Environmental genomics of Late Pleistocene black bears and giant short-faced bears

Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,^1-3 by allowing for parallel sequencing of DNA from all trophic levels.^4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,⁹ the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.^5,6,10,11 This is in contrast to data from fossils^12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.^14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.