Data from: Rapid diversification of the Variable Seedeater superspecies complex despite widespread gene flow

Disentangling the evolutionary relationships of rapidly radiating clades is often challenging because of low genetic differentiation and potentially high levels of gene flow among diverging taxa. The genus Sporophila consists of small Neotropical birds that show, in general, relatively low genetic divergence, but particularly high speciation rates and pronounced variation in secondary sexual traits (e.g., plumage color), which can be important in generating premating reproductive isolation. In cases like these, the use of genome-wide sequence data can increase the resolution to uncover a clade's evolutionary history. Here, we used a phylogenomic approach to study the evolutionary history and genetic structure of the Variable Seedeater superspecies complex, which includes S. corvina, S. intermedia, and S. americana. Using ~25,000 genome-wide single nucleotide polymorphisms (SNPs), we confirmed that the Variable Seedeater superspecies complex is monophyletic. However, a phylogenetic reconstruction based on a mitochondrial marker (ND2) resulted in a discordant tree topology, particularly in the position of the Wing-barred Seedeater, S. americana, suggesting a possible mitochondrial capture event. Our results suggest historical gene flow among lineages, particularly between species with conflicting topologies. Among the four phenotypically variable S. corvina subspecies, our structure analyses identified three main distinct genetic groups (K = 3) and that the entirely black subspecies, S. c. corvina, is derived from within a pied-colored clade. Further, we inferred widespread gene flow across the whole species' distribution, including between subspecies. However, gene flow was about 20 times lower at the geographic boundaries of the entirely black and the pied subspecies, suggesting an important role for plumage divergence in limiting gene flow. Overall, our findings suggest that the early diversification of the Sporophila genus occurred rapidly despite historical gene flow between lineages and that divergence in plumage color possibly influences the extent of gene flow among taxa.ND2 sequences and Genomic SNPs from the publication "Rapid diversification of the Variable Seedeater superspecies complex despite widespread gene flow". Individual's ID corresponds to the museum catalog numbers, complete localities are available in the publication's supplementary material. Sporophila ND2 Mitochondrial Gene 1018bp This file contains sequences of the mtDNA gene ND2 for 53 individuals from 8 species of Sporophila seedeaters. Each sequence is 1018bp in length. Sporophila_ND2_1018bp.NEX Sporophila Genomic SNP file This vcf file contains 24,968 SNPs from GBS sequencing of genetic samples from 33 individuals from 8 species of Sporophila seedeaters. Sporophila_SNPs_24968.vcf Sporophila corvina Genomic SNP file This vcf file contains 33,142 SNPs from GBS sequencing of genetic samples from 47 individuals the Variable Seedeater Sporophila corvina. S.corvina_SNPs_33142.vc