Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates

Julie M Allen; Charlotte C Germain-Aubrey; Narayani Barve; Kurt M Neubig; Lucas C Majure; Shawn W Laffan; Brent D Mishler; Hannah L Owens; Stephen A Smith; W Mark Whitten; J Richard Abbott; Douglas E Soltis; Robert Guralnick; Pamela S Soltis

doi:10.1016/j.isci.2018.12.002

Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates

iScience. 2019 Jan 25:11:57-70. doi: 10.1016/j.isci.2018.12.002. Epub 2018 Dec 8.

Authors

Affiliations

¹ Department of Biology, University of Nevada Reno, Reno, NV 89557, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. Electronic address: [email protected].
² Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
³ Department of Plant Biology, Southern Illinois University, Carbondale, IL 62901, USA.
⁴ Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ 85008, USA.
⁵ School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, Australia.
⁶ University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-2465, USA.
⁷ Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen O, Denmark.
⁸ Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103, USA.
⁹ Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; School of Mathematical and Natural Sciences, The University of Arkansas at Monticello, Monticello, AR 71655, USA.
¹⁰ Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA.
¹¹ Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA.
¹² Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA.

Abstract

Recent availability of biodiversity data resources has enabled an unprecedented ability to estimate phylogenetically based biodiversity metrics over broad scales. Such approaches elucidate ecological and evolutionary processes yielding a biota and help guide conservation efforts. However, the choice of appropriate phylogenetic resources and underlying input data uncertainties may affect interpretation. Here, we address how differences among phylogenetic source trees and levels of phylogenetic uncertainty affect these metrics and test existing hypotheses regarding geographic biodiversity patterns across the diverse vascular plant flora of Florida, US. Ecological niche models for 1,490 Florida species were combined with a "purpose-built" phylogenetic tree (phylogram and chronogram), as well as with trees derived from community resources (Phylomatic and Open Tree of Life). There were only modest differences in phylodiversity metrics given the phylogenetic source tree and taking into account the level of phylogenetic uncertainty; we identify similar areas of conservation interest across Florida regardless of the method used.

Keywords: Biogeography; Plant Biology; Spatial Phylogenetics.