Elucidating evolutionary processes in North American gray wolves: genetic subdivision, local adaptation, and coat coloration

A fundamental question in evolutionary biology concerns how organisms adapt to challenges in their environment and how genetic variation is acted upon by natural selection. Thus, the gray wolf (Canis lupus) is an excellent study species in this regard because coat color and morphological variation exists throughout its range, and a variety of genetic resources are available. In this doctoral dissertation, we explored three facets of evolution in North American gray wolves. First, we determined environmentally-related genetic subdivision and evidence for local adaptation through the use of 42K single nucleotide polymorphisms (SNPs) genotyped on a SNP array in 111 wolves from six ecotypes, and identified consistent signals of selection on genes related to morphology, coat coloration, metabolism, vision and hearing. Second, we designed a targeted capture of 1040 genes, including all exons and flanking regions, as well as 5000 1kb non-genic neutral regions and resequenced these regions in 107 wolves. Using selection tests, we identified potentially functional variants related to local adaptation. Finally, we focused on understanding positive selection at the K locus, a gene responsible for black coat color in wolves and domestic dogs. A previous study suggested that the melanistic KB allele was introduced into the genome of North American wolves from the domestic dog via interbreeding, and then underwent positive selection. We designed a custom capture array to resequence five megabases surrounding the K locus core deletion in a larger sample of North American wolves from multiple areas to assess patterns of nucleotide and haplotype diversity, population-specific decay in linkage disequilibrium, and hierarchical patterns of genetic divergence among populations. From these data we infer that adaptive introgression most likely occurred first in the Northwest Territories or Yukon area of Canada, when native dogs and humans were co-existing in the Arctic. Furthermore, we find evidence for a strong, ongoing selective sweep in Yellowstone wolves that may be related to immunity and disease prevalence. These analyses set an important precedent for the use of cutting-edge genetic techniques to solve long-standing evolutionary questions about wild populations