cell division ecdysone: hormone in Ecdysozoa inducing moulting, metamor-
cytoplasm: cell contents excluding cell nucleus and organelles phosis and reproduction
cytoskeleton: network of microtubules and microfilaments which ECM: extra cellular matrix
serves to provide shape, mechanical resistance to deformation, ecological fitness: adaptation of an individual to its environment
and aids cell migration; it aids intracellular transport and mo- ecoregion: a relatively large area of the earth’s surface 'containing
vement. a geographically distinct assemblage of species, natural commu-
nities, and environmental conditions' (WWF definition); the term
370 Glossary
‘ecoregion’ was originally used in the context of geographical erosion: exogenic processes leading to the removal of soil and
scholarship (meaning a 'recurring pattern of ecosystems associ- rock from the Earth’s surface and its transportation from one
ated with characteristic combinations of soil and landform that location to another
characterize that region') erythrocytes: (Grk.: erythros = red, kytos = container) red blood
ectoderm: (Grk.: ektos = outside, derma = skin) the first or ou- cells
termost germ cell layer which differentiates to form the skin, estuary: (Lat.: aestuarium = bay) broad body of water where a
nervous system and sensory organs river flows into the sea
elaters: spiral-shaped cells in plant spore capsules which serve to euphotic zone: the uppermost layer of water, the sunlight zone
disperse spores eusporangiate: wall of the mature sporangium arising from se-
electron microscopy: a form of microscopy which reveals the veral cell layers
surface or the interior of an object using electrons instead of euthermic: maintaining an optimal temperature
light; an electron microscope achieves a much higher resolution evaporation: vaporisation of moisture from unvegetated land or
than light microscopes the surface of a body of water
ellagic acid: a polyphenol exoskeleton: (Grk.: exo = outside, skeletos = frame) external sup-
emulsifier (emulgent): an agent which enables two normally un- port structure (e.g. shells in molluscs and brachiopods)
mixable materials to be mixed together and stabilised extinction rate: number of species that become extinct in a given
enation: (Lat.: enatere = float out) formation of outgrowths on time period (year, decade…)
the surface of leaves extrapolation: process of estimating variables outside a given in-
endemic: occurrence of organisms within a defined restricted geo- terval based on the known variables inside the interval
graphical area extremophile: organisms which thrive in extreme environmental
endobenthic: living in the sediment conditions
endocommensalism: (Grk.: endon = inside, skeletos = frame: exudation: (Lat.: exsudatio = sweating out) process of emitting or
com = together, mensa = table) commensal relationship inside losing organic molecules through a cell membrane
the body of the host; for one partner the commensal relation- facies: characteristics of rocks related to the history of rock for-
ship is beneficial, for the other it is neutral mation
endocytobiosis: the term given to the absorption of prokaryotes faunal provinces: a term similar in meaning to fauna kingdoms;
by eukaryotic cells and their subsequent evolution into organel- regions that differ markedly from other regions due to their en-
les. This term is more precise than endosymbiosis because, in the demic taxa
case of organelles, they are no longer independent organisms felsic: coinage from feldspar and quartz (silicate); light coloured,
and therefore do not conform to the definition of symbiosis as igneous minerals rich in silicic acid
being the association of cells of different species fertile strobili: fertile cones
endoderm: (Grk.: endon = inside, derma = skin) inner germ cell fertility: the ability to produce offspring
layer which differentiates to form the respiratory system and the flagellin: a protein used as a building block for bacterial flagel-
digestive tract la in contrast to eukaryotic flagella, flagellin is not associated
endophytes: organisms which live on the inside of a plant in with motor proteins – independent movement is therefore not
which the relationship between plant and organism can be eit- possible
her symbiontic or parasitic flood basalts: usually the result of inviscid lava flows, coating lar-
endoskeleton: (Grk.: endon = inside, skeletos = frame) inner sup- ge expanses of land with basalt lava
port structure (e.g. bones in vertebrates) floristic kingdom: biogeographical region that differs markedly
endosymbiotic bacteria: symbiotic bacteria living in other or- from other regions due to its endemic floristic taxa
ganisms flower constancy: preference of individual pollinators for the flo-
endothermic: regulation of body temperature from within (such wers of specific plant species
animals are usually warm-blooded (homeothermic)) fluviates: stones carried downriver by currents
ephemeral: (Grk.: ephemeros = for one day) having a short life flysch: sequence of claystone and sandstone formed during oroge-
span nesis in a deep marine facies
epibenthic: on the bottom of a body of water (in contrast to end- foliose: a growth form with leaf-like structures
obenthic: in the sediment at the bottom of a body of water) food vacuole: vacuole which has formed by phagocytosis within
epilithic: (Grk.: epi = on, litho = stone) growing on the surface which food particles are digested by lysosomal enzymes
of rocks founder population: usually just a few individuals of a species
epiphytic: (Grk.: epi = on, phyton = plant) growing on plants which become established in a new area and form the basis of a
epithelium: tissue which lines cavities; the outermost cell layer or new, larger population
layers in Metazoa frost dessication: dessication (of plants) due to a lack of water
equinox: point in time at which the sun stands directly above the as the result of frost, and simultaneous loss of water due to
equator when day and night are of equal duration transpiration
ER: endoplasmatic reticulum gallery forest: a forest which forms a corridor along a river, bor-
erniettomorphs: sessile, flat but non-fractal forms of Ediacaran dering on a landscape with markedly different vegetation, a dif-
fossils ferent type of forest, or no vegetation
Glossary 371
gametangium: (Grk.: gamos = wedding, marriage) organ in hematite: Fe2O3, a common iron oxide
which the gametes are formed in sexual reproduction hemicryptophytes: plants with a growth-point (bud) near the
gametangiogamy: growing together and fusion of two entire soil surface
gametangia hemiparasite: parasitic plants which obtain water and nutrients
gamete: haploid reproductive cell from their host but which are still capable of photosynthesis
gametocyte: sex type developing from merozoites themselves
gametophyte: the gamete-forming, haploid stage in the change herbivores: (Lat.: herba = plant, vorare = to eat) plant-eaters:
of generations in land plants animals subsisting exclusively on plants
ganglion: a nerve cell cluster, also known as a nerve-knot heterokonts: term referring to differently shaped flagella, espe-
gap junctions: protein channels between the membranes of two cially in stramenophiles
adjacent animal cells heterophasic: generational change between the haploid and the
gastrolith: hard objects, usually rocks, which are swallowed by diploid generations
vertebrates to help them grind food in their gizzard heterospore: possessing different spores
generalists: organisms able to survive under a variety of condi- heterotrophy: (Grk.: heteros = different, trophe = nutrition) abi-
tions lity of organisms to use existing organic carbon to form nutri-
geochronology: the science of dating the absolute temporal age ents and store energy
of rock layers hibernation: active/passive strategy for surviving winter in selec-
geophyte: plant with concealed storage organs ted mammals
germ layer: in animals, the three embryonic tissue types (ecto- histones: basic proteins forming part of the structure of nucle-
derm, endoderm and mesoderm); in plants, cotyledons are osomes
known as seed leaves holoparasite: parasitic plant which is completely dependent on its
glacial: (Lat.: glacies = ice) interval of time marked by cold tem- host and is incapable of photosynthesis
peratures holotype: a single individual organism which was used as the
glacial till: heterogeneous glacial sediment which has been abra- name-bearing type when a species or sub-species was first de-
ded and deposited by a glacier scribed
Glossopteris: dominant plant genus on the Gondwana continent homeothermy: the ability to maintain a stable body temperature
during the Permian period hominisation: the evolution of modern man, particularly in the
glucan: glucose-based polysaccharide last five to seven million years, including the development of
glycocalyx: capsule or plasma coating; coating on the surface of physical and mental characteristics such as the ability to walk
the cell membrane or cell wall upright and an enlarged brain
glycogen: reserve polysaccharide in unikonts; linked by α (1-3) and homorhizy: phenomenon in plants where all of the roots stem
α (1-6) glycosidic bonds; similar to but more extensively bran- from the shoot
ched than starch Horizontal Gene Transfer (HGT): the transfer of genes between
glycoproteins: macromolecules consisting of a protein and car- organisms without reproduction; also between species
bohydrate groups hotspot: limited, stationary geographical location with anoma-
gradualism: concept in evolutionary theory assuming that the lously hot areas in the asthenosphere due to mantle plumes
rate of evolutionary change is (roughly) constant, and that va- hotspot volcanism: particularly active volcanism at hotspots,
riation takes place across several continuous processes rather also at great distances from the edges of tectonic plates
than in sudden leaps forward HOX genes (homeotic genes): genes which are responsible for
graptolites: extinct fossil colonial animals with a chitin-like exo- controlling particular segment structures and the head-tail axis
skeleton (thecae) humid: relatively high level of water vapour in the atmosphere
Great Oxidation Event: great oxygen crisis 2.45 billion years ago humin: high-molecular weight substances in humus soil types, in-
caused by the appearance of dioxygen cluding humins (insoluble), fulvic acids (soluble in alkali, acid
greenhouse gases: gaseous matter which absorbs infrared radi- and water) and humic acids (soluble in alkali)
ation emitted from the Earth, thereby contributing to the war- humus: the totality of dead organic matter in soil
ming of the atmosphere Hun-Superterrane: small terrane which split from Gondwana in
gynoecium: (Grk.: gyne = woman, oikos = house) collective term the late Silurian
for the parts of a flower that produce ovules Huntington / Chuckanut Formation: 1.2 billion-year-old fluvial
habitat: area inhabited by a particular species sedimentary formation in Canada (Summerset Island, Nunavut,
habitat fragmentation: process by which habitat loss results in Canada)
the division of large habitats into a greater number of smaller hyaline: with a glassy or translucent appearance
patches hybrid: (Lat.: hybrid = mixture) offspring resulting from cross
halophile: preferring high salt concentrations breeding by parents of different species
haplobiontic: organisms with either one haploid or one diploid hydrogen carbonates: simple salts in carbonic acids containing
generation, but not both the HCO3– anion
haploid: (Grk.: haploeides = simple) a single set of chromosomes hydrogen carbonate anion: HCO3–
heavy rain: intensive precipitation over a certain time span; over hydroids: non-woody cells in mosses for transporting water
10mm precipitation per hour
372 Glossary
hydrolysis: (Grk.: hydro = water, lysis = separation) cleavage of kleptoplastidy: process in which plastids are sequestered by an
molecules through a reaction with water organism but are not passed on to the next generation (not en-
hydronium ion: positively charged water molecule (H3O+) dosymbiosis)
hydrothermal: relating to the action of heated water in the Lagerstätte: (German: Lager = storage; Stätte = place) is a sedi-
Earth’s crust (under pressure to temperatures above 100 °C) mentary deposit that exhibits extraordinary fossils with excepti-
hymenium: tissue layer where meiospores develop in basidiomy- onal preservation. In German the corresponding term would be
cetes and ascomycetes Fossillagerstätte whereas Lagerstätte in German refers to diffe-
Hymenoptera: order of flying insects (bees and wasps) rent kinds of deposits including ore deposits
hypha: filamentous structure in fungi which grow at the tip and lateral: sideways or a side part of something
remain unbranched or branch laterally latitudinal: distance north or south of the equator measured
hypodermal endothecium: fibrous layer under the epidermis of along a meridian
pollen sacs in Magnoliopsida Laurentia: North American continental shield
Iapetus: early Paleozoic ocean between Baltica and Laurentia bet- leaching: the loss of fine nutrients from the soil due to water see-
ween 700–400 million years ago ping into the ground from the upper soil horizon
idioblast: cells that differ in form and/or function from their leaf litter: mostly undecayed dead plant material on the ground
neighbours in surrounding tissue Lepidoptera: Insect order which includes butterflies and moths
igneous rock: rock formed by the solidification of lava leptosporangiates: sporangia consisting of a single layer of cells
incertae sedis: (Lat.: incerta sedes = uncertain placement) uncer- life: life is a self-sustaining system capable of Darwinian evolution
tain systematic taxonomy (working definition used by NASA)
indehiscent fruit: fruit which does not open at maturity life form: integrates organisms with a similar morphological struc-
index fossils: fossil types and species which are particularly well- ture and way of life; term most frequently used in botany
suited to correlating different sediments; they can be easily lignin: (Lat.: lignum = wood) various phenolic macromolecules
identified at the species level, have a broad geographical distri- which are stored in the cell walls of plants and which make them
bution, are widespread and existed within a narrow time period woody
infertility: the inability to produce offspring ligule: part of the leaf at the junction of sheath and leaf
infraciliature: the entire root structure of cilia in ciliates lithostratigraphy: spatial and temporal classification of rock
to ingest: consume, take in strata based on the characteristics of the rock; subdiscipline of
integument: (Lat.: integumentum = covering, shell) protective stratigraphy
layer covering the ovule loamification: process of soil formation yielding smaller clasts as
interglacial: interglacial period; warmer period between two gla- the result of silicate weathering and the new formation of clay
cial periods minerals
interstitial: fluid-filled porous spaces in aquatic sediments lobe: clearly identifiable anatomical extension or projection
Intertropical Convergence Zone (ITCZ): low-pressure trough lobe lines: suture lines between the shell and the chambers in the
near the equator where the northeast and southeast trade phragmocone (septa) in fossil Ammonoidea and nautiloids
winds converge loess: aeolian sediment (without layers) consisting of silt
intraspecific: occurring or existing within a species or between longitudinal: relating to length or longitude
individuals of the same species lorica: shell-like, protective outer layer in various protists
intron: uncoded genetic sequence lying between two encoded ge- luciferin: compounds which generate light (bioluminescence)
netic sequences (= exons) Luvisols: soil with eluvial horizons which are not as leached or
involucre: protective structure made of bracts in certain flowering acidic as acrisol
plants mafic: dark, rock-forming minerals which are rich in magnesium
