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 allopatri..., , , # Selection on a single locus drives plumage differentiation in the Rufous-collared Sparrow (Zonotrichia capensis)

[https://doi.org/10.5061/dryad.dz08kps7s](https://doi.org/10.5061/dryad.dz08kps7s)

## Description of the data and file structure

Here you will find raw genomic data and processed data used for analyses from the manuscript titled Selection on a single locus drives plumage differentiation in the Rufous-collared Sparrow (Zonotrichia capensis).

**Contents**

1\) Raw genomic reads obtained for 18 individuals (PL1 to PL18) on an Illumina NextSeq 500 lane at the Cornell Institute for Biotechnology core facility. All individuals were pooled and sequenced (2x150 paired end), so you will find two files (fastq.gz) per individual. File names follow this scheme: 9641_3270_75521_HWYTKBGX5_PL1_ATCACG_R1.fastq.gz, where PL1 is the sample (PL1 to PL18), ATCACG is the adapter index used for that sample, and R1 is read one (you will see two reads, R1 and R2, per sample). All other informa...,