Million-year-old DNA sheds light on the genomic history of mammoths

Tom van der Valk (), Patrícia Pečnerová, David Díez-del-Molino, Anders Bergström, Jonas Oppenheimer, Stefanie Hartmann, Georgios Xenikoudakis, Jessica A. Thomas, Marianne Dehasque, Ekin Sağlıcan, Fatma Rabia Fidan, Ian Barnes, Shanlin Liu, Mehmet Somel, Peter D. Heintzman, Pavel Nikolskiy, Beth Shapiro, Pontus Skoglund, Michael Hofreiter, Adrian M. Lister, Anders Götherström and Love Dalén ()
Additional contact information
Tom van der Valk: Centre for Palaeogenetics
Patrícia Pečnerová: Swedish Museum of Natural History
David Díez-del-Molino: Centre for Palaeogenetics
Anders Bergström: The Francis Crick Institute
Jonas Oppenheimer: University of California Santa Cruz
Stefanie Hartmann: University of Potsdam
Georgios Xenikoudakis: University of Potsdam
Jessica A. Thomas: University of Potsdam
Marianne Dehasque: Centre for Palaeogenetics
Ekin Sağlıcan: Middle East Technical University
Fatma Rabia Fidan: Middle East Technical University
Ian Barnes: Natural History Museum
Shanlin Liu: China Agricultural University
Mehmet Somel: Middle East Technical University
Peter D. Heintzman: UiT – The Arctic University of Norway
Pavel Nikolskiy: Russian Academy of Sciences
Beth Shapiro: University of California Santa Cruz
Pontus Skoglund: The Francis Crick Institute
Michael Hofreiter: University of Potsdam
Adrian M. Lister: Natural History Museum
Anders Götherström: Centre for Palaeogenetics
Love Dalén: Centre for Palaeogenetics

Nature, 2021, vol. 591, issue 7849, 265-269

Abstract: Abstract Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

Date: 2021
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DOI: 10.1038/s41586-021-03224-9

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