isoprenoids: natural compounds arising from isoprenes (2-me- and iron (Lat.: ferrum)
thyl-1.3-butadiene) mangrove: ecosystem in tropical mangroves; saline-tolerant trees
isospory: having identical spores and shrubs in a mangrove
isotherm: (Grk.: isos = same, therme = heat) line on a map indi- mannan: β (1-4) linkages
cating the same temperature mastigonemes: (Grk.: mastigo = thread, whip) hairs which cover
isotope: different variants of an element which have the same flagella
number of protons in each atom but which differ in neutron megafauna: large or giant species of animals from the Neogene
number and the early Quaternary
karyogamy: fusion of two nuclei meiosis: (Grk.: meiosis = lessening) cell division in which the num-
kinetid: structure in eukaryotic cells used for locomotion ber of chromosomes is halved
kinetoplast: network of circular DNA in the mitochondrium of ki- meiospores: spores produced by meiosis
netoplastids mesoderm: (Grk.: derma = skin) middle germ layer in embryo-
kinetosome: basal body of flagella; kinetosomes consist of a cy- blasts; the mesoderm forms muscles, skeleton, vascular system,
lindrical array of microtubules; they serve as a nucleation site for excretive organs, and part of the gonads
the microtubules of flagella and cilia mesophilic: preferring moderate conditions (mostly in respect to
temperature and humidity)
metamerism: having a series of repeated segments
Glossary 373
metamorphic rock: rock formed by being subjected to high pres- NADPH: reduced form of nicotinamide adenine dinucleotide phos-
sure or temperatures without losing its solid form phate (NADP)
metamorphism: (Grk.: metamorphosis = transformation) Altera- Nagelfluh: (regional Germanism) geologically recent conglomera-
tion of the composition or structure of rock, usually by heat, te consisting of compacted pebbles
pressure, or other natural phenomena nanoplankton: (Grk.: planktos = errant) organisms between
metanephridia: excretory glands connected to the coelom by a 4–40µm which float/swim in water
ciliated funnel; filtration takes place by the blood vessels near nemoral: deciduous
the metanephridia using blood pressure; the nephron, as the neural tube: first stage in the formation of the central nervous
functional and anatomical unit in vertebrates, originates from system in the embryonic development of chordates
the metanephridia neurocranium: part of the skull protecting the brain
metapopulation: group of several individual populations bet- niche: (Lat.: nidus = nest) totality of abiotic and biotic factors
ween which gene flow is restricted which are necessary for a species to survive and reproduce
methane clathrate: (Lat.: clatratus = latticed) also methane hy- nitrogen oxides: gaseous compounds of oxygen and nitrogen
drate; clathrates are chemical substances in gases (in this case norm of reaction: width of phenotypic variation which can deve-
methane) which trap host molecules (in this case water) in a lat- lop from a distinct genotype
tice. Methane clathrates exist in permafrost and on the sea-bed notochord: cartilaginous skeletal rod supporting the body in all
microaerophiles: organisms that require oxygen to survive but in embryonic and some adult chordate animals (=Chorda dorsalis)
smaller concentrations than are present in the atmosphere obligate endoparasite: (Lat.: obligare = to bind, to tie) parasites
microgametocyte: male gametocyte living inside their host and are totally dependent on their host,
microphyll: small leaves with a single, unbranched vein i.e. they cannot survive independently
micropyle: canal between the integuments at the tip of the ovu- obligatory: necessary, essential
lum in seed plants oil shale: sedimentary rock rich in liquid or gaseous hydrocarbons
microtubules: protein filaments which, together with microfi- ontogeny: the individual development of an organism
laments and intermediate filaments, serve to maintain a cell’s oocyst: (Grk.: oo = egg, kystis = bladder) developmental stage of
structure, to facilitate intracellular transport and the cell’s ability the apicomplexa containing sporocysts
to move oogamy: fertilization of the ovum; union of an egg cell (large, im-
microvilli: membrane protrusions in cells with microfilaments motile gamete) with a sperm cell (smaller, highly motile gamete)
consisting of clusters of actin filaments in sexual reproduction
mineral: homogeneous, naturally-occurring solid, usually anorga- oospore: (Grk.: oo = egg, spora = seed) fertilised oogonia, zygo-
nic with a crystal structure tes (etc) in Peronosporomycetes
mitosis: (Grk.: mito = thread) process in which the chromosomes opisthosoma: posterior part of the body behind the prosoma
double in number before a cell nucleus is divided, the ploidy organelle: a structurally distinct subunit within a cell with a spe-
(number of chromosomes) therefore remaining unchanged cialised function; strictly speaking, an organelle is a cell com-
mixotrophy: (Grk.: mixis = mixture, trophe = nutrients) ability of partment which is surrounded by a membrane formed from pro-
some organisms to absorb both carbon dioxide and to survive karyotes in a process of endocytobiosis: this narrower definition
on organic sources of energy only includes plastids and mitochondria
molecular oxygen: molecule consisting of two oxygen atoms (O2) osmotrophy: the process of obtaining nutrition by taking in dis-
monad: flagellated, single-celled solved organic compounds; in contrast to phagotrophy
monomers: (Grk.: monos = single, meros = part) individual mo- ovary: (Lat.: ovum = egg) female organ which holds the ovules
lecules which can bind together to make polymers (macromole- oxidation: the loss of electrons
cular bonds) oxygenation: provision of oxygen; oxidation where the electron
monopodial: plant growth type in plants with a single trunk or acceptor is oxygen
stem palaeontology: (Grk.: palaios = old, logos = discourse) the scien-
moraine: accumulation of debris transported and deposited by tific study of life before the Holocene
glaciers Paleo-Tethys Ocean: ancient ocean between Laurussia and Gond-
morphology: form or shape of organisms; related to external ap- wana; it began to form in the Upper Silurian, was most expansi-
pearance/shape ve in the Lower Carboniferous (Mississippian) and closed in the
motility: (Lat.: motio = movement) ability to move freely and ac- Triassic
tively palmelloid: colony of algae in which the cells are embedded in
mRNA (messenger RNA): molecule in cells that carries a porti- a gelatinous matrix; in contrast to coenobia, there is no fixed
on of the DNA code containing information for the synthesis number of cells
of proteins parabasal apparatus: equivalent to a specialized Golgi appara-
murein: cell wall in bacteria made from peptidoglycan (N-acetyl- tus consisting of parabasal bodies (dicotysomes) which are as-
glucosamin and N-acetylmuraminic acid) sociated with the parabasal filaments. The parabasal filaments
mycelium: the entirety of hyphae; the vegetative part of a fungus grow out of basal bodies which are themselves not part of the
mycotroph: feeding on fungi or nutrition in a symbiotic associa- parabasal apparatus. The parabasal bodies can possess up to 20
tion with fungi flattened vesicles known as cisterna
374 Glossary
paramylon: a storage polysaccharide in Euglenida and Haptophy- plesiomorphy: ancestral trait which was already present before
ta. In contrast to starch in plants and red algae, paramylon is the formation of the ancestral line under consideration
made from β 1,3-glucan pleura: lateral part of body segments in trilobites
paraxonemal rod: protein structure running parallel to the fla- pleurodont: dentition consisting of rootless teeth that are fused
gella to the jaw bone by their outer surface
parenchymula larvae: a type of larva which has a flagellated plutonism: geological process in which a pluton develops as the
front section (later endoderm) and an unflagellated rear section result of magma crystalising under the Earth’s surface
(later ectoderm) polar ring: thickening of the membrane complex at the anterior
partial pressure of carbon dioxide: the degree of pressure and posterior ends of the cells in Apicomplexa
exerted by carbon dioxide in a mixture of gases Polymerase Chain Reaction (PCR): laboratory technique used
peak: the highest point or level to make multiple copies of a segment of DNA
pedoturbation: soil perturbation not caused by illuviation (the polyploidisation: multiplication of the number of sets of chro-
re-distribution of water) mosomes in a cell
pelagic: relating to the open water ppm: parts per million
pelliclula: (Lat.: pellicula = little skin) hard but flexible layer (usu- PQ-Cycle: the result of redox reactions influenced by plastoqui-
ally made of proteins) under the cell membrane none (PQ)
pentacyclic: flowers with five whorls primary producers: autotrophic organisms that synthesise com-
PEP carboxylase: phosphoenolpyruvate carboxylase plex organic molecules from inorganic compounds
perhumid: extremely wet climate, including ten to twelve humid primary production: the synthesis of biomasses from inorganic
months compounds
periplast: intracellular layer made of protein plates which form a primary succession: plant life occurring on substrate devoid of
strong cell membrane vegetation or on newly formed substrate
phagocytosis: (Grk.: phagein = to devour, cytos = cell) process in primers: primers are short strands of nucleic acid with comple-
which eukaryotic cells actively consume particles mentary reverse sequences directed at a target sector which
phagotrophy: form of nutrition which involves consuming parti- they bind onto, thereby serving as the starting point for poly-
culate matter merase enzymes to catalyse the polymerase chain reaction (PCR)
pharynx: (Grk.: pharyngs = throat, gullet) in animals, the initial primeval ocean: generic term referring to Earth's first oceans,
part of the alimentary canal which formed around 4 billion years ago; the Panthalassic Ocean
photo-oxidation: oxidation caused by the action of light in the Paleozoic is often referred to as the primeval ocean
photorespiration: (Grk.: phos = light, Lat.: respiratio = brea- primordium: (Lat.: primordium = the beginning, origin) an organ
thing) a process in plant metabolism in which oxygen instead of or tissue at its earliest developmental stage
carbon dioxide is added to RubisCO during which phosphogly- prosoma: anterior part in Chelicerata
colate is created prothallium: haploid gametophyte in ferns
phragmoplast: microtubuli assembled perpendicularly to the cell protists: a large group of unrelated eukaryotic organisms with no
plate during cell division specialised tissue
phycobilisome: large protein complex associated with colour pig- protocyanobacteria: extinct ancestors of current cyanobacteria
ments involved in photosynthesis; in contrast to chlorophylls, protonema: earliest stage (haploid phase) in moss gametophytes
the phycobilines absorb green and yellow light protonephridia: simple excretory gland beginning with a termi-
phycoplast: microtubuli assembled parallel to the cell plate du- nal cell; a bundle of flagella create an outward current which
ring cell division; microtubule structure during cytokinesis in leads to pressurisation which in turn removes waste fluids from
members of the Chlorophyceae the animal
phyllotaxis: the alternate arrangement of leaves on a plant stem protoplanet: (Grk.: protos = first) large body of matter in orbit
phylogenetics: the study of the evolutionary relationships bet- around a star and thought to be developing into a planet
ween organisms and the evolution of species during the history provincialism: term given to the division of animal communities
of the Earth into distinct fauna provinces (roughly equivalent to faunal king-
phytoplakton: (Grk.: phyton = plant, planktos = drifting) photo- doms)
trophic organisms which float in water (plankton) pseudo-parenchyma: tissue-like complex of cells; in contrast to
planation: relocation in one plane real tissues, cell-to-cell structures such as plasmodesmata are
planktic or planktonic: planktic organisms float or drift in the only connected by the individual (intertwined) cell filaments
water column and cannot swim against the current pseudo-plasmodium: aggregation of numerous cells to form a
planktivorous: feeding on plankton grex; the individual cells retain their cell membrane in contrast
plant litter: dead organic material on the top layer of soil to real plasmodia, in which a multinucleate mass of cytoplasm
plant litter decomposition: breaking down and mineralisation is formed
of organic substances by decomposers pseudopodia: temporary projections of plasma to enable move-
planula: a free-swimming ciliated larva in various cnidarian species ment or attachment to a surface; also used for ingesting nutri-
plasmodesmata: channels between two plant cells enabling the ents
transport of matter between them psychrophilic: preferring low temperatures (from –20 °C to 10 °C)
plasmogamy: the fusion of the cytoplasms of two cells
Glossary 375
punctiform distribution: only in one place or at a point, little ribosome: protein/rRNA complexes which enable protein synthesis
spatial distribution RNA polymerase: enzyme which acts as a catalyst in the synthesis
pusules: tubular system of membranes in dinoflagellates of RNA (ribonucleic acid)
pygidium: posterior body part in trilobites and other anthropods; rock: mixture of minerals occurring in solid form
also the unsegmented section of annelids rock metamorphism: changes in rocks under high pressure and
pyrenoid: structure in the plastids in several algae and hornworts temperatures without them melting into liquid magma
largely consisting of RubisCO (ribulose-1,5-bisphosphate carbo- r-strategists: species which focus on producing a high quantity
xylase/oxygenase); act as centres of carbon dioxide enrichment (r) of offspring
pyroclasts: fragmented material consisting of volcanic (eruptive) RuBisCo: Ribulose-1,5-bisphosphate carboxylase/oxygenase, the
clasts to a degree of more than 75 % (e.g. ash) enzyme in photosynthesis which is involved in carbon fixation
pyruvate: anion of pyruvic acid; provides energy for the citric acid Rugosa: 'wrinkled' coral; Palaeozoic coral taxon with additional
cycle and is the end-product of glycolysis septa in only four of the six sectors, therefore displaying bila-
quadruped: an animal which has four feet teral symmetry
Quarternary: the most recent period in the Cenozoic Era spanning sailing ballast: water used by ships (voyaging without cargo) to
the last 2.588 million years and including the present keep the vessel upright
quasispecies (viral): a group of virus genotypes which have re- saproby: collective term given to all digestive processes of dead
sulted from the same viral genome in a host organic matter
radiation: rapid diversification of a taxon giving rise to an array saprophytes: heterotrophic organisms which feed on dead orga-
of new forms nic matter and in doing so break it down into its constituent
rangeomorphs: flat, sessile, fractal Ediacaran fossils parts
reactive oxygen species (ROS): on the one hand free radicals, saprotrophic: feeding on dead organic matter and in doing so,
such as the hyperoxide anion, the hydroxyl radical, and the per- breaking it down into its constituent parts
oxyl radical, on the other hand stable molecular oxidising agents SAR-clade: clade including Stramenopiles, Alveolata and Rhizaria
such as peroxide, ozone and the hypochlorite anion, as well as schizogony: asexual reproduction in which daughter cells are for-
unstable oxygen molecules, also known inaccurately as oxygen med by mitosis in the mother cell; these are then freed when the
radicals mother cell disintegrates
recent: (Lat.: recens = fresh, new) having happened not long ago Scleractinia: stony corals; they dominate modern coral reefs; sep-
red sediment: sediment which is coloured red due to the pre- ta are present in all six sectors, therefore displaying radial sym-
