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https://doi.org/10.1038/s41586-021-03224-9
Received: 3 July 2020
Accepted: 11 January 2021
Published online: 17 February 2021
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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 780560 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 ofthese 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.
The recovery of genomic data from specimens that are many thousands of years old has improved our understanding of prehistoric population dynamics, ancient introgression events and the demography of extinct species3-5. However, some evolutionary processes occur over timescales that have often been considered beyond the temporal limits of ancient DNA research. For example, many present-day mammal and bird species originated during the Early and Middle Pleistocene6,7. Palaeogenomic investigations of their speciation process would thus require recovery of ancient DNA from specimens that are at least several hundreds of thousands of years old.
Mammoths (Mammuthus sp.) appeared in Africa approximately five million years ago (Ma), and subsequently colonized much of the Northern Hemisphere8,9. During the Pleistocene epoch (2.6 Ma to 11.7 thousand years ago (ka)), the mammoth lineage underwent evolutionary changes that produced the southern mammoth (Mammuthus meridionalis) and steppe mammoth (Mammuthus trogontherii), which later gave rise to the Columbian mammoth...