Data from: Selection on a single locus drives plumage differentiation in the Rufous-collared Sparrow (Zonotrichia capensis)

The Rufous-collared Sparrow (Zonotrichia capensis) shows phenotypic
variation throughout its distribution. In particular, the Patagonian
subspecies Z. c. australis is strikingly distinct from all other
subspecies, lacking the black crown stripes that characterize the species,
with a uniformly grey head and overall paler plumage. We sequenced whole
genomes of 18 individuals (nine Z. c. australis and nine from other
subspecies from northern Argentina) to explore the genomic basis of these
color differences and to investigate how they may have evolved. We
detected a single ~465-kb divergence peak on chromosome 5 that contrasted
with a background of low genomic differentiation and contains the ST5
gene. ST5 regulates RAB9A, which is required for melanosome biogenesis and
melanocyte pigmentation in mammals, making it a strong candidate gene for
the melanic plumage polymorphism within Z. capensis. This genomic island
of differentiation may have emerged because of selection acting on
allopatric populations or against gene flow on populations in physical and
genetic contact. Mitochondrial DNA indicated that Z. c. australis diverged
from other subspecies ~400,000 years ago, suggesting a putative role of
Pleistocene glaciations. Phenotypic differences are consistent with
Gloger’s rule, which predicts lighter colored individuals in colder and
drier climates like that of Patagonia.