Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon

Birds and other vertebrates display stunning variation in pigmentation patterning, yet the genes controlling this diversity remain largely unknown. Rock pigeons ( ) are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: T-check, checker, bar (ancestral), or barless....

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Bibliographic Details
Published in:eLife 2018-07, Vol.7
Main Authors: Vickrey, Anna I, Bruders, Rebecca, Kronenberg, Zev, Mackey, Emma, Bohlender, Ryan J, Maclary, Emily T, Maynez, Raquel, Osborne, Edward J, Johnson, Kevin P, Huff, Chad D, Yandell, Mark, Shapiro, Michael D
Format: Article
Language:English
Subjects:
Age
Alleles
Amino acids
Animal behavior
Animal coloration
Animals
Birds
Blindness
Chromosomes and Gene Expression
Codons
Color
Columba livia
Columbidae - genetics
Domestication
Family
Feathers
Feral populations
Gene Flow
Gene mutation
Genes
Genes, Regulator
Genetic aspects
Genetic regulation
Genetic research
Genetic Variation
Genetics
Genetics and Genomics
Genomes
Genomics
Haplotypes
introgression
Melanism
Mutation
Mutation, Missense
NDP
Norrie disease
Ornithological research
Phenotypes
pigeon
Pigeons
Pigmentation
Pigments, Biological - metabolism
Plumage
Population genetics
Public spaces
Random variables
Regulatory sequences
Rock pigeon
Urban populations
Variation
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Description
Summary:Birds and other vertebrates display stunning variation in pigmentation patterning, yet the genes controlling this diversity remain largely unknown. Rock pigeons ( ) 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 as a candidate gene for this variation. Allele-specific expression differences in indicate -regulatory divergence between ancestral and melanistic alleles. Sequence comparisons suggest that derived alleles originated in the speckled pigeon ( ), 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 . 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.
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.34803