Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Yucheng Wang, Mikkel Winther Pedersen, Inger Greve Alsos, Bianca Sanctis, Fernando Racimo, Ana Prohaska, Eric Coissac, Hannah Lois Owens, Marie Kristine Føreid Merkel, Antonio Fernandez-Guerra, Alexandra Rouillard, Youri Lammers, Adriana Alberti, France Denoeud, Daniel Money, Anthony H. Ruter, Hugh McColl, Nicolaj Krog Larsen, Anna A. Cherezova, Mary E. Edwards, Grigory B. Fedorov, James Haile, Ludovic Orlando, Lasse Vinner, Thorfinn Sand Korneliussen, David W. Beilman, Anders A. Bjørk, Jialu Cao, Christoph Dockter, Julie Esdale, Galina Gusarova, Kristian K. Kjeldsen, Jan Mangerud, Jeffrey T. Rasic, Birgitte Skadhauge, John Inge Svendsen, Alexei Tikhonov, Patrick Wincker, Yingchun Xing, Yubin Zhang, Duane G. Froese, Carsten Rahbek, David Nogues Bravo, Philip B. Holden, Neil R. Edwards, Richard Durbin, David J. Meltzer, Kurt H. Kjær, Per Möller and Eske Willerslev ()
Additional contact information
Yucheng Wang: University of Cambridge
Mikkel Winther Pedersen: University of Copenhagen
Inger Greve Alsos: UiT— The Arctic University of Norway
Bianca Sanctis: University of Cambridge
Fernando Racimo: University of Copenhagen
Ana Prohaska: University of Cambridge
Eric Coissac: UiT— The Arctic University of Norway
Hannah Lois Owens: University of Copenhagen
Marie Kristine Føreid Merkel: UiT— The Arctic University of Norway
Antonio Fernandez-Guerra: University of Copenhagen
Alexandra Rouillard: University of Copenhagen
Youri Lammers: UiT— The Arctic University of Norway
Adriana Alberti: Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)
France Denoeud: CEA, CNRS, Université Evry, Université Paris-Saclay
Daniel Money: University of Cambridge
Anthony H. Ruter: University of Copenhagen
Hugh McColl: University of Copenhagen
Nicolaj Krog Larsen: University of Copenhagen
Anna A. Cherezova: St Petersburg State University
Mary E. Edwards: University of Southampton
Grigory B. Fedorov: St Petersburg State University
James Haile: University of Copenhagen
Ludovic Orlando: Université Paul Sabatier, Faculté de Médecine Purpan
Lasse Vinner: University of Copenhagen
Thorfinn Sand Korneliussen: University of Copenhagen
David W. Beilman: University of Hawaii
Anders A. Bjørk: University of Copenhagen
Jialu Cao: University of Copenhagen
Christoph Dockter: Carlsberg Research Laboratory
Julie Esdale: Colorado State University
Galina Gusarova: UiT— The Arctic University of Norway
Kristian K. Kjeldsen: Geological Survey of Denmark and Greenland
Jan Mangerud: University of Bergen
Jeffrey T. Rasic: US National Park Service, Gates of the Arctic National Park and Preserve
Birgitte Skadhauge: Carlsberg Research Laboratory
John Inge Svendsen: University of Bergen
Alexei Tikhonov: , Russian Academy of Sciences
Patrick Wincker: CEA, CNRS, Université Evry, Université Paris-Saclay
Yingchun Xing: Chinese Academy of Fishery Sciences
Yubin Zhang: Jilin University
Duane G. Froese: University of Alberta
Carsten Rahbek: University of Copenhagen
David Nogues Bravo: University of Copenhagen
Philip B. Holden: The Open University
Neil R. Edwards: The Open University
Richard Durbin: University of Cambridge
David J. Meltzer: University of Copenhagen
Kurt H. Kjær: University of Copenhagen
Per Möller: Lund University
Eske Willerslev: University of Cambridge

Nature, 2021, vol. 600, issue 7887, 86-92

Abstract: Abstract During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1–8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe–tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe–tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

Date: 2021
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DOI: 10.1038/s41586-021-04016-x

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