Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role

Abstract

Background: Polar bears are uniquely adapted to an Arctic existence. Since their relatively recent divergence from their closest living relative, brown bears, less than 500,000 years ago, the species has evolved an array of novel traits suited to its Arctic lifestyle. Previous studies sought to uncover the genomic underpinnings of these unique characteristics, and disclosed the genes showing the strongest signal of positive selection in the polar bear lineage. Here, we survey a comprehensive dataset of 109 polar bear and 33 brown bear genomes to investigate the genomic variants within these top genes present in each species. Specifically, we investigate whether fixed homozygous variants in polar bears derived from selection on standing variation in the ancestral gene pool or on de novo mutation in the polar bear lineage. Results: We find that a large number of sites fixed in polar bears are biallelic in brown bears, suggesting selection on standing variation. Moreover, we uncover sites in which polar bears are fixed for a derived allele while brown bears are fixed for the ancestral allele, which we suggest may be a signal of de novo mutation in the polar bear lineage. Conclusions: Our findings suggest that, among other mechanisms, natural selection acting on changes in genes derived from a combination of variation already in the ancestral gene pool, and from de novo missense mutations in the polar bear lineage, may have enabled the rapid adaptation of polar bears to their new Arctic environment.

Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator

“…The dietary plasticity of polar bears indicated by our findings may be a key attribute in the resilience of the species, acting to buffer the relatively low levels of genetic variation on which selection can act ( 21 , 28 , 54 ). Prey abundances are much lower in east Greenland, and, therefore, bears in this region may be especially prone to dietary shifts ( 55 ).…”

Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation

“…This lends to the idea that the variants we discuss here may not have been pivotal in the early adaptation, but may have been driven by increased selective pressures during the last glacial period. Other genes showing a strong signal of selection in the polar bear lineage, such as ABCC6 and COL5A3, also have functions related to the cardiovascular system and metabolism [4]. Only they have alleles fixed in the Late Pleistocene bears, and they may therefore have played a key role in driving the early adaptation of polar bears to a lipid-rich diet.…”

The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations

“…Adapters, stretches of Ns, and low-quality bases in reads were trimmed and filtered with AdapterRemovalv2 [33] using default parameters. BWA-backtrack v0.7.15 [34] was used to map the cleaned reads to the polar bear pseudo-chromosome genome [35,36] (based on Genbank accession: GCA_000687225.1), which included a mitochondrial genome (Genbank accession: NC003428), with default parameters. Reads with mapping quality < 30 were filtered using SAMtools [37].…”