Strengthening global-change science by integrating aeDNA with paleoecoinformatics

John W Williams; Trisha L Spanbauer; Peter D Heintzman; Jessica Blois; Eric Capo; Simon J Goring; Marie-Eve Monchamp; Laura Parducci; Jordan M Von Eggers; Contributing authors

doi:10.1016/j.tree.2023.04.016

Strengthening global-change science by integrating aeDNA with paleoecoinformatics

Trends Ecol Evol. 2023 Oct;38(10):946-960. doi: 10.1016/j.tree.2023.04.016. Epub 2023 May 23.

Authors

John W Williams¹, Trisha L Spanbauer², Peter D Heintzman³, Jessica Blois⁴, Eric Capo⁵, Simon J Goring⁶, Marie-Eve Monchamp⁷, Laura Parducci⁸, Jordan M Von Eggers⁹; Contributing authors

Collaborators

Contributing authors:
Inger Greve Alsos, Chris Bowler, Marco J L Coolen, Nicola Cullen, Sarah Crump, Laura Saskia Epp, Antonio Fernandez-Guerra, Eric Grimm, Ulrike Herzschuh, Alessandro Mereghetti, Rachel Sarah Meyer, Kevin Nota, Mikkel Winther Pedersen, Vilma Pérez, Beth Shapiro, Kathleen R Stoof-Leichsenring, Jamie Wood

Affiliations

¹ Department of Geography, University of Wisconsin-Madison, Madison, WI 53704, USA. Electronic address: [email protected].
² Department of Environmental Science and Lake Erie Center, University of Toledo, Toledo, OH 43606, USA.
³ The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway; Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden.
⁴ Department of Life and Environmental Sciences, University of California -Merced, Merced, CA 95343, USA.
⁵ Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 4-6, 907 36 Umeå, Sweden.
⁶ Department of Geography, University of Wisconsin-Madison, Madison, WI 53704, USA.
⁷ Department of Biology, McGill University, Montreal, QC, Canada.
⁸ Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.
⁹ Department of Geology and Geophysics, University of Wyoming, Laramie, WY 82071, USA.

PMID: 37230884
DOI: 10.1016/j.tree.2023.04.016

Abstract

Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.

Keywords: ancient environmental DNA; community-curated data resources; global change ecology; metabarcoding; paleoecoinformatics.

Publication types

Review
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Biodiversity*
Computational Biology
DNA Barcoding, Taxonomic
DNA, Ancient*

Substances

DNA, Ancient