Environmental variation among isolated populations can drive genetic differentiation by selection, while isolation alone results primarily in genetic drift. Genetic analyses can aid in identifying genetically isolated populations and population structure of a species across its range. Additionally, such analyses can provide indirect evidence of local adaptation through the comparison of allele frequencies at neutral and functional genetic markers, with the aim of identifying outlier loci consistent with the effects of selection. Here, we examine the genetic divergence and patterns of functional divergence among six breeding populations of arctic-breeding snow buntings (Plectrophenax nivalis). We genotyped 221 birds at 9 microsatellite markers and at 101 single nucleotide polymorphisms (SNPs) located within known-function genes. We identified substantial population differentiation using both marker types with relatively greater divergence and hence finer population structure using the microsatellite markers. While population structures resulting from the two marker types were in general agreement, functional SNPs showed evidence of stabilizing selection at both global and population pairwise levels, with a few key SNPs showing signatures of pairwise divergent selection, consistent with expectations of local adaptation. The observed complex and inconsistent pattern of pairwise divergence (selection) at key candidate-gene loci may reflect rapid environmental change decoupling locally adapted genotypes from actual local environmental conditions. Our work highlights microevolutionary changes that are likely to be very important not only in arctic-breeding songbirds, but in Arctic and Sub-Arctic vertebrates in general, which are experiencing strong environmental effects from accelerated climate change and human-induced stressors.

After establishing secondary contact, recently diverged populations may remain reproductively isolated or hybridize to a varying extent depending on factors such as hybrid fitness and the strength of assortative mating. Replicated contact zones between hybridizing taxa offer a unique opportunity to explore how different factors interact to shape patterns of hybridization. Here, we used genomic and phenotypic data from three independent contact zones between subspecies of the Variable Seedeater (Sporophila corvina), to examine how coloration and genetic divergence shape patterns of hybridization. We found that plumage coloration has limited introgression across contact zones, but the degree of plumage divergence does not explain overall patterns of introgression. Across two parallel contact zones between populations with divergent phenotypes (entirely black vs. pied plumage) populations hybridized extensively across one contact zone but not the other, suggesting that plumage divergence is not sufficient to maintain reproductive isolation. Where subspecies hybridized, hybrid zones were wide and formed by later-generation hybrids, suggesting that hybrids present similar or higher fitness than parental subspecies. Moreover, contemporary gene flow has played an important role in shaping patterns of genetic diversity between populations. Overall, our results demonstrate that divergence in plumage coloration is important in reducing gene flow but insufficient in maintaining reproductive isolation in this clade, and that other factors such as divergence in song and time since secondary contact may also play an important role in driving patterns of reduced hybridization and gene flow.