Data from: Genetic subdivision and candidate genes under selection in North American gray wolves

Previous genetic studies of the highly mobile gray wolf (Canis lupus)
found population structure that coincides with habitat and phenotype
differences. We hypothesized that these ecologically distinct populations
(ecotypes) should exhibit signatures of selection in genes related to
morphology, coat color, and metabolism. To test these predictions, we
quantified population structure related to habitat using a genotyping
array to assess variation in 42,036 SNPs in 111 North American gray
wolves. Using these SNP data and individual-level measurements of 12
environmental variables, we identified six ecotypes: West Forest, Boreal
Forest, Arctic, High Arctic, British Columbia, and Atlantic Forest. Next,
we explored signals of selection across these wolf ecotypes through the
use of three complementary methods to detect selection: FST/haplotype
homozygosity bivariate percentile, BayeScan, and environmentally
correlated directional selection with Bayenv. Across all methods, we found
consistent signals of selection on genes related to morphology, coat
coloration, metabolism, as predicted, as well as vision and hearing. In
several high-ranking candidate genes, including LEPR, TYR, and SLC14A2, we
found variation in allele frequencies that follow environmental changes in
temperature and precipitation, a result that is consistent with local
adaptation rather than genetic drift. Our findings show that local
adaptation can occur despite gene flow in a highly mobile species and can
be detected through a moderately dense genomic scan. These patterns of
local adaptation revealed by SNP genotyping likely reflect high fidelity
to natal habitats of dispersing wolves, strong ecological divergence among
habitats, and moderate levels of linkage in the wolf genome.