Environmental genomics of Late Pleistocene black bears and giant short-faced bears
Mikkel Winther Pedersen, Bianca De Sanctis, Nedda F. Saremi, Martin Sikora, Emily E. Puckett, Zhenquan Gu, Katherine L. Moon, Joshua D. Kapp, Lasse Vinner, Zaruhi Vardanyan, Ciprian F. Ardelean, Joaquı́n Arroyo-Cabrales, James A. Cahill, Peter D. Heintzman, Grant D. Zazula, R. D. E. MacPhee, Beth Shapiro, Richard Durbin, Eske Willerslev
Abstract
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.