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

作者：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, Joaquín Arroyo‐Cabrales, James A. Cahill, Peter D. Heintzman, Grant D. Zazula, R. D. E. MacPhee, Beth Shapiro, Richard Durbin, Eske Willerslev · 发表于：Current Biology · 年份：2021 · DOI：10.1016/j.cub.2021.04.027 · 被引用次数：91 · 研究领域：Wildlife Ecology and Conservation、Species Distribution and Climate Change、Genetic diversity and population structure

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 demonst...