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

Abstract

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.

Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

“…To estimate population genetic differentiation of loci identified as CNVs, we calculated the variant fixation index V ST (Redon et al 2006). V ST is an analog of F ST estimator of population differentiation (Wright, 1949;Weir & Cockerham, 1984) and is commonly used to identify differentiated CNV profiles between populations (Redon et al, 2006;Dennis et al, 2017;Rinker et al 2019). For each pairwise population comparison, V ST was estimated considering (V T -V S )/V T , where V T is the variance of normalized read depths among all individuals from the two populations and V S is the average of the variance within each population, weighed for population size (Redon et al 2006).…”

“…diseases, pathogen susceptibility, drug response, ancestry ;Feuk, Carson & Scherer 2006;Wong et al, 2007;Ionita-Laza et al, 2009), CNVs have since been studied in a few other pecies, notably to understand domestication or speciation processes (Clop et al, 2012). Nevertheless, the role of CNVs in local adaptation relative to SNPs in non-model species is poorly understood and remains mostly restricted to a very limited number of animal and plant species in terrestrial environments (Tigano et al, 2018;Rinker et al, 2019;Nelson et al, 2018, Prunier et al, 2019, making this issue still largely unexplored in marine species. CNVs are also rarely studied on a large subset of individuals due to financial and technical constraints because classical approaches to detect CNVs, such as paired-end mapping, split read, de novo assembly or depth of coverage, required a reference genome and whole-genome resequencing at deep coverage (Roca et al, 2019).…”

Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex)

“…Although we find a strong signal of environmental niche differentiation, we find no SNPs that deviate from expectations of neutral population divergence. Future analyses could elucidate the role of selection in maintaining population differentiation by using targeted sequencing of functional loci (Christmas, Biffin, Breed, & Lowe, 2016;Namroud, Bealieu, Juge, Laroche, & Bousquet, 2008) or whole genome sequence data to explore the role of structural genomic variation in relation to local adaptation to different climatic regimes (Lucek, Gompert, & Nosil, 2019;Rinker, Specian, Zhao, & Gibbons, 2019). (Pearson, Raxworthy, Nakamura, & Townsend Peterson, 2007).…”

Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

“…CNVs encompass such more nucleotides than other types of variations (e.g., SNPs and InDels) that they can result in more remarkable effects on the functional gene through perturbing the long-range regulation of gene expression, altering gene dosage or coding sequences, and creating new genes, consequently contributing to phenotypic variations (Redon et al, 2006;Innan and Kondrashov, 2010;Bickhart and Liu, 2014;Shwan et al, 2017). A growing body of evidence shows that CNVs are crucial drivers of phenotypic diversity, evolution, and adaptation in humans and animals (Perry et al, 2008;Iskow et al, 2012;Sudmant et al, 2015;Romero et al, 2017;Rinker et al, 2019).…”