RESULTS
We generated genomic data for 9 individuals breeding in coastal North Carolina (putative S. v. waynei) , and 20 individuals from the nominate subspecies, S. v. virens , which were distributed across their breeding range. Genome-wide F ST indicated low (0.027) overall differentiation across the S. virens complex. However, principal component analysis revealed three highly clustered groups, one of which consisted of only S. v. waynei (Figure 2). Samples from coastal North Carolina (S. v. waynei) were distinct along PC1, which explained 8% of the total variance in the data, and strongly separated from S. v. virens . Samples of S. v. virens from the Uwharrie National Forest in central North Carolina separated along PC2 (4.1% variance) with the remaining group composed of S. v. virens samples from Arkansas, Tennessee, Indiana, and New York (Figure 2).
Differentiation was not homogenous across the genome (Figure 3A). We identified two regions of the genome, one on chromosome 6 (Figure 3B) and one on the sex (Z) chromosome (Figure 3C) that showed elevated differentiation above the background. On chromosome 6, the elevated region spanned 16,950,000bp and 17,040,000bp (a length of 80,000bp) and had six windows with F ST above 0.15 (the maximum windowed F ST in this region was 0.28). The region on the Z chromosome, between 11,910,000bp and 12,150,000bp (a length of 240,000bp) contained 10 windows above F ST 0.15 (the maximum windowed F ST in this region was 0.32). The chromosome 6 region included five annotated genes that were bounded by the region of elevated divergence; the Z chromosome region had four annotated genes, and one gene of unknown function (Figure 4).
Phylogenetic relatedness among the samples clustered most samples by geographic locality (Figure 5). The initial split within the species occurred between samples from New York and other samples from southern populations. Samples from putative S. v. waynei formed a monophyletic group, which was sister to birds breeding in the Uwharrie National Forest of central North Carolina.