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, by allowing for parallel sequencing of DNA from all trophic levels. However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species, the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies. This is in contrast to data from fossils where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable. Here, we report the retrieval of three low coverage (0.03x) genomes from American black bear (Ursus americanus) and a 0.04x genome of an 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 (26x) and two lower coverage giant short-faced bear genomes from ~22-30 cal kyr BP old Yukon fossils. 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 analyse 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.