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 from all trophic levels. However, because samples contain sparse fragmented data multiple individuals, often closely related species, the field eDNA so far been limited organellar genomes its contribution population phylogenetic studies. This is contrast fossils where full-genome studies are routine, despite these being rare their destruction undesirable. Here, we report retrieval three low coverage (0.03x) American black bear (Ursus americanus) a 0.04x genome an extinct giant short-faced (Arctodus simus) cave sediment northern Mexico dated 16-14 thousand calibrated years before present (cal kyr BP), which contextualize with new high (26x) two lower ~22-30 cal BP old Yukon fossils. We show that Late Pleistocene ancestrally day eastern population, bears were deeply divergent earlier Beringian population. Our findings demonstrate separately analyse genomic-scale sequences species co-preserved samples, brings use into era genomics phylogenetics.