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

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 intothe Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale(1), the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago(2). 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.

Automated summary

This study reveals the presence of two distinct mammoth lineages in eastern Siberia during the Early Pleistocene, with one lineage giving rise to the woolly mammoth and another representing an unrecognized lineage ancestral to the first mammoths to colonize North America. Additionally, the study shows that the Columbian mammoth of North America can trace its ancestry back to a hybridization event between these two lineages during the Middle Pleistocene, with roughly equal admixture proportions. Moreover, the majority of protein-coding changes associated with cold adaptation in woolly mammoths were found to be present as early as one million years ago.