Evidence of positive selection and a novel phylogeny among five subspecies of song sparrow (<i>Melospiza melodia</i>) in Alaska

Local adaptation occurs when populations evolve traits in response to local environmental challenges. Isolated island populations often experience different selection pressures than their mainland counterparts, which enables the study of how phenotypes and genotypes respond to differing selection regimes. We studied a group of five phenotypically differentiated subspecies of song sparrow (<i>Melospiza melodia</i>) in Alaska that demonstrate striking body size, color, and migratory behavioral differences to examine the effects of local adaptation on phenotypes and genotypes. We examined the phenotypic attributes of these populations and used whole-genome data to determine relationships and test candidate loci for evidence of selection. Phenotypic measurements of museum specimens (<i>n</i> = 227) quantified the dramatic size differences among these populations, with westernmost <i>M. m. maxima</i> being ~1.6 times larger than easternmost <i>M. m. rufina</i>. Using ultraconserved elements (UCEs) and McDonald-Kreitman tests, we showed that seven candidate genes associated with bill size, circadian rhythm regulation, plumage color, and salt tolerance exhibited signs of putative positive selection. Phylogenetic analysis of UCEs identified <i>M. m. maxima</i> as sister to the other Alaska <i>M. melodia</i> subspecies. This suggests <i>M. m. maxima</i> colonized earliest, perhaps before the last glacial maximum, and that Alaska was later recolonized by ancestors of the remaining four subspecies.