Replicate contact zones suggest a limited role of plumage in reproductive isolation among subspecies of the Variable Seedeater (Sporophila corvina)

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 ..., 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...,