DOI: 10.5061/dryad.kb610
title: Data from: Plumage genes and little else distinguish the genomes of hybridizing warblers

description: When related taxa hybridize extensively, their genomes may become
 increasingly homogenized over time. This mixing via hybridization creates
 conservation challenges when it reduces genetic or phenotypic diversity
 and when it endangers previously distinct species via genetic swamping [ 1
 ]. However, hybridization also facilitates admixture mapping of traits
 that distinguish each species and the associated genes that maintain
 distinctiveness despite ongoing gene flow [ 2 ]. We address these dual
 aspects of hybridization in the golden-winged/blue-winged warbler complex,
 two phenotypically divergent warblers that are indistinguishable using
 traditional molecular markers and that draw substantial conservation
 attention [ 3–5 ]. Whole-genome comparisons show that differentiation is
 extremely low: only six small genomic regions exhibit strong differences.
 Four of these divergence peaks occur in proximity to genes known to be
 involved in feather development or pigmentation: agouti signaling protein
 (ASIP), follistatin (FST), ecodysplasin (EDA), wingless-related
 integration site (Wnt), and beta-carotene oxygenase 2 (BCO2). Throat
 coloration—the most striking plumage difference between these warblers—is
 perfectly associated with the promoter region of agouti, and genotypes at
 this locus obey simple Mendelian recessive inheritance of the
 black-throated phenotype characteristic of golden-winged warblers. The
 more general pattern of genomic similarity between these warblers likely
 results from a protracted period of hybridization, contradicting the
 broadly accepted hypothesis that admixture results from solely
 anthropogenic habitat change in the past two centuries [ 4 ]. Considered
 in concert, these results are relevant to both the genetic architecture of
 avian feather pigmentation and the evolutionary history and conservation
 challenges associated with these declining songbirds.
description: Genotype and Plumage
 information for NY State Sample SetThe data file shows the
 individual genotype information for mtDNA and the six divergent loci
 assayed with an RFLP. Plumage information is also given, the scoring
 criteria can be found in the supplemental experimental
 proceedures.Genotypes_phenotypes_NY_2015_samples.csvGenotypes from the range wide sample setGenotypes from mtDNA and the six divergent loci assayed using RFLP for samples collected across the range of both taxa. See "Readme" for NY sample set for additional information.Genotypes_Range_wide_samples.csvPlumage Scoring CriteriaAdapter from Gill (1980), this table includes the criteria we applied for scoring various plumage characters.plumage_criteria.docxRFLP Enzyme informationSNP information, primer sequences, cut site information, and product size for the six divergent RFLP lociVariant Call Format file for ddRAD dataset151 Individuals with genotype information generated from the ddRAD protocol, with individuals sampled across the range of both species. In the Readme csv the species name corresponds to the coarse scale phenotype, classified in the hand as either: BWWA - blue-winged warbler; GWWA - golden-winged warbler; BRWA - Brewster's warbler hybrid.GWWA_BWWA.GATK.filtered.removed.minGQ.20.removed.indv.max.missing.4.maf.02.vcf.recode.vcfVariant Call Format file for resequencing datasetGenotype information for 24 individuals sampled in NY State in 2015 with re-sequencing data. In the readme CSV, the "species" corresponds to the coarse scale phenotype information: BWWA - blue-winged warbler; GWWA - golden-winged warbler; BRWA - Brewster's warbler hybrid; INTR - intermediate hybrid, mostly GWWA characters with additional yellow on the breast.GWWA_BWWA.reseqeuncing.variant.dryad.vcf