Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift

Copy number variation describes the degree to which contiguous genomic regions differ in their number of copies among individuals. Copy number variable regions can drive ecological adaptation, particularly when they contain genes. Here, we compare differences in gene copy numbers among 17 polar bear and 9 brown bear individuals to evaluate the impact of copy number variation on polar bear evolution. Polar bears and brown bears are ideal species for such an analysis as they are closely related, yet ecologically distinct. Our analysis identified variation in copy number for genes linked to dietary and ecological requirements of the bear species. These results suggest that genic copy number variation has played an important role in polar bear adaptation to the Arctic.

Polar bear (Ursus maritimus) and brown bear (Ursus arctos) are recently diverged species that inhabit vastly differing habitats. Thus, analysis of the polar bear and brown bear genomes represents a unique opportunity to investigate the evolutionary mechanisms and genetic underpinnings of rapid ecological adaptation in mammals. Copy number (CN) differences in genomic regions between closely related species can underlie adaptive phenotypes and this form of genetic variation has not been explored in the context of polar bear evolution. Here, we analyzed the CN profiles of 17 polar bears, 9 brown bears, and 2 black bears (Ursus americanus). We identified an average of 318 genes per individual that showed evidence of CN variation (CNV). Nearly 200 genes displayed species-specific CN differences between polar bear and brown bear species. Principal component analysis of gene CN provides strong evidence that CNV evolved rapidly in the polar bear lineage and mainly resulted in CN loss. Olfactory receptors composed 47% of CN differentiated genes, with the majority of these genes being at lower CN in the polar bear. Additionally, we found significantly fewer copies of several genes involved in fatty acid metabolism as well as AMY1B, the salivary amylase-encoding gene in the polar bear. These results suggest that natural selection shaped patterns of CNV in response to the transition from an omnivorous to primarily carnivorous diet during polar bear evolution. Our analyses of CNV shed light on the genomic underpinnings of ecological adaptation during polar bear evolution.