15Birds and other vertebrates display stunning variation in pigmentation patterning, yet the 16 genes controlling this diversity remain largely unknown. Rock pigeons (Columba livia) 17 are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: 18 T-check, checker, bar (ancestral), or barless. Using whole-genome scans, we identified 19 NDP as a candidate gene for this variation. Allele-specific expression differences in NDP 20indicate cis-regulatory differences between ancestral and melanistic alleles. Sequence 21 comparisons suggest that derived alleles originated in the speckled pigeon (Columba 22 guinea), providing a striking example of introgression of alleles that are favored by 23 breeders and are potentially advantageous in the wild. In contrast, barless rock pigeons 24have an increased incidence of vision defects and, like two human families with 25 hereditary blindness, carry start-codon mutations in NDP. In summary, we find 26 unexpected links between color pattern, introgression, and vision defects associated with 27 regulatory and coding variation at a single locus. 28