10.5061/DRYAD.KB610
Toews, David P. L.
Cornell University
Taylor, Scott A.
University of Colorado Boulder
Vallender, Rachel
University of Manitoba
Brelsford, Alan
University of California System
Butcher, Bronwyn G.
Cornell University
Messer, Philipp W.
Cornell University
Lovette, Irby J.
Cornell University
Data from: Plumage genes and little else distinguish the genomes of
hybridizing warblers
Dryad
dataset
2017
blue-winged warbler
Vermivora cyanoptera
Vermivora chrysoptera
golden-winged warbler
2017-08-24T00:00:00Z
2017-08-24T00:00:00Z
en
https://doi.org/10.1016/j.cub.2016.06.034
6609569014 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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
New York