DOI: 10.5061/dryad.fj6q573z5
title: Data from: Replicate contact zones suggest a limited role of plumage in reproductive isolation among subspecies of the Variable Seedeater (Sporophila corvina)

description: After establishing secondary contact, recently diverged populations may
 remain reproductively isolated or may hybridize to a varying extent
 depending on factors such as hybrid fitness and the strength of
 assortative mating. Here, we used genomic and phenotypic data from three
 independent contact zones between subspecies of the Variable Seedeater
 (Sporophila corvina) to examine how coloration and genetic divergence
 shape patterns of hybridization. We found that differences in plumage
 coloration are likely maintained by divergent selection across contact
 zones; however, the degree of plumage differentiation does not match
 overall patterns of hybridization. Across two parallel contact zones
 between populations with divergent phenotypes (entirely black vs. pied
 plumage), populations hybridized extensively across one contact zone but
 not the other, suggesting that plumage divergence is not sufficient to
 maintain reproductive isolation. Where subspecies hybridized, hybrid zones
 were wide and formed by later-generation hybrids, suggesting frequent
 reproduction and high survivorship for hybrid individuals. Moreover,
 contemporary gene flow has played an important role in shaping patterns of
 genetic structure between populations. Replicated contact zones between
 hybridizing taxa offer a unique opportunity to explore how different
 factors interact to shape patterns of hybridization. Overall, our results
 demonstrate that divergence in plumage coloration is important in reducing
 gene flow but insufficient in maintaining reproductive isolation in this
 clade, and that other factors such as divergence in song and time since
 secondary contact may also play an important role in driving patterns of
 reduced hybridization and gene flow.
description: Scorvina_SNPs_1.vcf: SNP data from Genotype-by-Sequencing
 approach (GBS). We called SNP variants using TASSEL version 5.2.65
 following the GBSv2 SNP discovery and production pipeline. Then, we
 filtered genome-wide single-nucleotide polymorphisms (SNPs) using VCFTOOLS
 version 0.1.16. Our filtered criteria consisted of including biallelic
 SNPs with no indels, minimum read depth ≥ 3, minimum allele frequency ≥
 0.05, a maximum proportion of missing data ≤ 0.25, and SNPs that were ≥
 100 bp apart to reduce the effect of highly linked markers. We further
 filtered the data file in TASSEL, keeping SNPs with a maximum
 heterozygosity ≤ 0.8 to exclude potential paralogs, and removed
 individuals with ≥40% missing data. The resulting data set retained 255
 individuals and 14,839 SNPs. Scorvina_SNPs_2.vcf: SNP
 data from Genotype-by-Sequencing approach (GBS). We called SNP variants
 using TASSEL version 5.2.65 following the GBSv2 SNP discovery and
 production pipeline. Then, we filtered genome-wide single-nucleotide
 polymorphisms (SNPs) using VCFTOOLS version 0.1.16. Our filtered criteria
 consisted of including biallelic SNPs with no indels, minimum read depth
 of ≥ 3, maximum proportion of missing data of ≤ 0.15, and SNPs that were ≥
 1000 bp apart to obtain a complete site frequency spectrum (not truncated
 due to minimum allele frequency filtering) while keeping a manageable SNPs
 sample size, due to computer processing. This second data set retained
 8,437 SNPs from 10 randomly selected genotypically pure individuals per
 subspecies Scorvina_B2.txt: We measured the spectral
 properties from the three body patches that differ between subspecies
 (i.e., rump, throat, and belly), collecting five reflectance measurements
 (from 300 to 700 nm) per patch. We used an Ocean Optics USB2000
 spectrophotometer, and a PX-2 pulsed Xenon light source (Ocean Optics
 Inc., Dunedin, FL, USA), with the average reading set at 50, integrating
 time at 16 msec, boxcar smoothing at 10, and correction for electric dark
 noise activated.  We then estimated mean brightness (B2) for each
 individual patch from the reflectance reads, using the R package
 PAVO2. Scorvina_morph.txt: We measured seven
 morphometric traits (i.e., body mass, total culmen length, beak depth and
 width at the nares, right wing chord, right tarsus length, and tail
 length) using a caliper (accuracy ± 0.1mm) from 193 males, 125 females,
 and nine individuals of unknown sex.