Population Structure
Although the Atlantic coast population was most distinct in our dataset, the nested structure of S. v. waynei within the clades in the south suggests a relatively recent origin of this group. Our results also suggest that S. v. waynei are most closely related to other southern populations (Figure 5), especially to S. v. virensbreeding <150 km away in the Uwharrie National Forest. This pattern is consistent with post-glacial geographic dispersal from north to south. However, the Uwharrie population does not appear to be directly intermediate between the coastal populations and the inland group—as would be expected if it was intergrades of the two subspecies—but instead shows evidence of independent evolution (e.g., divergence along PC2 in Figure 2).
Despite substantial geographic isolation from the contiguous S. v. virens breeding distribution (e.g., the Arkansas population is separated by >900 km), the fact that the other isolated populations did not cluster or provide as clear a signal of isolation-by-distance as S. v. waynei, could be explained in several ways. First, it is possible that these locations have been only recently colonized, thus not providing enough time for genetic differentiation to occur. This is likely the case in Arkansas, whereS. v. virens was only first documented breeding in the mid-1990s (Rodewald, 1997). Additionally, unlike the ecological conditions of the southern Atlantic Coastal Plain, the habitats in these other disjunct areas are not as clearly different from the rest of S. v. virens’breeding range—at least south of the Boreal Forest—so selective pressures may not have promoted rapid differentiation. Finally, despite rather extensive geographic separation, it is possible that isolation in these areas is incomplete, with gene flow occurring occasionally when individuals forgo the rest of their migratory journey (natal or breeding dispersal from the contiguous breeding distribution) and choose to breed at these locations. In support of this possibility, most birds sampled in Arkansas were young male (second-year or first-time breeding) birds—the age at which dispersal distance for many birds is greatest (Greenwood & Harvey, 1982).
From a conservation perspective, the genetic diagnosability of S. v. waynei supports its subspecific taxonomic status, and likely the validity of a unique evolutionary history as a population that exhibits fixed genetic differences. Thus, it would also be appropriate to manageS. v. waynei as an independent management unit for conservation actions to maintain the unique diversity that this subspecies exhibits. Our use of low-coverage sequencing and genotype likelihoods (within the ANGSD pipeline) makes it challenging to estimate per-SNP FST values. However, using successively smaller genomic windows (Figure S1) we show that many dozens of SNPs within the Z chromosome region have FST values >0.7, and within the chromosome 6 region at least one SNP with FST>0.7. Thus, these nearly fixed genetic differences are consistent with S. v. waynei having a unique evolutionary history worthy of conservation even though genome-wide divergence is low overall.