The genetic basis of plumage coloration and elevation adaptation in a clade of recently diverged alpine and arctic songbirds

Trait genetic architecture plays an important role in the probability that
variation in that trait leads to divergence and speciation. In some cases,
speciation may be driven by the generation of novel phenotypes through the
recombination of genes associated with traits that are important for local
adaptation or sexual selection. Here, we investigate the genetic basis of
three plumage color traits, and one ecological trait, breeding elevation,
in a recent avian radiation, the North American rosy-finches (Leucosticte
spp.). We identify unique genomic regions associated with each trait and
highlight 11 candidate genes. Among these are well-characterized
melanogenesis genes, including Mitf and Tyrp1, and previously reported
hypoxia-related genes including Egln1. Additionally, we use mitochondrial
data to date the divergence of rosy-finch clades which appear to have
diverged within the past 250 ky. Given the low levels of genome-wide
differentiation among rosy-finch taxa, and evidence for extensive
introgression in North America, plumage coloration and adaptation to high
elevations have likely played large roles in generating the observed
patterns of lineage divergence. The relative independence of these
candidate regions across the genome suggests that recombination might have
led to multiple phenotypes, and subsequent rosy-finch speciation, over
short periods of time.