sence of Fe(III) minerals metry
redox reaction: reduction-oxidation-reaction; chemical reaction sclerites: hard parts in the body of invertebrates
in which electrons are transferred between species sclerophytes: evergreen arboraceous plants in the tropics and
reducing equivalent: unit of measurement used to quantify the subtropics which have adapted to periods of drought
reduction capacity by reducing agents; one reducing equivalent secondary endosperm: nutritional tissue created by the fertilisa-
corresponds to one mole of electrons (due to the transfer of tion of polar nuclei in the seeds of most Magnoliopsida
electrons and oxygen atoms, one mole of NADH corresponds to secretory enzymes: enzymes secreted by excretory glands
two reducing equivalents) sediments: deposits of material on the Earth’s surface, transpor-
reduction: gain of electrons or a decrease in oxidation state by a ted by wind, water or ice
molecular, atom, or ion semi-arid: mostly arid climate; evaporation is greater than precipi-
regression: marine regression takes place when the sea retreats tation over six to nine months
from continental regions and is caused by a rise in the sea floor semi-humid: mostly humid climate; precipitation is greater than
or a decline in sea level evaporation over six to nine months
relative frequency: the number of individuals in a given species septum: dividing wall in hyphae, basidia, spores and konoids
relative to all the individuals of all species living in that habitat series: stratigraphic timescale
reproductive isolation: a set of barriers impeding the gene flow serrated leaf: leaf possessing sharp sub-teeth between the teeth
between two populations; examples of such barriers might be on its margin
geographical separation, genital incompatibility, or behavioural sesquiterpines: subgroup of terpenes
differences sessile: sessile organisms are attached to a substrate and cannot
rhabdosomes: rod-like colonies of graptolites move about independently, in contrast to motile organisms
rhizoids: similar to roots, serving primarily to anchor the plant to sexual dimorphism: (Lat.: sexus = gender; Grk.: dimorphos =
the ground; to a lesser extent they also serve to absorb nutrients having two forms) differences in appearance between male and
and water as they possess no specialized vascular tissue female individuals of the same species
rhizopodal: organisms with no fixed cell wall or flagella which shortgrass prairie: prairie dominated by short grasses
have an amoeboid form of movement using pseudopods; the siderite: (Grk.: sideros = iron) mineral composed of iron carbonate
obsolete name for amoeboid organisms ('rhizopoda') stems (FeCO3)
from this term sieve elements: the type of cell in the phloem in Magnoliopsida
rhoptries: club-shaped secretory organelles in the apical complex in which organic metabolites are transported
in Apicomplexa containing lytic enzymes siphonal: polynuclear, single-celled
rhyolite: acid igneous rock
376 Glossary
S-layer: layer of paracrystalline protein lining the cell wall in many stratotype: layer of rock in a particular location on the basis of
prokaryotes which a stratigraphic unit is defined
Small Subunit (SSU): the small subunit of ribosomes; the term strobili: cone-shaped sporangia-bearing structures
refers to both the 16S subunit of prokaryotic ribosomes as well stromatoliths: (Grk.: stroma = blanket, lithos = stone) biogenic
as the 18S subunit of eukaryotic ribosomes sedimentary rock formed by the trapping and binding of sedi-
Snowball Earth: term given to the hypothesis that the Earth’s mentary particles or the accumulation of salts resulting from the
surface, including the equatorial region, was once completely growth of microorganisms
covered in ice; the term is used in discussions relating to several Stromatoporoida: extinct, colony-forming organisms classified
Precambrian ice ages, but it remains a moot point whether the as sponges which were important reef-formers in the Silurian
equator was indeed covered in ice and Devonian
soil horizon: a layer of soil with common physical characteristics subduction zone: convergent boundary between one tectonic
differing from the horizons above and below it plate of the lithosphere and another on the Earth’s upper crust
solar climatic zones: classification of climate zones based exclu- substitution: (Lat.: substituere = put in place of another) repla-
sively on the intensity of solar radiation; the lines of division bet- cement, exchange
ween the solar climate zones are the tropics and the polar circles substrate: surface onto which sessile organisms can attach them-
solar nebula: thick clouds of interstellar matter remaining fol- selves
lowing the explosion of a supernova succulent: (Lat.: sucus = juice, suculentus = juicy) having thick
solitary: living alone fleshy leaves or stems adapted to storing water
somatogamy: sexual reproduction in which the haploid somatic supercontinent: large landmass formed from several continents
cells (not gametes) from several organisms fuse together, crea- or cratons
ting a diploid cell suspensor: connection between endosperm and embryo in seed
sorus (pl. sori): cluster of sporang-ia (fungi, ferns) plants; formed by asymmetrical division of the zygote
species concept: the idea of categorising living organisms into suture: (Lat.: sutura = sew together) seam; the lobe line in cepha-
small, formal groups, usually based on a specific definition; ex- lopods
amples are: sympetalae: having fused petals in flowering plants
biological species complex: taxa which are reproductively isola- symplesiomorphy: term given to homologous plesiomorphic
ted from other species; characteristics exhibited by two or more taxa
evolutionary species complex: a lineage that evolves indepen- synapomorphy: an evolved characteristic common to a mono-
dently from other lineages; phyletic group
morphological species concept (as per Darwin): varieties with a syngamy: sexual reproduction through the fusion of two gametes
lack of or total absence of transitional forms between them; synthesis: (Grk.: synthesis = composition) combination of various
ecological species complex: a lineage occupying an adaptive components to form a new whole
zone differing minimally from others of similar lineages Tabulata: Paleozoic group of corals; they always possess six septa
spliceosome: structure in eukaryotic cells which acts as a catalyst (therefore displaying radial symmetry) but they are often incom-
during splicing (the removal on introns from the pre-mRNA) plete
splicing: modification of the pre-mRNA by removing introns du- tallgrass prairie: prairie dominated by tall grasses, such as that
ring transcription native to central North America
spontaneous generation: spontaneous emergence of life from taxonomy: (Grk.: taxis = order, nomos = law, ordinance) (usually
inanimate matter hierarchical) classification of organisms
sporangium: (Grk.: spora = seed, aggeion = vessel) a structure in teloblastic growth zone: teloblasty is the term describing the
which one or more spores are formed process in which new segments are formed in a growth zone at
spore: (Grk.: spora = seeds) asexual reproductive cell the rear of the embryo and work their way forwards; teloblasty
sporocarp: spore-forming fruiting body is common in all Articulata
sporophyte: spore-producing diploid generation in the alternati- telome: axial plant structure in land plants
on of generations in land plants Tethys: ocean that existed between Laurasia and Gondwana bet-
sporoplasm: cell plasm in a spore ween the Permian and the Tertiary
sporopollenin: main component of the exospores in the spores tetraspores: grouping of the four spores generated by meiosis
of spore-producing plants (mosses, ferns) and the external wall tetrasporophyte: the second sporophytic generation in red algae
(exine) of pollen grains formed from a carpospores
sporozoite: infectious stage in parasitic Apicomplexa thallose: thalloid vegetative tissue with no distinct parts or 'leaves'
starch: reserve polysaccharide in Archaeplastida and Alveolates; α thallus: multicellular undifferentiated vegetative tissue in plants,
(1-3) and α (1-6) glycosidic bonds; similar to but less branched algae and fungi without the organisation of a cormus (sections
than glycogen incl. stem, root, leaf)
stomata: pore in a plant which serves to regulate gas exchange thecodont: possessing dentition consisting of teeth set in bony
with the environment; the resultant transpiration cools the tis- sockets in the jawbone
sue thermophile: preferring relatively warm temperatures, i.e. bet-
stratigraphy: branch of geology which studies the relative ages of ween 45-80 °C; hyperthermophiles prefer temperatures over
rock layers and strata 80 °C
Glossary 377
thioredoxin: small proteins which function as cofactors in the undergrowth: vegetation in a forest growing underneath the ca-
transfer of electrons nopy
thoracic respiration: inhalation by expanding the rib-cage and undifferentiated soils: soils are not or only weakly differentiated
increasing the volume of the chest cavity; in contrast to buccal into horizons
respiration, thoracic respiration takes place through an open unsaturated fatty acids: in contrast to saturated fatty acids, un-
mouth saturated fatty acids possess at least one carbon-carbon double
thylakoids: (Grk.: thylakoeides = sack-like) systems of membranes bond in their chain
in chloroplasts uridine monophosphate: an intermediate product in pyrimidine
tight junctions: cell-to-cell conjunctions with no gap between biosynthesis
epithelial cells, forming a barrier to diffusion uroid: posterior bulb in amoebae
tillite: sedimentary rock composed of compacted glacial till (rock Variscan orogeny: a mountain-building event in the Paleozoic
material deposited by glacial ice) caused by the collision of Gondwana and Laurussia
torpor: decreased physiological activity with reduced metabolic vesicle: (Lat.: vesicula = diminutive of bladder, blister)
rate viviparity: term describing organisms which produce their off-
toxins: (Lat.: toxicum = poison) poisonous substances produced spring in live births (as opposed to laying eggs); both fertilisa-
by living organisms tion and the development of the embryo take place inside the
tracheae: (Lat.: trachea = wind pipe) in animals, tube allowing mother’s body
the passage of air to be transported to tissue; in plants, water- volcanism: geological processes connected to volcanoes; magma-
conducting tissue tic processes near the Earth’s surface
transcription: part of gene expression when a DNA segment is weathering: the breaking down of rocks in mechanical or chemi-
copied into RNA cal processes
transcriptome: the total set of all RNA molecules in a cell, in tis- whorl: arrangement of leaves in which two or more leaves arise
sue or in an organism during a given developmental stage from a single node
transgression: marine transgression takes place when the sea ad- xeromorph: plant which has adapted to arid habitats
vances rapidly into continental regions and is caused by a drop yolk sac: organ providing nourishment attached to the embryo in
in the sea floor or a rise in sea level various animals
transition: point mutation in which a purine nucleotide is repla- zoochlorellae: endosymbiontic green algae
ced by another purine, or a pyrimidine nucleotide is replaced by zoospore: asexual spore with a flagellum
another pyrimidine zooxanthellae: endosymbiontic dinophytes
translation: the synthesis of proteins in the cells of living orga- zygote: (Grk.: zygotos = yoked together) the cell formed from two
nisms using mRNA molecules gamete cells in sexual reproduction
transversion: point mutation in which a purine is substituted for
a pyrimidine or vice versa
trichal: filamentous (branched or unbranched) organisation of al-
gae
trichocyst: filamentous rods filled with secretions which explode;
they are used for defence or to capture food
triploblastic: organism with three primary germ layers
trochophore larvae: free-swimming, pear-shaped larvae with se-
veral bands of cilia in various Spiralia
Tropical Convergence Zone: low-pressure trough near the equa-
tor measuring only a few hundred kilometres across; it appears
as a band of thick cloud and is an area of high precipitation
true diversity: term describing the number of species that accord
with a certain value of a biodiversity index when all species are
distributed equally (i.e. when all species are equally abundant)
trunked mammals: Order Proboscidea, the only living family is
the Elephantidae (elephants)
tubulin: a protein, the main constituent of microtubuli
tussock grasses: grasses which grow close together in tufts or
clumps
type locality: the place where a particular rock type is first iden-
tified
ubiquitous: broadly distributed, to be found everywhere
ultraviolet: radiation having a wavelength shorter than that of
the violet end of the visible spectrum but longer than that of
X-rays (100–380 nm)
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Mechanic, Wikimedia Commons, GFDL&CC-BY-3.0; © Armin
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Index 387
Index
A Agnostida 88 Definition 230, 238
Air embolism 372 Animalcules 230
Abiogenesis 188, 235 Akashiwo 347 Anisokont 367
Abiotic 367 Albertosaurus 134 Anisotremus 183
Acanthamoebida 293 Aldehydes 50, 367 ANITA clade 324, 326
Acantharia 332, 336 Algae 236, 287, 367 Ankylosauria 133
Acanthocephala 273 Origins 56 Annelida 269, 273
Acanthoceratophytina 316 Proterozoic 58 Annual plants 367
Acanthodii 94, 276 Algal blooms 347, 363 Anoxia 367
Acanthostega 112 Alismatales 327 Anoxygenic 367
Accumulation 367 Alisol 216, 367 Antheridium 316, 355, 367
Acephala 285 Alkaliphilic 367 Anthracocrinus 107
Acer 143 Allantois 129, 367 Anthracoidea 291
Acervulina 338 Allogromiida 80 Anthropogenic 367
Acetyl-CoA 52 Allopatric speciation 182 Apatite 102, 337
Acetylglucosamine 281 Allorrhiza 367 Aperture 367
Acetylmuramic 281 Allosaurus 133 Aphelidea 260
Achene 367 Alps 18, 140, 142 Aphotic zone 367
Acidophilic 367 Alpine belt (Alpine-Himalayan orogenic Apiaceae 330
Acineta 309 belt) 140 Apical 367
Acoelomate 272, 367 Aluminium silicate 22 Apical complex 348, 367
Acorales 327 Alveolata 247, 255, 257, 340, 342 Apicomplexa 257, 340, 342, 348
Acorn worms. See Enteropneusta Alveoli 340, 342, 347, 365, 367 Apicoplast 348, 367
Acrania 274 Alytes 129 Apomorphy 242, 367
Acrasidae 300 Amaranthus 155 Apusomonas 259
Acrisol 216f, 367 Amasia 154 Apusozoa 256, 258
Acrispumella 357 Amastigote 305 Arabidopsis thaliana 343
Acritarchs 59, 101, 105 Amber 72, 141 Aragonite 26, 102, 337, 367
Acrodont 278, 367 Ambitisporites 107 Araukariales 322
Acrogymnosperms 322 Amborellales 326f Arbor vitae 322
Actinopterygii 94, 276 Ambulacral groove 367 Arbuscular mycorrhiza 284
Adaptation 128, 248, 314, 367 Ambulacraria 274 Arcellinida 293
Adaptive mutation 367 Ambulakral system 274, 367 Archaea 248, 252
Adaptive radiation 367 Ammonitida 85, 131 Archaeocyatha 82
Adaptive zone 367 Ammonoidea 84, 112, 131 Archaeopteris 113
Adenine 36 Amnion 129, 278 Archaeopteryx 95, 130
Adenosine diphosphate. See ADP Amniota 94, 277f, 367 Archaeplastida 247, 255f, 306
Adhesion 367 Amoeba 293 Archamoebae 294
ADP 39, 43, 53, 147 Amoebae 292 Archean 28–40
Adventitious 367 Amoebozoa 247, 258, 292 Atmosphere 32
Aegocrioceras 135 Amorphea 256, 258. See Unikonta Earth’s crust 32
Aerobe 367 Amorphous 367 Genetic expansion 38
Aerobic respiration 52 Amphibians 276 Archegonium 316, 367
African lungfish 277 Amphisorus 339 Arecales 327
Afrotropical 195 Anaerobes 367 Arid 367
Agaricomycotina 290 Anapsida 94, 116, 278, 367 Aril 367
Age (geochronological) 28, 74. See also Anatexis 20, 367 Aristotle 230
Stratigraphic layer Ancyloceratina 135 Armillaria ostoyae 280
Agglutinated 367 Angiosperms 8, 96, 134, 277, 324. See also Armoured fish. See Placodermi
Aggregation 367 Magnoliopsida Arthropoda 88, 269
Agnatha. See jawless Animal. See Metazoa Articulata 268

