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

The A rctic skua ( S tercorarius 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 ( MC 1 R ) that is strongly associated with plumage colour variation in Arctic skuas using patterns of nucleotide variation and comparison to neutral loci (nuclear introns and mt DNA ). We find that three linked nonsynonymous mutations in MC 1 R , including the single mutation described previously, are associated with plumage colour in the A rctic skua. The position of nonsynonymous mutations on a MC 1 R haplotype network implies that divergent selection drove the initial evolution of the colour morphs. Comparisons of F ST s of MC 1 R vs. nuclear introns among five skua populations differing in proportion of dark morphs along an approximate north–south cline reveal a signature of divergent selection on MC 1 R . In contrast, we find limited evidence for balancing selection on MC 1 R within populations, although the power is low. Our results provide strong evidence for both past and ongoing selection on MC 1 R , and, by implication, plumage colour in A rctic skuas. The results suggest that a fruitful avenue for future ecological studies will be analysis of selection on morphs in colonies at the extremes along the morph ratio cline.