Michael Shapiro and colleagues report the reference genome for the domestic rock pigeon, Columba livia (Science, published online 31 January 2013; doi:10.1126/science.1230422). The authors sequenced the whole genome of a male Danish tumbler pigeon to over 60-fold coverage using the Illumina HiSeq 2000 platform and carried out de novo assembly. They also resequenced 40 additional rock pigeon genomes, representing 36 domestic breeds and 2 feral pigeons, with 8- to 26-fold coverage each. They report estimates of genetic diversity and mutation rate that are comparable to those found in other avian species, as well as a large and stable effective population size. Their annotation identified 17,300 genes, with most of these also found in other avian genomes. Phylogenetic analysis was used to define the origins of rock pigeon breeds and their relationships with the hill pigeon, Columba rupestris. The authors also identified a common variant in EphB2 associated with the head crest phenotype, in the resequenced panel, as well as in an additional 61 crested and 69 uncrested birds. They suggest a mechanism by which EphB2 may influence feather polarity during development and demonstrate that the pigeon is a useful model to characterize derived traits in domesticated birds.