388 Index
Articulated 367 Basilosauridae 141 Brassica 329

Asaphida 88, 107 Batrachospermum 311 Brassicales 329
Ascetosporea 335 Belemnitida (or belemnites) 85, 135 Bread mould 286
Ascokarp 288, 367 Belesodon 95 Breathing, buccal (Buccal pumping) 116,
Ascomycota 60, 256, 280, 288 Bennettitopsida 322 368
Ascus 289 Benthic 368 Breviatea 294
Asparagales 327 Benthic zone 221 Brittle stars 90, 274
Assimilation 367 Berberidopsidales 329 Bronze Age 153
Asteraceae 330 Bicosoecida 257, 350 Brown algae 237. See Phaeophyceae
Asterids 330 Big Bang 14 Brown earth 204
Asterionellopsis 315 Bigyra 350 Brunification 204
Asterococcus 313 Bilateral symmetry 267 Bryophytina 316
Asteroid belt 15 Bilateria 260 Bryozoans 115, 368
Asteroidea 90, 274 Binary nomenclature 232, 368 Buddleja 331
Asterophyllites 65 Biodiversity 4, 157, 368 Bundle sheath cells 368
Asthenosphere 14 Definition 4 Buntsandstein 124
Carbon dioxide concentrations 138, 144 Distribution 174 Buoyancy 110, 355
Oxygen content 48 Fossils 78 Burgess Shale 71
Oxygen concentrations 30, 44, 114, 126 Hotspots 178 Burial metamorphism 368
Primordial 14 Water availability 174 Buttress root 219, 368
Atlantic 140, 225. See also Ocean Biodiversity index/indices 166 Buxales 329
Atmosphere. See also Oxygen evolution Bio-formation 157
ATP 38, 40, 52, 147, 367 Biogenic 9, 337, 368 C
ATPase 38, 40 Biogeography 158, 194
Australasia 195 Microorganisms 188 C4-plants. See Photosynthesis: C4-photo-
Australopithecines 152 Bioluminescence 9, 347 synthesis
Australopithecus 143, 153 Biome 157, 194, 198 C5-sugar 42, 368
Austrobaileyales 326f Biomineralisation 9, 12, 101f, 224, 339 Calamites 114
Autapomorphy 242, 367 Biostratigraphy 74, 368 Calcarea 82, 264
Autospores 367 Biotically 368 Calcareous 82
Autotrophy 47, 367 Biozone 75 Calcisol 210, 212f, 368
Avalon-type biota 100 Biped 368 Calcite 26, 102, 337, 368
Aves. See Birds Birds 130, 133f, 276, 278 Calcium 47
Axopodia 293, 332 Bitumen 73, 368 Calcium carbonate 26, 337
Axostyle 298, 367 Bituminous shale 368 Calcium detoxification 102
Bivalvia 86 Calcium phosphate 337
B Bivetiella 143 Caledonian mountains 68
Black smokers 34 Calvin cycle 43, 147, 368
Babesiosis 283 Blastopore 260, 274, 368 CAM 368
Bacillariophyceae 224, 254, 257, 350, 358, Blepharisma 345 Cambisol 204f, 211
365 Bodo 305 Cambrian 77, 98, 104
Bacillariophyta 135 Body symmetry 267 Beginning 98, 100
Bacteria 248, 250 Bony fishes. See Osteichthyes Cambrian explosion 100
Ballast water 367 Bootstrap method 242 Campanula 330
Baltica 68, 104, 106, 108, 367 Boraginaceae 330 CAM-plants. See Photosynthesis: CAM-
Banded iron ore 48f, 368 Boraginales 331 photosynthesis
Bangiomorpha pubescens 58, 59 Boreal forest 202 Canellales 327
Bangiophyceae 310 ‘Boring billion’ 58 Cantharellus 241
Baragwanathia 108 Bothrosomes 351, 368 Capensis 194, 210
Barcoding 164 Boundary stratotype 28 Capsal 368
Basal bodies 289, 294, 299, 304f, 312, 368. Brachiopoda 86, 113, 273 Capsoid 368
See also Kinetosome Brachiopods See Brachiopoda Carbon dioxide 20, 26. See also Green-
Basalt 22, 368 Brachiosaurus 133 house gases
Base triplet 246, 368 Brachiozoa 272f Carbon dioxide concentration 20, 26
Basidia 290 Brachythecium 123 Carbon dioxide partial pressure 368
Basidiomycota 60, 256, 280, 290 Branchial gut 371 Carbon metabolism 38
Index 389
Carbonate 26, 46 Chain silicate 17 Cistern 368

Carbonate equilibrium 26 Chamaecyparis 322 Citric acid cycle 52f
Carbonate precipitation 20, 26 Chara 315 Cladogram 244
Carbonate-silicate cycle 20, 46, 154 Charniodiscus 101 Cladonia 173
Carbonic acid 20, 26 Charophytina 314 Cleithrolepis 65
Carbonic acid weathering 47 Chelicera 368 Climate 196
Carbonic acid-carbonate equilibrium 26 Chelicerata 271 Zones 198
Carboniferous 77, 98, 114 Chemical evolution 34 Climate diagram 197
Carboxysome 308 Chemical weathering 368 Closterium 315
Carduus 331 Chemocline 364, 368 Cloudinia 101
Carnivore 237, 286, 368 Chemoorganotroph 368 Clubmoss. See Lycopodiopsida
Carnivory 9, 327 Chemosynthesis 47 Clypeus 131
Carnosauria 133 Chernozem 206f Cnidaria 266
Carnotaurus 133 Chernozem or Black soils 206 Cnidarians. See Cnidaria
Carotinoid 256, 368 Chitin 256, 280f Coal forests 114
Carpel 368 Chlamydomonas reinhardtii 343 Coalification 72, 368
Carpels 368 Chloranthales 326 Coccal 368
Carpinus grandis 65 Chlorarachnion 335 Coccoid 368
Carposporophyte 311, 368 Chlorarachniophyta 257, 333f Coccolithales 362
Cartilaginous fishes. See Chondrichthyes Plastids 56 Coccoliths 135, 257, 362
Caryophyllales 329 Chlorella 161 Coelacanth 112, 277
Castericystis 105 Chlorobiota, Chlorobionta. See Viridi- Coelacanthimorpha 277
Catalysis 368 plantae Coelom 268–270, 273, 368
Cauloid 316 Chlorodendrales 313 Coelurosauria 133
Cavosteliida 293 Chloroflexi 40 Coenobium 368
Celastrales 329 Chlorokybophytina 313, 314 Coenococcum 285
Cell Chlorophyceae 313 Coevolution 9, 331
Multinucleate 8, 281 Chlorophyll 41, 220, 256, 307, 311 Coiled 368
Origin 34 Chlorophyta 62, 256, 306, 365 Coleochaete 315
Cell adhesion 60, 295, 368 ‘Core’ Chlorophyta 313 Coleochaetophytina 314
Cell communication 60 Chloroplast ER 362 Coleoidea 84
Cell organelles 341 Chloroplastida. See Viridiplantae Coleoptera 137, 368
Cell wall 317 Chlorosome 43 Coleps 345
Cell wall materials 8, 281 Choanocytes 265 Collodaria 336
Cellulose 256, 281 Choanomonada 256, 260, 262 Collozoum 337
Cenophytic 64 Chondrichthyes 106, 276 Colonisation of land 106, 110, 128, 314
Cenozoic 64, 138, 368 Chondroma 55 Colorado potato beetle (also potato bug)
Centrales 358 Chorda dorsalis 274, 368 191
Centramoebida 293 Chordata 105, 274 Columbia 18
Centrioles 368 Chorion 129, 368 Columella 317, 368
Centripedal 368 Chromalveolata 257, 368 Commelinales 327
Centrohelida 360 Chromalveolate-hypothesis 340, 360 Commensalism 369
Cephalochordata 274 Chromera 341, 343 Communication 60
Cephalon 89 Chromerida 257, 342 Chemical 8, 295
Cephalopoda 84 Chronostratigraphy 74, 368 Compaction 25, 72, 369
Cephalotaxales 322 Chronozone 74 Companion cells 370
Ceratites 127 Chroomonas 365 Compartmentalisation 9, 349, 369
Ceratitida 127 Chrysochromulina 362 Compensation depth 26, 224
Ceratium 347 Chrysolaminarin 257, 358, 368 Competitive exclusion principle 180
Ceratophyllales 327 Chrysophyceae 257, 350, 356 Conglomerate 25, 124, 373
Ceratopsia 133 Chytridiomycota 256, 280, 282 Conglomerate 369
Ceratosauria 133 Cilia 344 Conidia 172, 369
Cercomonadida 334 Ciliophora 257, 340, 342, 344 Conifer 202, 204, 322
Cercozoa 257, 332, 334 Cingulum 347 Coniferopsida 322
CH4. See Methane, Greenhouse gases Circulation (lakes) 220 Conjugation 288, 345, 369
Chaetetida 83 Circumpolar 368 Conodont animals 70, 92, 107
390 Index
Conodonts 75, 77, 92, 369 Plastids 56 Detoxification 102, 110, 369
Conoid 348, 369 Crystallization, differential 17 Detoxification enzymes 51
Conosa 256, 292, 294 Crystals 22 Detritivore 369
Consumers 369 Ctenophora 266 Detritus particle 369
Contact metamorphism 372 Ctenophores. See Ctenophora Deuterostomia 274
Continent 18. See also Supercontinent Cucurbitales 329 Devon 98, 112
Continental crust 16, 18, 20, 48 Cupressales 322 Diagenese 20, 24, 369
Continental or tectonic plate Cupressus 322 Diapir 63
Adriatic 18 Cuticula or cuticle 9, 317 Diapsida 94, 116, 278, 369
African 18 Cuttlefish 84, 355, 369 Diatoms. See Bacillariophyceae
Eurasian 18, 68, 130, 142, 154, 195 Cyanelles 308 Dicerorhinus 193
Indian 18, 138 Cyanidiophytina 310 Dichotomous 369
Nazca 18 Cyanobacteria 40, 50, 201, 236, 250 Dickinsonia 100f, 267
Pacific 18 Plastid origins 56 Dicksonia 121, 123, 321
Continental shelf 369 Cyanobiont 172 Dicot 325
Convection 369. See also Earth’s mantle, Cyanophora 308f Dicranoweisia 123
Ocean Cycadopsida 96, 130, 322 Dicroidium 127
Convergence 369 Cyclidium 345 Dictyochophyceae 350
Convergence zone, tropical 369 Cycliophora 273 Dictyonema 92, 105
Cooksonia 108f Cycloclyperus 338 Dictyosome 298, 309, 334, 369
Corals 82 Cycloneuralia 270 Dictyosphaerium 313
Cordaitopsida 96, 323 Cynaobacteria 201 Dictyostelia 293f
Core chromalveolates 360 Cynodontia 127 Didymograptus 93, 107
Corms 118, 369 Cynognathus 127 Differential Interference Contrast (DIC)
Development 118 Cypress 322 369
Cornales 330 Cysts 369 Differentiated soils 369
Corrosion protection 9, 261, 315 Cysts 369 Digitalis 331
Corvus 159 Cytochrome-b6f-complex 41 Dilleniales 329
Corynexochida 88 Cytokinesis 369 Dimetrodon 117
Cosmoclaina 109 Cytoplasma 369 Dinobryon 357
Cosmopolitan 369 Cytosine 36 Dinoflagellates. See Dinophyta
Costa 299, 369 Cytoskeleton 369 Dinophysis 347
Cotyledon 369 Cytosol 369 Dinophyta 257, 340, 342, 346
Craniata 94, 274 Cytostome 369 Plastids 56
Craniformea 86 Dinosaurs 8, 130, 132, 134, 277, 279
Craton 18, 32, 369 D Dionaea 237, 327
Crenal 222 Dioscoreales 327
Cretaceous 77, 125, 134, 362 Dactylopodida 293 Diphasiastrum 318
Cretaceous-Paleogene boundary 64 Daphnia 315 Diplobiontic 369
Crinoidea 90, 107, 274 Dark brown soil 207 Diplograptidae 92
Cristae 296, 300, 306, 334, 361, 369 Darwin, Charles 234 Diplograptus 93
Crocus 327 Dating 74 Diploid 369
Crommium 141 Daucus 331 Diplomonadida 298
Crossosomatales 329 Decomposers 369 Diplonemea 302
Crude oil 73, 131 Deep sea 34 Diplonts 120
Prospecting 92 Demospongiae 264 Diplophyllum 317
Crurotarsi 279 Dendroidea 92 Dipnoi or Lungfish 277
Crustacea 271 Dentalium 143 Diptera 137, 369
Cryogenian 100 dentate leaves 369 Discoba 296, 300, 304
Cryopreservation 271 Deoxyribonucleic acid. See DNA Discosauriscus 95
Cryosol 200 Deposits 70 Discosea 256, 292
Cryoturbation 200 Dermamoebida 293 Dissociation 369
Cryptomonadales 361 Desert 212 Distigma 303
Cryptomonas 365 Desilication 218, 369 Distribution area 158
Cryptophyceae 360, 364 Desmin 277, 369 Ditomopyge 117
Cryptophyta 257, 333, 360, 364 Dessication 370 Diversity 4, 8
Index 391
α-diversity 168, 369 Edrioasteroidea 90 Ephedra 322

