Genomic variation in the Black-throated Green Warbler (Setophaga virens) suggests divergence in a disjunct Atlantic Coastal Plain population (S. v. waynei)

We used whole-genome resequencing to estimate genetic distinctiveness in the Black-throated Green Warbler (Setophaga virens)-including S. v. waynei-a putative subspecies that occupies a narrow disjunct breeding range along the Atlantic Coastal Plain. Despite detecting low-global differentiation (F-ST = 0.027) across the entire species, the principal components analysis of genome-wide differences shows the main axis of variation separates S. v. waynei from all other S. v. virens samples. We also estimated a low-migration rate for S. v. waynei, but found them to be most similar to another disjunct population from the Piedmont of North Carolina, and detected evidence of a historical north-to-south geographic dispersal among the entire species. New World wood warblers (family: Parulidae) can exhibit strong phenotypic differences among species, particularly, in song and plumage; however, within-species variation in these warblers-often designated as subspecies-is much more subtle. The existence of several isolated Black-throated Green Warbler populations across its eastern North American breeding range offers an excellent opportunity to further understand the origin, maintenance, and conservation status of subspecific populations. Our results, combined with previously documented ecological and morphological distinctiveness, support that S. v. waynei be considered a distinct and recognized subspecies worthy of targeted conservation efforts. Lay Summary center dot We used whole-genome resequencing to quantify genetic structure in Black-throated Green Warblers (Setophaga virens) throughout their North American breeding range. center dot We detected low differentiation across all samples but found discrete genetic clustering of S. v. waynei populations that breed along the Atlantic Coastal Plain. center dot We provide evidence of a geographic north-to-south dispersal among the entire species, and found S. v. waynei to be of relatively recent origin within the southern clade. center dot We estimated reduced gene flow in the region separating S. v. waynei from other S. virens populations, but found they were most closely related to a disjunct population from the Piedmont of central North Carolina. center dot We identified two specific regions of the genome that showed elevated differentiation, one on a sex chromosome (Z) and the other on chromosome 6. center dot Our findings provide clarity to the subspecific status of S. virens and bolster conservation efforts for S. v. waynei populations and their habitats.