Insights into bear evolution from a Pleistocene polar bear genome

Abstract

The polar bear (Ursus maritimus) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population history, including evidence for ancient admixture between polar bears and brown bears (Ursus arctos). Here, we extend our earlier studies of a 130,000-115,000-year-old polar bear from the Svalbard Archipelago using 10X coverage genome sequence and ten new genomes of polar and brown bears from contemporary zones of overlap in northern Alaska. We demonstrate a dramatic decline in effective population size for this ancient polar bear's lineage, followed by a modest increase just before its demise. A slightly higher genetic diversity in the ancient polar bear suggests a severe genetic erosion over a prolonged bottleneck in modern polar bears. Statistical fitting of data to alternative admixture graph scenarios favors at least one ancient introgression event from brown bears into the ancestor of polar bears, possibly dating back over 150,000 years. Gene flow was likely bidirectional, but allelic transfer from brown into polar bear is the strongest detected signal, which contrasts with other published works. These findings have implications for our understanding of climate change impacts: polar bears, a specialist Arctic lineage, may not only have undergone severe genetic bottlenecks, but also been the recipient of generalist, boreal genetic variants from brown bear during critical phases of Northern Hemisphere glacial oscillations.

A Beary Good Genome: Haplotype-Resolved, Chromosome-Level Assembly of the Brown Bear (Ursus arctos)

“…Moreover, inconsistencies with previous estimates of total N e across species appear to be attributable to differences in the selected mutation rate. Here, we predict a nearly doubled N e compared to previous results ( Cahill et al 2013 ; Liu et al 2014 ; Kumar et al 2017 ; Zhu et al 2020 ; Endo et al 2021 ; Lan et al 2022 ), which is consistent with expectations for having a mutation rate that is approximately halved ( Nadachowska-Brzyska et al 2016 ). This mutation rate is likely more accurate since it was calculated directly through trio sequencing (Wang et al 2022).…”

“…In order to investigate the synteny between our genome and the polar bear (the closest relative to the brown bear with an estimated divergence date of more than one million years ( Bidon et al 2014 ; Cronin et al 2014 ; Lan et al 2022 ), we performed a whole-genome alignment. A total of 38 autosomal scaffolds comprising 2.17 Gb were identified as the major autosomal scaffolds in the brown bear.…”

A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos)

“…Moreover, inconsistencies with previous estimates of total N e across species appear to be attributable to differences in the selected mutation rate. Here, we predict a nearly doubled N e compared to previous results (Cahill et al 2013;Kumar et al 2017;Endo et al 2021;Zhu et al 2020;Liu et al 2014;Lan et al 2022), which is consistent with expectations for having a mutation rate that is approximately halved (Nadachowska-Brzyska et al 2016). This mutation rate is likely more accurate since it was calculated directly through trio sequencing…”

“…In order to investigate the synteny between our genome and the polar bear (the closest relative to the brown bear with an estimated divergence date of more than one million years (Lan et al 2022; Bidon et al 2014; Cronin et al)), we performed a whole-genome alignment. Both the polar bear and the brown bear are ursine bear species, which are known to have a stable karyotype of 2n = 74 (Nash et al 1998; Wurster-Hill & Bush).…”

“…In order to investigate the synteny between our genome and the polar bear (the closest relative to the brown bear with an estimated divergence date of more than one million years (Lan et al 2022;Bidon et al 2014;Cronin et al)), we performed a whole-genome alignment.…”