β-diversity 168, 369 Ejectosome 364 Ephemeral 370
γ-diversity 168, 369 Elater 317, 370 Epibenthic 370
Molecular 164, 246 Electron microscopy 370 Epilithic 370
True diversity 168, 369 Electron transport Epilobium 121
DNA 36 Cyclic 40 Epimastigote 305
DNA bank 369 Non-cyclic 40 Epiphytic 370
DOC 369 Eleutherozoa 90 Epitheca 347, 358
Dogfish sharks. See Acanthodii Elginerpeton 95 Epithelium 370
Dogger 124 Ellagic acid 370 Epoch 28, 74. See also Stratigraphic layer
Dolipore 61 Ellipsocephalus 105 Equisetopsida 96, 114, 320
Dolomite 26 Elphidium 143 Equisetum 121, 321
Domains 248, 369 Elysia 239 ER 370. See also Endoplasmic reticulum
Dominance structure 369 Embryo sac 121 Era 28, 74. See also Stratigraphic layer
Dorudon 141 Embryonic development 128 Eranthis 137
Doushantuo Formation 369 Embryophytes 60, 306, 316. See also Land Erathem 28, 74. See also Stratigraphic layer
Downy mildew 352 plants Eremosphaera 313
Dracaena 326 Emergences 118 Ericales 330
Drifting 369 Emiliania 362 Erniettomorpha 101, 370
Drosera 327 Emulsifier 370 Erosion 21, 24, 370
Drosophila melanogaster 343 Enation 118, 370 Chemical 24
Durisol 212 Enation theory 118 Physical 24
Dynein 259, 369 Endemic 370 Erythrocytes 370
Endobenthic 370 Escherichia coli 343
E Endocommensals 350, 370 Estuary 220, 222, 368
Endocytobiosis 55, 370 Euamoebida 293
Earth Endocytosis 297 Euarthropoda 271
Atmosphere 16 Primary 56, 254, 306, 308 Euasterids 325, 330
Core 15f Secondary 56, 348 Euastrum 165
Crust 14, 16 Serial secondary 346 Eubodonida 305
Hydrosphere 16 Tertiary 346 Eudicots 324, 328, 330
Mantle 14, 16 Endomembrane system 54 Euglena 302f
Internal structure 14, 16 Endomycorrhiza 285 Euglenoids 256, 302
Origins 14 Endomyxa 334 Plastids 56
Earth History 11 Endoparasites 298, 301, 348, 370 Euglenozoa 300, 302, 304
Biodiversity 12 Endophytes 370 Euglypha 335
Reconstruction 74 Endoplasmic reticulum 60, 255, 311, 341 Eukarya, Eukaryotes 248, 254, 256
Earth’s mantle. See also Earth: Mantle Endoskeleton 274, 337, 370 Radiation 58
Convection 18 Endosperm 129 Eukaryotic cells 54, 248
Eastmanosteus 95 Endosymbiosis. See Endocytobiosis Euphotic zone 370
Ecdysone 268, 369 Endosymbiotic algae 9, 345 Eurhodophytales 310
Ecdysozoa 268, 270 Endosymbiotic bacteria 370 Eurosids 325
Echinacea 331 Endotherm 370 Eurosporangiates 370
Echinoderes 309 Entamoebidae 293 Eurypteridae 109
Echinodermata 90, 274 Enteromorpha 313 Eurypterus 109
Echinoidea 90, 274 Enteropneusta 274 Eusthenopteron 113
ECM 369 Entoderm 370 Eustigmatales 350
Ecological fitness 182, 369 Entomophthoromycotina 286 Eutheria 278
Ecological niche. See niche Entoprocta 270 Euthermic 370
Ecoregion 174, 195f, 369 Eoarchean 33 Eutracheophytes 318
Ecozone 157, 195 Eocene 140 Evaporation 370
Ectoderm 370 Eocercomonas 335 Evenness 166. See also Coevolution
Ectomycorrhiza 285 Eocrinoidea 90 Evolution 4, 6, 8, 162, 234
Ectoprocta 273 Eon 28, 74 Excavata 247, 255f, 296
Ediacara hills 71 Eonothem 28, 74 Exocytosis 297
Ediacaran 29, 100, 344 Eophyllophyton 112 Exon 55
392 Index
Exoskeleton 102, 128, 337, 370 345 Glacial 148, 150, 371
Extinction 66, 184f, 192, 370 Forests 112 Glacial till 25, 371
Extremophile 370 Boreal 202 Glaciation 24, 30, 32, 38, 48, 62, 68, 101,
Exudation 361, 370 Deciduous 204 106, 114, 140. See also Ice age
Eye 303 Temperate 204 Glaucocystis 308f
Eyespot 303 Tropical rainforest 218 Glaucocystophyta 306, 308
Xerophytic 216 Glaucophyta 256
F Fornicata 256, 299 Glissomonadida 335
Fossil deposits 70 Global Stratotype Section and Point 76
Fabaceae 329 Fossilisation 72, 273 Globigerinida 80, 338
Fabales 329 Fossils 8, 78, 273 Gloeochaete 308
Fabomonas 259 Founder population 184, 370 Glomeromycota 256, 280, 284, 286
Facies 98, 100, 370 Frost shattering 25 Glossopteridopsida 322
Fagales 329 Fucus 237, 355 Glossopteris 114, 116f, 322, 371
Fatty acids, unsaturated 370 Fungi 247, 280. See also Mushrooms Glucan 371
Faunal 86, 88, 134, 370 Definition 240 Glucose 38, 281
Fauna-rich 194 Diversity 177 Glugea 283
Feldspar 13, 16, 23f Fusulinida 80, 115 Glycimeris 143
Felsic 16, 22, 370 Future 154 Glycocalyx 371
Fenton reaction 51 Fynbos 210 Glycogen 256, 371
Fermentation 38, 47 Glycolysis 38, 47
Alcoholic 39 G Glycoproteins 371
Lactic acid (or Hydroxypropionic acid) Glyoxylate 50
39 Gabbro 16, 22 Glyptodon 149
Ferns 122, 287. See also Polypodiopsida Gallery forest 370 Gnathifera 273
Ferralisation 218 Gametangiogamy 371 Gnathostomata 94, 108, 274, 276
Ferralsol 219 Gametangium 371 Gnathostomulida 273
Ferredoxin 41 Gamete 371 Gnetales 96, 322, 325
Fertile strobili 370 Gametocytes 371 Gnetum 322, 325
Fertility 370 Gametophyte 120, 317, 319, 321, 371 Golden algae. See Chrysophyceae
Fertilization, inner 129 Ganglia 371 Golden Spike 29
Fig wasp 331 Gap junctions 60, 371 Gondwana 18, 68, 104, 106, 108, 112, 114,
Filasterea 260 Garnet 22 130, 134
Filopodia 293, 332 Garrulus 159 Goniatitida 84, 113, 115
Filoreta 335 Garryales 331 Goniomonadales 361
Filosa 334 Gas planets 15 Goniomonas 364
Fire 6, 215 Gaskiers glaciation 63 Gradualism 234, 371
Flabellinia 292 Gastrotricha 273 Granatpteridotid 23
Flagallum 259. See also Cilia Gemuendia 95 Granite 23
Flagellar groove 302 Generalists 370 Granofilosea 334
Flagellation 256 Generational alternation 8f, 120–123, 283, Graptolites 92, 105, 107, 274, 371
Flagellin 259, 370 319 Graptoloidea 92
Flagellum 55, 259 Genesis 230 Grasses 134, 141, 143
Floating appendages 329 Genesis 230 Grasslands 141, 144
Flood basalt 66, 126, 370 Genome size 8, 301 Flooded 208
Flora-rich 194, 370 Gentianales 331 Montane 208
Floridean starch 310 Geochemical cycles 46 Subtropical 214
Florideophyceae 310 Geochronology 28, 74, 371 Temperate 206
Flower constancy 368 Geophytes 371 Tropical 214
Fluviate 24, 370 Geraniales 329 Great Oxidation Event 32, 371
Flysch 25, 370 Giardia 298 Green algae 312
Folioceros 317 Giganotosaurus 133 Green non-sulfur bacteria 40, 43
Foliose 316, 370 Gini-Simpson Index 166, 168 Green sulfur bacteria 40, 43
Food vacuole 345, 370 Ginkgo 137, 322 Greenhouse effect 26, 46
Foramen 87 Ginkgoopsida 322 Carbon dioxide 38, 46, 63
Foraminifera 79, 80, 257, 332, 336, 338, Giraffa 309 Methane 38, 46, 48
Index 393
Greenhouse gases 38, 371 Hippuritoida 82, 87 I

