Abstract
Birds and other vertebrates display stunning variation in pigmentation patterning, yet the genes controlling this diversity remain largely unknown. Rock pigeons (Columba livia) are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: T-check, checker, bar (ancestral), or barless. Using whole-genome scans, we identified NDP as a candidate gene for this variation. Allele-specific expression differences in NDP indicate cis-regulatory divergence between ancestral and melanistic alleles. Sequence comparisons suggest that derived alleles originated in the speckled pigeon (Columba guinea), providing a striking example of introgression. In contrast, barless rock pigeons have an increased incidence of vision defects and, like human families with hereditary blindness, carry start-codon mutations in NDP. In summary, we find that both coding and regulatory variation in the same gene drives wing pattern diversity, and post-domestication introgression supplied potentially advantageous melanistic alleles to feral populations of this ubiquitous urban bird.
Highlights
Vertebrates have evolved a vast array of epidermal colors and color patterns, often in response to natural, sexual, and artificial selection
The domestic rock pigeon (Columba livia) displays enormous phenotypic diversity among over 350 breeds, including a wide variety of plumage pigmentation patterns that vary within breeds (Shapiro and Domyan, 2013; Domyan and Shapiro, 2017)
Mutations in the NDP gene in humans typically cause a range of neurological problems in addition to loss of sight, but in barless pigeons, the mutation appears to cause only vision defects. These findings suggest that a specific part of the gene is important for vision in birds and humans, and shed light on the surprisingly complex evolutionary history of the rock pigeon
Summary
Vertebrates have evolved a vast array of epidermal colors and color patterns, often in response to natural, sexual, and artificial selection. Variation in wing shield color pattern among pigeons with checker alleles in the Scaffold 68 candidate region.
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