DOI: 10.5061/dryad.dz08kps7s
title: Data from: Selection on a single locus drives plumage differentiation in the Rufous-collared Sparrow (Zonotrichia capensis)

description: 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.
description: # 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 information in the name corresponds to details of the sequencing run that do not have any relevance for the analyses. 9641_3270_75523_HWYTKBGX5_PL3_TTAGGC_R2.fastq.gz  2\) "adpaters.txt" : adapters list to be removed with AdapterRemoval 3\) Processed data used for analyses: a) SNPs_whole_genome.vcf : file containing 10,798,248 SNPs after all filtering. This set of SNPs was used for PCA and the location of divergence peaks across the entire genome. See main text and supporting information for details on how we obtained this set of SNPs from raw sequencing data. b) thin25kb.vcf : thinned dataset of 41,778 SNPs (one per 25,000 bp) used for STRUCTURE and K-means analyses. c) all_sites_whole_genome.vcf.gz: compressed file containing ALL SITES (SNPs and invariant) used for genome-wide nucleotide diversity calculations (after filtering) d) scaffold42_ALL_SITES.vcf : file contanining ALL SITES (SNPs and invariant) for scaffold 42 after filtering used to investigate the emergence of the genomic island of differentiation containing ST5 gene. e) scaffold42_SNPs.vcf : file containing 49,646 SNPs from scaffold 42 after filtering e) mtDNA.fas: fasta file containing the alignment of mtDNA used for phylogenetic analyses. For more details on sequence length and how these sequences were obtained see main text and Supporting information. ### Files and variables #### File: 9641\_3270\_75522\_HWYTKBGX5\_PL2\_CGATGT\_R2.fastq.gz **Description:** raw sequencing data  #### File: 9641\_3270\_75522\_HWYTKBGX5\_PL2\_CGATGT\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75521\_HWYTKBGX5\_PL1\_ATCACG\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75538\_HWYTKBGX5\_PL18\_GTGGCC\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75538\_HWYTKBGX5\_PL18\_GTGGCC\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75537\_HWYTKBGX5\_PL17\_GTGAAA\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75537\_HWYTKBGX5\_PL17\_GTGAAA\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75536\_HWYTKBGX5\_PL16\_GTCCGC\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75536\_HWYTKBGX5\_PL16\_GTCCGC\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75535\_HWYTKBGX5\_PL15\_ATGTCA\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75535\_HWYTKBGX5\_PL15\_ATGTCA\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75534\_HWYTKBGX5\_PL14\_AGTTCC\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75534\_HWYTKBGX5\_PL14\_AGTTCC\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75533\_HWYTKBGX5\_PL13\_AGTCAA\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75533\_HWYTKBGX5\_PL13\_AGTCAA\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75532\_HWYTKBGX5\_PL12\_CTTGTA\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75532\_HWYTKBGX5\_PL12\_CTTGTA\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75531\_HWYTKBGX5\_PL11\_GGCTAC\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75531\_HWYTKBGX5\_PL11\_GGCTAC\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75530\_HWYTKBGX5\_PL10\_TAGCTT\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75530\_HWYTKBGX5\_PL10\_TAGCTT\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75529\_HWYTKBGX5\_PL9\_GATCAG\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75529\_HWYTKBGX5\_PL9\_GATCAG\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75528\_HWYTKBGX5\_PL8\_ACTTGA\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75528\_HWYTKBGX5\_PL8\_ACTTGA\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75527\_HWYTKBGX5\_PL7\_CAGATC\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75527\_HWYTKBGX5\_PL7\_CAGATC\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75526\_HWYTKBGX5\_PL6\_GCCAAT\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75526\_HWYTKBGX5\_PL6\_GCCAAT\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75525\_HWYTKBGX5\_PL5\_ACAGTG\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75525\_HWYTKBGX5\_PL5\_ACAGTG\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75524\_HWYTKBGX5\_PL4\_TGACCA\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75524\_HWYTKBGX5\_PL4\_TGACCA\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75523\_HWYTKBGX5\_PL3\_TTAGGC\_R2.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75523\_HWYTKBGX5\_PL3\_TTAGGC\_R1.fastq.gz **Description:** raw sequencing data #### File: 9641\_3270\_75521\_HWYTKBGX5\_PL1\_ATCACG\_R2.fastq.gz **Description:** raw sequencing data #### File: adapters.txt **Description:** adapters list to be removed from raw sequencing data with AdapterRemoval ##### Variables * AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG: * AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT: #### File: scaffold42\_ALL\_SITES.vcf **Description:** file contanining ALL SITES (SNPs and invariant) for scaffold 42 after filtering used to investigate the emergence of the genomic island of differentiation containing ST5 gene. #### File: scaffold42\_SNPs.vcf **Description:** file containing 49,646 SNPs from scaffold 42 after filtering #### File: thin25kb.vcf **Description:** thinned dataset of 41,778 SNPs (one per 25,000 bp) used for STRUCTURE and K-means analyses. #### File: SNPs\_whole\_genome.vcf **Description:** file containing 10,798,248 SNPs after all filtering. This set of SNPs was used for PCA and the location of divergence peaks across the entire genome. See main text and supporting information for details on how we obtained this set of SNPs from raw sequencing data. #### File: mtDNA.fas **Description:** fasta file containing the alignment of mtDNA used for phylogenetic analyses. For more details on sequence length and how these sequences were obtained see main text and Supporting information. #### File: all\_sites\_whole\_genome.vcf.gz **Description:** compressed file containing ALL SITES (SNPs and invariant) used for genome-wide nucleotide diversity calculations (after filtering)