The Genetic Basis Of Recurrent Evolution In Domestic Pigeons

The domestic rock pigeon is spectacularly diverse and arguably exhibits variation in more traits than any other bird species. Since its initial domestication thousands of years ago, pigeon breeders have selected striking differences in behavior, vocalizations, skeletal morphology, feather ornaments, colors, and color patterns to establish over 350 modern breeds. Despite intense historical interest in pigeon genetics, little is known about the molecular basis of their vast diversity. We used genome-wide scans of allele frequency differentiation and a probabilistic gene-finder (VAAST, originally developed for human genomics), to identify regions of the pigeon genome associated with derived traits. Strikingly, one such scan revealed a shared haplotype in all pigeons with derived head crest phenotypes, suggesting that a causative mutation occurred just once and spread to multiple breeds by ancient and recent introgression. A single shared variant is perfectly associated with the crest phenotype across 79 diverse breeds of domestic pigeon, and is therefore a convincing candidate for the crest (cr) locus of classical pigeon genetics. This locus appears to act as a developmental switch for the trait, but the tremendous variation in crest phenotypes suggests that other loci must contribute as well. Many of the traits that vary among pigeon breeds also vary among wild species of birds and other animals. Thus, the domestic pigeon represents a model for identifying the genetic basis of variation in traits of broad interest.