Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

Abstract

SUMMARY Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyperlipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479–343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardio-vascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

“…The Alpine individual was born in South Slovenia but sampled about 400 km west in the Adamello National Park in Italy, where it was released in year 2000 during a reintroduction project (21). Paired-end Illumina sequences were aligned to the polar bear reference genome (22), and data analyses were performed on these and other available whole-genome data (SI Appendix, Table S1) from two Swedish brown bears, six polar bears, one black bear, and the panda. Four individuals (one from the Apennine, one from the Alps, one from Slovakia and one from Spain) were sequenced at an average depth of coverage of ~15X, versus ~5X for all other individuals.…”

“…S4). This is probably a consequence of a longer history at low density and high connectivity in polar compared to Apennine bear (22,27). Apennine bear genomes likely accumulated the effects of strong inbreeding occurring recently, but the fraction of their genomes at high variation still reveals a past history at much higher effective population size.…”

“…A total of ~2.14 billion reads were uniquely mapped (SI Appendix, section S1.3) to 357 autosomal scaffolds (~2.16Gb: 95.3% of the whole assembly) of the polar bear reference genome (22) with high confidence (Q>=25). We included in our analyses two European brown bears from Sweden, six polar bears and one black bear data from previously published studies (22,75). Eight individuals were sequenced at low coverage with an average sequencing depth of 2.4 to 6.3X, whereas the four remaining individuals were sequenced at higher coverage (from 14.4 to 16.5X).…”

The Geography of Ecological Niche Evolution in Mammals

“…species harbouring divergent traits) within Carnivora generally inhabit very distinct environments, for instance with one living in a temperate or tropical region, and another inhabiting arctic regions (e.g. polar bear vs. other bears [22]), which suggests an interplay between high dispersal capabilities followed by strong natural selection, especially for top predators in the Arctic.…”

“…species harbouring divergent traits) within Carnivora generally inhabit very distinct environments, for instance with one living in a temperate or tropical region, and another inhabiting arctic regions (e.g. polar bear vs. other bears [22]), which suggests an interplay between high dispersal capabilities followed by strong natural selection, especially for top predators in the Arctic.While trait convergence and divergence patterns at the species scale seem to be present in mammals, it remains unknown whether and how these species scale patterns contribute to the trait structure of entire species assemblages, and in particular to trait similarity between different biotas [5]. We define here species assemblages as the sets of species whose range maps intersect with grid cells defined at 200x200 km resolution.…”