Gromia 335 Histone 346, 371
Gruberellidae 300 Hjulström curve 25 Iapetus 104, 106, 372
Guanine 36 Holomycota 280 Ice Age 148, 150. See also Glaciation
Gulf stream 150 Holoparasite 371 Ichthyobodo 304
Gunnerales 329 Holothuroidea 90, 127, 274 Ichthyopterygia 133
Gymnodinium 343 Holotypus 161, 371 Ichthyosporea 260
Gymnosperms Holozoa 260 Ichthyostega 111f
Gymnosperms 96, 322 Homeothermy 278, 371 Ichtyosauria 132
Gymnosphaerida 332 Hominins 149, 152 Idioblast 371
Gynoecium 371 Hominisation 148, 152, 371 Iguanodon 133
Gypsisol 212 Homo. See Hominisation Ilium 133
Homo erectus 153 Imbricatea 334
H Homo habilis 153 Incertae sedis 372
Homo heidelbergensis 153 Incertae sedis Eukaryota 360
Habitat 371 Homo neanderthalensis 149 Index fossils 76, 78, 372
Habitat fragmentation 190, 371 Homo rudolfensis 153 India 134
Hacrobia 255, 257, 340, 360, 364 Homo sapiens 153 Indian Ocean 225
Hadean 14, 28–31 Homorhizy 371 Indomalaya 195
Hadrosaurus 133 Horizontal gene transfer 371 Infraciliature 372
Hagen-Vorhalle Brickworks 71 Hornworts. See Acanthoceratophytina Ingestion 372
Hagfish. See Myxini Horsetails. See Equisetopsida Integument 129, 136, 325, 372
Half-life 75 Horst grasses 371 Interglacial 148, 150, 192, 372
Halophile 371 Hotspot volcanism 62, 371 Intermediate disturbance hypothesis 180
Haplobiontic 371 HOX gene 266, 371 Interstitial 372
Haploid 371 Huerteales 329 Intertropical convergence zone 216, 372
Haplonts 120 Humic substances 371 intraspecific 372
Haptonema 362 Humid 371 Intron 54f, 372
Haptophyta 135, 257, 360, 362, 365 Humus or topsoil 371 Invasive species 190
Plastids 56 Hun superterrane 109, 371 Invertebrates, total number of species 177
Hard sediments 21 Huntington formation 59, 371 Involucre 372
Harpetida 88 Huronic Glaciation 48 Iridaceae 326
Heavy rain 371 Hyalin 371 Iris 327
Heliobacteria 40, 43 Hybrids 9, 371 Iron Age 153
Heliozoa 360 Hydrogen 34 Iron ore. See Banded iron ore
Heliozoa 360 Hydrogen carbonate 26, 371 Iron oxide 337
Hematite 49, 218, 371 Hydrogen carbonate anion 371 Iron-sulfur minerals 34
Hemichordata 79, 92, 105, 274 Hydrogen sulphide 40 Iron-sulfur proteins 40
Hemicryptophytes 371 Hydrogenosome 256 Isarcicella 93
Herbivory 371 Hydrogenosomes 8, 254, 256, 298f Ischium 133
Hercosestria 117 Hydroid 316, 371 Isidia 172
Herrerasauria 133 Hydrolysis 372 Island biogeography 184
Herrerasaurus 133 Hydronium ion 372 Island silicate 17
Heterodontosauridae 133 Hydrothermal 372 Isochrysidales 362
Heterodontosaurus 133 Hydrothermal field 34 Isoetales 318
Heterokont 371 Hydroxyl radical 51 Isoetes 318
Heterolobosea 300 Hymenium 289f, 372 Isoetopsida 318
Heterophasic 371 Hymenoptera 137, 372 Isoprenoid 372
Heterosporous 371 Hyolomenus 115 Isospore 372
Heterotrichea 345 Hypercycles 36 Isotherm 372
Heterotrophy 9, 357, 371 Hyphae 172, 282, 284, 286, 288, 290, 352, Isotope 372
Hexactinellida 264 372 Isthmus of Panama 150, 183
Hexagonaria 113 Hyphochytridiomycetes 350
Hexapoda 271 Hypodermal endothecium 372 J
Hibernation 205, 209, 371 Hypotheca 347, 358
Himalaya 18, 138, 140, 142, 145 Jaccard Index 168
394 Index
Jakobida 256, 300 Total number of species 177 Litoral 221

Jamoytius 109 Land snails 111 Litter decomposition 372
Jaw 322 Larix 322 Litter, plant 372
Jawless 95, 106, 274, 277 Lateral 372 Liverworts. See Marchantiophytina
Joenia 299 Laterite 218 Living beings 6
Juniper 322 Lateritisation 218 Lixisol 215
Juniperus 322 Latitudinal 372 Loamification 218, 372
Jupiter 15 Laurales 327 Lobe-finned fish. See Sarcopterygii
Jurassic 77, 125, 130 Laurasia 18, 131 Lobes 88, 372
Laurentia 68, 104, 106, 108, 372 Lobopodia 293
K Laurussia 68, 108, 112, 114 Lobosa 292
Lava 22 Locomotion 9, 359
Kaiyangites 101 Layer 28, 74. See also Stratigraphic layer Loess 24, 372
Karyogamy 289, 291, 372 Lazarus effect 126 Longamoebia 292
Kathablepharidaceae 360, 364 Leaching 211, 217 Longipteryx 135
kDNA 305 Leaching 372 Longitudinal 372
Kenorland 18 Leaf litter 372 Loose sediments 21
Kerona 343, 345 Leaves. See dentate leaves Lophocolea 121, 123
Keuper 124 Leeuwenhoek, Antonie van 230 Lophotrochozoa 272
Kickxellomycotina 286 Leishmania 304 Lorica 262, 372
Kimberella 101 Lemna 237 Loricifera 271
Kimberlite 22 Lenodus 107 Lower Jurassic 124
Kinetid 297f, 372 Lepidodendrales 318 Luciferin 347, 372
Kinetoplast 304, 372 Lepidodendron 97, 114, 318f Lunularia 317
Kinetoplastea 256, 302–305 Lepidoptera 137, 372 Luvisol 205, 210f, 372
Kinetoplast-Kinetosome flagellar pocket Lepidosauria 278 Lycopodiophytina 318
complex 8, 305 Lepidosauromorpha 132 Lycopodiopsida 96, 114, 318
Kinetosome 258, 262, 294, 297f, 304, 351, Lepidozia 317 Lycopodium 318f
372. See also Basal bodies Lepospondyli 94
Kinorhyncha 271 Leptinotarsa 191 M
Klebsormidiophyceae 313–315 Leptomyxida 293
Klebsormidium 315 Leptosporangiate 372 Macronucleus 344
Kleptoplastids 364, 372 Leucilla 265 Mafic 16, 22, 372
Kosmoceras 131 Lichen 108, 172, 201 Magma 21
Lichida 88 Magmatism 22
L Life 2, 4, 6, 372 Magmatite 20, 372
Chemical basis 9, 353 Magnetite 15
Labeotropheus 183 Definition 6, 170 Magnetostratigraphy 74
Labyrinthodontia 94 Origins 34 Magnolia 327
Labyrinthulida 257 Life form 372 Magnoliaceae 326
Labyrinthulomycetes 350 Ligabueino 133 Magnoliales 327
Lactarius 285 Light gradient 311 Magnoliids 324, 326
Laetiporus 241 Light perception 8, 303 Magnoliopsida 324
Lagenidiales 352 Light spectrum 311 Malaria 348
Lagurus 327 Lignin 110, 372 Mallomonas 356
Lake. See Standing water Lignite 142 Malm 124
Lamarck, Jean-Baptiste de 234 Ligula 372 Malpighiales 329
Lamellipodia 293 Liliaceae 326f Malvales 329
Lamiaceae 330 Liliales 327 Mamiellophyceae 313
Lamiales 331 Lilium 327 Mammalia 278. See also Mammals
Lamiiden 330 Limanda 283 Mammals 64, 94, 116, 127, 130, 134, 140,
Laminaria 355 Limestone 98 277f
Lamium 331 Linaria 331 Mammuthus 65
Lancelet 274 Linguliformea 86 Mandibulata 271
Land plants 50, 61f, 64, 67f, 96, 108–110, Linnaeus, Carl or Linné, Carl von 232 Manganese 40
112, 118, 120, 122, 178, 236, 254, 284, Linopteris 115 Manganese ions 51
306, 314, 319. See also Embryophytes Lissamphibia 94, 277 Mangrove 142, 218, 372
Zoochory 329 Lithostratigraphy 74, 372 Mannan 372
Index 395
Mantamonas 259 Methanogenesis 34, 38 Mould 286, 288

Mantle. See Earth, Earth’s mantle Metopus 335 mRNA 54, 373
Marattiopsida 320 Metriaclima 183 Mucoromycotina 258, 286
Marchantiophytina 316 Metromonadea 334 Mucrospirifer 113
Marine luminescence 346 Metzgeria 121, 317 Müllerian mimicry 9
Marinoan glaciation 29, 63, 101 Mica 17 Multicellularity 313
Mars 15 Micrasterias 315 Complex 60
Mass extinction 64, 66, 82, 126, 148 Microaerophilis 373 Simple 60
Devonian 66 Microbial food web 361 Multicilia 293f
Cenozoic 192 Microbial loop 361 Murein layer 56, 281, 317, 373
Cretaceous-Paleogene boundary 66 Microgametocyte 348, 373 Muscovite 17
Ordovician 66, 106 Micrognathozoa 273 Mushrooms 240, 280–291
Oxygen concentration 64 Micronucleus 289, 344 Mussels 78, 86, 127
Permian-Triassic boundary 66, 68, 126 Microorganisms 188, 230 Mutualism 8, 291
The ‘big five’ mass extinction events 66 Microphyll 373 Mycelium hyphae 373. See also Hyphae
Triassic 66, 126 Micropyle 129, 373 Mycetozoa 294
Mass proliferation 363 Microspheres 36 Mycobiont 172
Mastigamoebidae 293f Microsporidia 256, 280, 282 Mycorrhiza 8, 112, 284f, 290, 318, 321
Mastigonema 350, 357, 372 Microtubules 259, 262, 373 mycotroph 318, 373
Maximum-likelihood (estimation) 244 Microvilli 262, 373 Myelin sheath 106
Maximum-parsimony (estimation) 244 Miliolida 80 Myriapoda 269, 271
Mayorella 293 Mimicry 9 Myrtales 329
Mediterranean biome 210 Mineral 373 Myxini 274
Mediterranean Sea 140 Biogenic 9, 337 Myxogastria 293f
Medusa 267 Miocene 138, 142
Megaceros 317 Mitochondria 54, 250, 254, 256, 349 N
Megafauna 192, 372 Mitosis 373
Meganeura 114 Mitosomes 254, 256, 298 NAD 38
Megaphylls 112 Mixotrophy 9, 357, 373 NADH 38
Meiosis 9, 319, 372 Mnium 317 NADP 41
Meiospores 372 Model organisms 9, 343 NADPH 147, 373
Mercury 15 Mollusca 273 Naegleria 300f
Merismopedia 315 Molybdenum 58, 62 Nama-type biota 100
Mesoarchean 28, 32 Monad 373 Nanoplankton 350, 362, 373
Mesoderm 372 Monadofilosa 332, 334 Nassellaria 336
Mesohippus 141 Monilophytes 320 Nautilida (or Nautiloidea) 84, 113
Mesomycetozoa 260 Monocercomonoides 299 Nautilus 355
Mesophilic 250, 252, 372 Monocolpate 324 Nearctic (region) 195
Mesophytic 64 Monocot 325 Nebela 293
Mesoproterozoic 29, 31, 45, 54, 56, 310 Monocotyledons 324 Neighbour-joining (clustering method)
Mesostigmatophytina 312f Monograptidae 92 244
Mesozoic 64 Monograptus 93 Nematoda (or Nematoida) 270
Messel pit 71 Monomers 373 Nematomorpha 270
Metakinetoplastina 304 Monophyllites 127 Nemoral 373
Metameric 268, 373 Monopodial 96, 373 Neoarchaean 28, 32, 44
Metamonada 296, 298 Monosiga 263 Neobiota 190
Metamorphosis 21, 373 Monotropa 237 Neobodonida 305
Metanephridia 268, 270, 373 Moon Neogene 68, 77, 138, 142
Metapopulation 162, 373 Origins 14 Neoproterozoic 29, 31, 45, 60
Metarhodophytales 310 Stabilisation of Earth’s axis 14 Glaciation 62
Metatheria 278 Moraine 24, 373 Neotropics 195, 218
Metazoa 59–61, 67, 100, 164, 230, 238, 247, Morphology 373 Nepenthes 327
256–272 Mosses 120, 122, 287, 316 Nephroselmidophyceae 313
Meteorite impact. See Mass extinction Mosses. See Bryophytina Nephrozoa 268, 274
Methane 34, 38 Motile 265 Neptune 15
Methane clathrate 64, 100, 140, 373 Motility 236, 344, 373 Nereis 269
396 Index
Neural tube 106, 373 Ophiuroidea 90, 274 Pangea 18, 68, 114, 116, 126, 132
Neurocranium 274, 373 Opisthosoma 373 Panthalassic Ocean 104
Neutral Theory 180 Orciraptor 335 Parabasal apparatus 296, 298, 373
Niche 180, 373 Ordovician 68, 82, 84, 88, 98, 106 Parabasalia 256, 298
Differentiation 182 Organelle 9, 341, 349, 373 Parabodonida 305
Nicotinamide dinucleotide. See NAD Organisational form 8, 290, 316 Paradox of the plankton 180
Nitrogen oxides 373 Ornithiscians 130–134 Paramecium 239, 345
Nomenclature 160, 230, 232, 373 Ornithodira 130, 132, 278 Paramylon 257, 303, 374
North Atlantic 130 Ornithopoda 133 Paranthropus 153
Notochord 274, 368, 373. See also Chorda Orobanche 237 Paraphyletic 243
dorsalis Orogeny 26, 68, 140, 373 Paraphysomonas 189
Novopangaea 154 Alpine 140 Parasites 6, 240, 283, 286, 301, 304, 348,
Nuclear envelope 54 Variscan 114, 373 352
Nucleariidae 247, 280 Osmoregulation 9, 351 Paraxonemal rod 296, 302, 374
Nucleic acids 36 Osmotrophy 240, 373 Parenchymula larva 264, 374
Nucleomorph 9, 56, 333, 364 Osteichthyes 94, 276 Pasteur, Louis 188, 234
Nummulitidae 80 Otozamites 97 Paulinella 254, 257, 306, 334
Nymphaea 327 Outgroup 243 Pavlovophyceae 361f
Nymphaeaceae 326 Ovary 373 PCR (polymerase chain reaction) 160, 164,
Nymphaeales 326f Ovule 136 244, 374
Oxalidales 329 Peak 374
O Oxidases 46, 50, 52 Pecopteris 323
Oxidation 373 Pediastrum 313
Obligate 373 Oxidative decarboxylation 53 Pedospumella 357
Ocean 224 Oxygen 16, 30, 34, 47, 48 Pedoturbation 214, 374
Convection 42, 49 Cytotoxic effects 50 Pelagial 221, 374
Formation 14 Evolution geochemical feedback 46 Pelagophyceae 341, 350
Neoproterozoic 62 Molecular 373 Pelagothrix 345
Oxygenation 62, 100 Poisoning 46 Pellicula 296, 302, 374
Paleozoic 104 Radicals 50 Pelmatozoa 90, 274
Primordial 14, 34 Reactive oxygen species (ROS) 375 Pelomyxa 293
Proterozoic 58 Oxygenation 373 Pelycosauria 116
Oceania 195 Oxygenation of the oceans 62, 100 Pentacyclic 328, 374
Oceanic crust 16, 18, 20 Oxymonadida 298 PEP carboxylase 146, 374
Ochrophyta 350, 354, 356, 358 Peptidoglycan 57, 250, 281, 308
Octoglena 269 P Peranema 303
Odontopleurida 88 Percolomonas 300f
Oil shale 70, 373 Pachycephalosauria 133 Percolozoa 256, 300
Old Red Continent 68, 108 Pachycephalosaurus 133 Perhumid 374
Oligocene 138, 140 Pacific Ocean 225 Perhumid (climate) 210, 218, 374
Olivine 16, 22 Palaeocene 138, 140 Peridotite 17, 22
Ononis 329 Palaeoecology 78 Period 28, 74. See also Stratigraphic layer
Ontogeny 90, 373 Palaeogene 77, 138, 140 Periplast 257, 374
Onychophora 110, 271 Palaeolithic 152 Peritrichia 345
Oocyst 348, 373 Palaeoniscus 117 Perkinsiella 304
Oogamy 314, 373 Palaeontology 167, 192, 373 Permafrost 201f
Oogonia 352, 355 Palaeophytic 64 Permian 77, 98, 116
Oomycetes 350, 352 Palaeoproterozoic 29, 31, 45 Permian-Triassic boundary 64
Oospores 373 Palaeozoic 64, 98 Peronospora 352
Opal 337 Palearctic 195 Peronosporomycetes 257, 350, 352
Opalinata 350 Paleoarchean 33 Peroxisomes 51
Opalinida 257, 351 Palmelloid 350, 373 Petromyzontida 276
Operational Taxonomic Unit (OTU) 164 Palmophyllales 313 Petrosalviales 327
Ophioglossales 320 Panarthropoda 270 Pezizomycotina 288
Ophioglossum 321 Pandanales 327 Pfiesteria piscicida 346
Ophistokonta 258 Pangaea Ultima 154 Phacopida 88
Index 397
Phacus 302f Picocystis 313 Plutonite 22

