DOI: 10.5061/dryad.wwpzgmsm8
title: Data from: Rapid diversification of the Variable Seedeater superspecies complex despite widespread gene flow

description: 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.
description: 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 <em>Sporophila </em>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
 <em>Sporophila </em>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 <em>Sporophila corvina</em>.
 S.corvina_SNPs_33142.vcf