Comparative Whole Genome Phylogeography Reveals Genetic Distinctiveness of Appalachian Populations of Boreal Songbirds.

Intraspecific genetic diversity across a species' geographic range is relevant to adaptive potential and long-term population persistence, and identifying genetically distinct groups within species can direct management decisions focused on conserving species-level genetic diversity. Comparative phylogeography using whole genome techniques allows for investigation of whether co-distributed species exhibit shared spatial genetic differentiation at fine spatial scales, thereby facilitating a comparative approach to both landscape and conservation genetics. By sequencing over 900 low-coverage whole genomes, we evaluated the concordance of genetic structure and diversity from 12 co-occurring species of migratory birds whose breeding ranges span adjacent North American ecogeographic regions: the vast boreal forest belt and the temperate montane Appalachian forests. We detected concordant phylogeographic patterns in 11 of 12 species wherein populations from the southern Appalachians were genetically distinct from boreal belt populations. Our results reveal that small populations persisting in the southern Appalachian Mountains consistently harbor genetic diversity that is subtly distinct from much larger, widespread boreal populations of the same species. However, in most species, levels of standing genetic diversity were not significantly different between Appalachian and boreal populations despite the drastic difference in geographic extent of these populations. We found no evidence for shared signatures of selection across the genome, suggesting that the concordance of spatial genetic structure across species emerges from species-specific patterns of molecular divergence across the genome rather than parallel patterns of selection. Conservation of the Appalachian ecosystem would likely support maintenance of distinct genetic diversity in several migratory avian species with widespread distributions.