Phaeocystales 362 Picozoa 360 Poaceae 327
Phaeocystis 362 Picramniales 329 Poales 327
Phaeodactylum 343 Pigments, accessory 256, 310, 374 Podocarpales 322
Phaeophyceae 60, 122, 257, 350, 354 Pikaia 105 Podsol 202
Phaeothamniophyceae 350, 354 Pinales 322 Podzol 202
Phagocytosis 8, 297, 374 Pine pollen 355 Polar filament 283
Phagotrophy 304, 374 Pinguiophyceae 350 Polar rings 310, 348, 374
Phalansterium 293f Pinnularia 359 Polaroplast 283
Phanerozoic 28, 64 Pinocytosis 297 Pollen 120, 137
Climate 68 Pinus 143, 322 Pollen grain 120
Overview 66 Piperales 327 Pollination biology 9, 331
Pharetronida 83 Pit connections 60 Evolution 136
Pharynx 374 Placodermi 94, 108, 112, 276 Pollination drops 136
Phloem 321 Placozoa 266 Polycystinea 332, 336
Phoronida 273 Plagioclase 17, 22 Polyp 267
Phosphoglycolate 50 Plagiopus 129, 317 Polyploidisation 344, 374
Photobiont 172 Planation 118, 374 Polypodiopsida 96, 320
Photo-oxidation 42, 374 Planet 14 Polytrichum 121
Photopigments 9, 311, 364 Planktivore 374 Porifera 260–265
Photorespiration 50, 62, 144, 146, 374 Planktonic 180 Porphyridium 311
Photosynthesis 35, 40, 42 Plant geography. See Biogeography Potamal 222
Anoxygenic 38, 40, 46, 58 Plantae. See Viridiplantae Potassium (K)-feldspar 17
C3 42 Plantaginaceae 330 Potassium-argon (K-Ar) dating 75
C4 144-147, 154 Plants. See Land plants PQ-cycle 40, 374
CAM 68, 145f Definition 230, 236 Prasinococcales 313
Compartmentalisation 42 Planula larvae 266, 374 Preaxostyla 256, 297
Manganese 40 Plasmodesmas 60 Precambrian 30f
Oxygen 40, 46, 63 Plasmodesmata 314, 374 Overview 30
Photosystem I 40, 42 Plasmodia 294 Predation 8, 261
Photosystem II 40, 42 Plasmodium 343, 348 Priapulida 271
Phototrophy 9, 357 Plasmogamy 286, 289, 291, 374 Primary production, Primary producers
Phragmoplast 315, 374 Plasmopara 352 30, 35, 46, 64, 110, 112, 144, 170, 187,
Phycobilisome 57, 308, 374 Plastids 42, 54, 56, 254, 256, 333. See also 220, 224, 236, 346, 358, 361f, 374
Phycobillin 256 Paulinella Primary succession 180, 374
Phycoerythrin 57, 310 Glaucocystophyta 56 Primeval ocean 46, 374
Phycomeces 287 Peridinium type species 346 Primordium 330, 374
Phycoplast 313, 374 Primary 56, 306 Priscacara 273
Phylloid 316 Secondary 254, 346, 362 Proboscideans 142, 374
Phyllotaxis 374 Tertiary 346 Procryptobia 305
Phylloxera 191 Plastome 55, 255 Proetida 88, 117
Phylogenetic classification 228 Plate boundaries 16, 18, 22 Progymnosperms 96, 323
Phylogenetic distance 247 Convergent 19 Prokaryotic cell organisation 248, 250, 252
Phylogenetic tree 242, 244 Divergent (or Constructive) 19 Prokinetoplastina 304
Phylogeny 8, 287, 374 Plate tectonics 18, 154 Promastigote 305
Basics 234 Phanerozoic 68 Propagation rate 120
Phylogram 244 Plates, Continental. See Tectonic plates Prosoma 109, 374
Phytium 352 Plathelminthes 247, 273 Prostomatea 345
Phytobiont 172 Platyzoa 272 Proteales 329
Phytomonas 304 Plesiomorphy 242, 374 Proterozoic 28, 30, 44
Phytomyxea 334 Pleural 88, 374 Prothallium 319, 321, 374
Phytophtora infestans 191, 352 Pleurochrysis 363 Protists 228, 230, 374
Phytoplankton 101, 126, 170, 180, 221f, Pleurodont 278, 374 Diversity 177
346, 358, 374 Plicathyris 113 Proto-cell 36
Pica 159 Pliocene 142 Protocyanobacteria 42, 374
Picea 322 Plutonism 22, 374 Proto-Earth 32
398 Index
Protolyellia 105 Conifers 130 Rhodeus 191

Protonema 316, 374 Conodonts 107 Rhodophyta 60, 122, 254f, 256, 306, 310
Protonephridia 260, 270, 272, 374 Dinophyta 130 Rhodophytina 310
Protoperidinium 347 Echinodermata 90, 107 Rhodoplasts 310
Protoplanets 14, 32, 374 Eukaryotes 58 Rhoptries 349, 375
Protosporangiida 293 Flowering plants 137 Rhynchomonas 305
Protostelia 294 Fungi 284 Rhynchonelliformea 86
Protosteliida 293 Gymnosperms 96, 130 Rhynia 97
Protostomia 260, 268 Insects 111, 137 Rhynie chert 71
Provincialism 88, 374 Mammals 94 Rhyniophytina 96, 108, 318
Prunus 329 Reptiles 184 Rhyolite 22f, 375
Prymnesiales 362 Radiocarbon dating 75 Rib breathing 116
Prymnesiophyceae 361f Radioisotope 74f Ribonucleic acid. See RNA
Prymnesium 362 Radiolaria 332, 336 Ribosome 36, 54, 56, 168, 248, 375
Prysonympha 299 Rain, Acid 362, 375 16S 367
Pseudofungi 350 Rainfall distribution, global 196 18S 367
Pseudoparenchyma 310, 374 Rainforest. See Forest: Tropical rainforest 70S 367
Pseudoplasmodia 294, 374 Rangeomorpha 101, 375 Ribozyme 36f, 343
Pseudopodia 8, 293, 374 Ranunculales 329 Ripella 293
Pseudotropheus 183 Ranunculus 329 River continuum concept 222f
Psilotales 320 Raphanus 329 River. See Watercourses
Psilotopsida 320 Raphidophyceae 349f Rivularia 173
Psilotum 321 Ray-finned fishes. See Actinopterygii RNA 36
Psychrophilic taxa 252, 375 Reaction norm 180, 375 RNA-world (hypothesis) 36
Pterosauria 130, 132f Recent 375 Roccella 173
Ptychopariida 88, 105 Recombination rate 120 Rocks 370
Pubis 130, 133 Recrystallisation 25, 375 Age 74
Pucciniomycotina 290 Red iron ore 15 Cycles 20
Purple bacteria 40, 43 Red sediment 48f, 375 Deep subsurface 23
Pusules 375 Red tide 346 Formation processes 20
Pycnococcaceae 313 Redlichiida 88 Magma 20, 22
Pygidium 89, 375 Redox gene 52 Melting 17
Pyramimonadales 313 Redox reaction 38, 375 Metamorphosis 370
Pyramimonas 313 Reducing equivalent 38, 40f, 375 Surface 23
Pyrenoid 303, 334, 347, 365, 375 Reduction 375 Rocky Mountains 18, 140, 142, 196
Pyrite 34, 59 Reefs 82f, 108, 225 Rodinia 18, 44, 58, 62
Pyroclastics 22, 375 Reef builders 82 Romer Gap 114
Pyroxene 17, 22 Regression 64, 375 Rosaceae 329
Pyruvate 38, 53, 375 Reproduction 128 Rosales 329
Reproductive isolation 182, 375 Rosids 328
Q Reptiles 276, 278, 287 Rotaliida 80
Respiratory chain 47, 52 Rotifera 272f
Quadruped 130, 375 Respiratory system 110 Rotliegend 98
Quarternary 74, 138, 148, 150, 192, 375 Retaria 332, 334, 336 r-strategists 190, 375
Quasispecies 170, 375 Reticuloamoeba 335 Rubidium-strontium dating 75
Reticulopodia 293, 332 RuBisCO 50f, 144, 146, 375
Retortamonadida 298 Oxygen 50
R Rhabdinopora 93 Rubus 329
Rhabdosome 92, 375 Rudista 82
Radial symmetry 90, 267 Rheic Ocean 68, 108f, 112 Rugosa 82, 108, 375
Radiation 18, 29, 31, 103, 114, 128, 144, Rhithron 222 Rusts. See Pucciniomycotina
184, 323, 375 Rhizaria 246f, 254f, 257, 332f, 340
Amniota 116 Rhizidium 283 S
Angiosperms 96, 277 Rhizocarpon 173
Birds 94 Rhizoid 316, 375 Sabiales 329
Bivalvia 87 Rhizopoda 334 Sabre-toothed cats 149, 192
Brachiopods 106 Rhizopodial 334, 375 Sacabambaspis 107
Ceratitida 127 Rhizopus 286 Saccamoeba 239
Cichlids 183 Rhodellophytales 310 Saccharomycotina 288
Index 399
Saccorhiza 355 Sessile 265, 375 Disequilibrium theories 186

