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.

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