Molecular population genetics of the melanic plumage polymorphism in arctic skuas (Stercorarius parasiticus): evidence for divergent selection on plumage colour

The arctic skua (Stercorarius parasiticus) is a classic example of an avian plumage polymorphism, with variation in melanin-based ventral plumage coloration defining pale, intermediate and dark morphs in adults of both sexes. However, despite several decades of field research, there is an incomplete understanding of how the polymorphism in ventral plumage colour is maintained and the selective forces involved. Here we investigate selection on a locus (MC1R) that is strongly associated with plumage colour variation in arctic skuas using patterns of nucleotide variation and comparison to neutral loci (nuclear introns and mtDNA). We find that three linked non-synonymous mutations in MC1R, including the single mutation described previously, are associated with plumage colour in the arctic skua. The position of non-synonymous mutations on a MC1R haplotype network implies that divergent selection drove the initial evolution of the colour morphs. Comparisons of FSTs of MC1R vs. nuclear introns...