Sahelanthropus 143, 153 Sexual dimorphism 375 Equilibrium theories 186
Salt deposits 98 Shannon index 166, 168 Global gradients 186
Evaporation cycles 116 Sheet silicate minerals or phyllosilicate 16 Spermatophytina 322. See also Seed plants
Santalales 329 Short-grass steppe 375 Sphaerococcus 311
Sapindales 329 Siberia 58, 104, 126, 202 Sphagnum 317
Saprobiotic 375 Siberian trap volcanism 126 Sphinctozoa 83
Saprolegnia 241 Sicula 92 Spicules 264
Saprolegniales 352 Siderite 38, 375 Spinel 22
Saprophytes 375 Sieve elements 375 Spiniferites 347
SAR-clade 332, 340, 346–361, 375 Sigillaria 114f, 318 Spiralia 268, 272
Sarcopterygii 276 Silene 329 Spirotrichea 345
Sargassum 355 Silica 20 Spliceosome 54, 376
Saturn 15 Silicate 17, 20 Splicing 376
Sauria 132 Silicate weathering 62 Sponges. See Porifera
Saurischia 130, 132 Silicon 16 Spontaneous generation 234, 376
Sauropodomorpha 130, 132, 134 Silicon dioxide 337 Sporangium 376
Sauropsida 278 Silurian 77, 98, 108, 318 Spore 376
Sauropterygia 132f Simpson index 166 Trilete 107
Savannah 214 Sinraptor 133 Sporophyte 122, 317, 319, 321, 376
Saxifragales 329 Sinter 26 Sporoplasm 376
Scalidophora 270f Siphonal 375 Sporopollenin 376
Schizogony 348, 375 Sister group 243 Sporozoite 376
Schizoplasmodiida 293 Skeletal elements 102 Spumella 356
Schizopyrenida 301 S-layer (bacteria) 376 Spumellaria 336
Sciadaopitales 322 Sleeping sickness 304 SSU rRNA 227, 376
Scleractinia 82, 266, 375 Slime moulds 240, 293f Standing waters 220
Sclerite 375 Small shelly fauna or Small shelly fossils Starfish 90
Sclerophytes 210, 375 (SSF) 101–103 Staurikosaurus 130, 133
Scolelepis 269 Smilodon 149, 193 Staurocalyptus 265
Scrophulariaceae 330 Smut fungi. See Ustilaginomycotina Stegosauria 133
Scuticociliatea 345 Snails 79, 111, 141, 359 Stegosaurus 133
Sea cucumber 90 Snakes 134 Stephanopogon 300f
Sea urchin 90 Snowball Earth 48, 62, 376 Steppes 206
Seas 224. See also Oceans Soil horizon 376 Stomach stone or Gastrolith 376
Seawater 224 Solanales 331 Stomata 112, 316, 376
Sedimentary rocks 20, 24 Solar climatic zones 376 Stomatocysts 357
Sedimentation 24 Solar nebula 376 Storage polysaccharides 256
Sediments 20, 24, 375 Solar system 14f Stramenopiles 247, 255, 257, 340, 350–359
Chemical 25 Solitary 376 Plastids 56
Clastic rock 25, 368 Solnhofener Plattenkalk 91, 132 Stratigraphic layer
Seed coat 128f Solonchak 213 Archaean 33
Seed dormancy 201 Somatogamy 376 Cenozoic 139
Seed ferns 11f, 127, 322f Soredia 172 Mesozoic 125
Seed plants 96, 110, 120–129, 136, 322 Sorus 376 Palaeozoic 99
Origins 96 Species 4, 8 Proterozoic 45
Segmentation 8, 269 Coexistence 180 Stratigraphy 28, 74, 78, 376
Selaginella 318f Definition 8 Stratotype 28, 76, 376
Selaginellales 318 Description 160 Streptophyta 62, 256, 306, 314, 365
Semi-arid 375 Distribution 158 Strobili 108, 376
Semi-humid 375 Formation 182, 184 Strobylothyone 127
Semiochemicals 295 Total number 176 Stromatolites 31f, 48f
Semiparasite 330, 375 Species concept 8, 376 Stromatopores 376
Sepia 355 Biological 162, 376 Stromatoporoidea 82
Septum 375 Ecological 162, 376 Stuart glaciation 62
Series 28, 74, 375. See also Stratigraphic Evolutionary 162, 376 Stygamoebida 293
layer Morphological 162, 376 Subasaphus 107
Serrated leaves 375 Species Plantarum (Carl Linnaeus) 232 Subduction 18, 20
Sesquiterpenes 375 Species richness 166 Subduction zone 22, 376
400 Index
Substitution 246, 376 Temporomandibular joint (see Jaw) 276 Triceratops 133
Substrate 376 Terminal oxidation 52, 53 Trichal 310, 377
Succulence 213 Termites 214, 216 Trichocysts 344, 377
succulent 376 Terrestrial vertebrates. See Tetrapoda Trichomonas 298
Sulfate respiration 59f Tertiary 138. See also Neogene Trichophycus 44
Sulfide 64 Tesselaria 356 Trichoplax 266f
Summer rainy season 214, 216 Testudines 279 Tricolpate 324
Sunlight 49 Tethys 130, 376 Tridacna 239
Supercontinent 18,126, 323, 376 Paleo-Tethys Ocean 108, 126, 373 Trifolium 329
Superoxide dismutase 51, 52 Paratethys Ocean 140 Trigonia 131
Surface scales 9, 365 Tetrahymena 343 Trilobita 88, 105, 271
Suspensor 128, 376 Tetrapoda 94, 112, 276, 278 Trimastix 299
Suture 78, 88, 376 Tetraspores 376 Tripartite hairs 340
Sutures 84, 376 Tetrasporophyte 310, 376 Triploblastic 377
Symbiontida 302 Tetrastrum 313 Trochodendrales 329
Symbiosis 6, 172f, 258, 284, 291. See also Textulariida 80 Trochophore larvae 377
Endocytobiosis Thalassiosira 359 Trochozoa 272f
Sympatric speciation 182 Thallos or Thallus 316, 376 Trophy 220
Sympetaly 330, 376 Thallus 316, 376 Trypanosoma 304
Symplesiomorphy 242, 376 Thecamoeba 293 Trypanosomatida 304, 305
Synapomorphy 242, 376 Thecamoebida 292 Trypomastigote 304
Synapsids 94, 116, 278 Thecodont 278, 376 Tubulin 377
Synchromophyceae 350 Thecofilosea 334 Tubulinea 256, 292
Syngamy 120, 376 Theophrastus 230 Tuff 23
Synorisporites 107 Therapsida 94 Tundra 200
Synthesis 376 Theria 278 Tunicata 274
Synura 356 Thermophile 376 Turtles 278
Synurales 356 Theropoda 132f Type locality 76, 377
Synurophyceae 356 Thioredoxin 314, 377 Tyrannosauroidea 133
System 28, 74. See also Stratigraphic layer Thorax 88f Tyrannosaurus 65, 134
Systema Naturae 232, 236 Three-domain model 248
Systematics 160 Thrinaxodon 95 U
Fundamentals 232 Thuja 322
Thylacinus 193 Ubiquitous 377
T Thylakoid 42, 308, 310, 377 Ulothrix 313
Thylakoid membrane 42 Ulva 313
Tabulata 82, 108, 376 Thymine 36 Ulvophyceae 313
Taiga 202 Tight junctions 274, 377 Undergrowth 377
Tall-grass prairie 372 Tillite 24, 376 Unikonta 254–259
Tange 355 Timofeevia 105 Unio 191
Taphrinomycotina 288 Tomentella 285 Universe 14
Tardigrada 271 Torpor 200, 377 Ur 18
Tardigrades. See Tardigrada Toxins 377 Uracil 36
Taxales 322 Toxoplasma 348 Ural 116
Taxon, Taxa 8, 323 Toxoplasmosis 348 Uranium-lead dating 75
Taxonomy 160, 376 Trace fossil 59 Uranus 15
Rank 306 Tracheae 110, 205, 270, 325, 358, 377 Uridine monophosphate 258, 377
Taxus 322 Trachelomonas 303 Urochordata 274
Tectosilicates 17 Transcription 377 Uroid 292, 377
Teleoblastic growth zone 270, 376 Transcriptome 377 Uromyces 291
Teleostomi 276 Transgression 377 Ustilaginomycotina 290
Telome 376 Transition 377 UV radiation 14, 208, 377
Telome theory 118 Translation 377
Telonema 360 Transversion 377 V
Temperature distribution, global 196 Trebouxiophyceae 313
Temporal window 278 Triassic 77, 124f Vacuole, contractile 344, 351, 377
Index 401
Vahlkampfia 301 Z
Vahlkampfiidae 301
Vampyrella 335 Zamites 65, 131
Vampyrellida 334 Zea mays 155, 327
Vannellida 293 Zebra mussel 191
Variosea 294 Zechstein (rock layers) 98
Vascular bundle, types 9, 321 Zingiberales 327
Velociraptor 133 Zoochlorellae 312, 345, 377
Venus 15 Zoogeography. See Biogeography
Verbascum 331 Zoopagomycotina 286
Vertebrata 94, 106, 110, 178f, 274, 303 Zoophagus 286f
Species diversity 177 Zoospores 377
Vertisol 214 Zooxanthellae 345f, 377
Vesicles 60, 377 Zosterophyllopsida 96, 108
Viridiplantae 306, 312 Zygnema 315
Virion or Virus particles 170 Zygnematophytina 314
Virus 170 Zygomycota 256. See Zygospore-forming
Vitales 329 fungi
Viteus 191 Zygophyllales 329
Vitis 191 Zygospore 286
Vitrella 343 Zygospore-forming fungi 286
Viviparity 377 Zygote 377
Volcanism 22, 48, 377
Carbon dioxide 48
Volcano 22
Volvox 313, 343
Vorticella 345
Vulcanite 20, 23
Wallace, Alfred Russel 234

Watercourses 222
Weathering 21, 24, 377
Welwitschia 322
Whales 141
White Sea-type biota or Ediacara biota 100
Whorl 377
Wind dispersal 329
Wind patterns, global 198
Winter dry season 214
Xanthoria 173
Xantophyceae 350
Xeromorphic 202, 377
Xestospongia 265
Xylem 321
Yeasts 287
Yolk 129
Yolk sac 377

Biodiversity and Earth History - Boenigk, Wodniok, Glücksman

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Biodiversity and Earth History - Boenigk, Wodniok, Glücksman

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Jens Boenigk · Sabina Wodniok

ISBN 978-3-662-46393-2 ISBN 978-3-662-46394-9 (eBook)

Library of Congress Control Number: 2015936446

Springer Heidelberg New York Dordrecht London

Photo for Cover by Stuart Westmorland, Mill Creek, WA, USA

Printed on acid-free paper

Springer-Verlag GmbH Berlin Heildelberg is part of Springer Science+Business Media (www.springer.com)

1.1 How do I use this book? .............................................................................................................. 2

1.2 Biodiversity ..................................................................................................................................... 4

1.3 Life .................................................................................................................................................... 6

1.4 Species ............................................................................................................................................. 8

2 Earth‘s History ................................................................................................................................ 11

2.1 Fundamentals of the geosciences ............................................................................................ 12

2.1.1 Construction and formation of the Earth .................................................................................. 14

2.2 The Precambrian ........................................................................................................................... 30

2.2.1 The Archean eon ....................................................................................................................... 32

2.3 The Phanerozoic eon ................................................................................................................... 64

2.3.1 The Phanerozoic eon: an overview ........................................................................................... 66

2.3.5.7 Hominisation ..................................................................................................................... 152

3 Distribution of present-day biodiversity ....................................................................... 157

3.1 Basics of the biogeographical distribution of taxa ............................................................... 158

3.1.1 Species descriptions .................................................................................................................. 160

3.2 Biodiversity distribution .............................................................................................................. 174

3.2.1 Pattern and mechanisms .......................................................................................................... 176

4 Megasystematics .......................................................................................................................... 227

4.1 Basics of Megasystematics ......................................................................................................... 228

4.1.1 Historical and philosophical basis of megasystematics ............................................................. 230

4.2.1 Holozoa ..................................................................................................................................... 260

4.3.1 Metamonada ............................................................................................................................ 298

4.4 Archaeplastida ............................................................................................................................... 306

4.4.1 Glaucocystophyta ...................................................................................................................... 308

4.5.1 Cercozoa.................................................................................................................................... 334

4.6.1 Alveolata ................................................................................................................................... 342

Glossary ................................................................................................................................................... 367

References ............................................................................................................................................. 379

Index .......................................................................................................................................................... 387

List of subject boxes

Cilium/Flagellum ............................................................................................................................................... 259

Protection from predation ................................................................................................................................ 261

Predator-prey size relationships ........................................................................................................................ 263

Motile and sessile lifestyles ............................................................................................................................... 265

Symmetry and body structure ........................................................................................................................... 267

Segmentation .................................................................................................................................................... 269

Freezing and thawing ........................................................................................................................................ 271

Why can some fossils not be found? ................................................................................................................. 273

Protection from UV radiation ............................................................................................................................ 275

The development of dinosaurs and angiosperms ............................................................................................. 277

Size and dimensions .......................................................................................................................................... 279

Cell wall materials ............................................................................................................................................. 281

Generational shift in parasites .......................................................................................................................... 283

Organisational morphology and phylogeny....................................................................................................... 287

Multinucleate cells ............................................................................................................................................ 289

Symbiosis / mutualism ...................................................................................................................................... 291

Pseudopodia ...................................................................................................................................................... 293

Chemical communication and semiochemicals................................................................................................. 295

Phagocytosis ...................................................................................................................................................... 297

Reducing of genome size in parasites................................................................................................................ 301

Perception of light ............................................................................................................................................. 303

Position of the kinetoplast-kinetosome-flagellar pocket complex .................................................................... 305

Chlorophyll ........................................................................................................................................................ 307

Are higher-level organisms evolutionarily better-adapted? .............................................................................. 309

Photo pigments and vertical ecological niches.................................................................................................. 311

Multicellularity .................................................................................................................................................. 313