Grizzly bear population genomics across a coastal-interior ecotone in British Columbia, Canada.

Local adaptation research often focuses on discrete populations without extensive gene flow that are under differential selective pressures. By contrast, grizzly bears Ursus arctos in British Columbia (BC) are wide-ranging omnivores that span an environmental and resource ecotone from the coastal, salmon-enriched rainforest to dry interior plateau. This ecotone has been associated with local adaptation in other species and the different regions to morphological variation in grizzly bears. To understand genome-wide population genetic patterns across the ecotone and to identify loci or genomic regions associated with these different environments, here we use whole-genome resequencing to characterize 3.9 M SNPs in 31 grizzly bears spanning from central to northern latitudes in coastal and interior regions (to the west and east of the coastal mountain range [CMR], respectively). Clustering grizzly samples by genotypes identified 3 groups that generally correspond to the source geographic regions, with the greatest variation occurring from north to south. The data were best explained by a single ancestry cluster, but K = 3 recovered the 3 geographic groupings and were used to identify putative nonmigrant individuals. The presence of individuals with mixed ancestry (using K = 3) provides evidence for travel across the CMR, but significant differentiation between clusters (mean FST = 0.015 to 0.036) suggests some genetic separation between the regions, supporting an isolation-by-distance or clinal variation model. Putative close-kin were identified and removed, then multiple supervised outlier SNP detection methods were applied to identify regions of the genome consistently segregating between coastal and interior regions. Several associated genomic regions and candidate genes were identified, including a consistently identified outlier region near the gene creatine kinase, m-type. This work provides the first genome-wide analysis of grizzly bears in the studied region. These findings will be useful for connectivity planning and research on the adaptability of coastal and interior grizzlies to future climate change scenarios.