Revisiting a cryptic species complex: interspecific gene flow among woodland salamanders in the Blue Ridge Mountains of northern Georgia, USA

Abstract The complex topography of mountainous landscapes can create biogeographical barriers and promote allopatric speciation—even among morphologically cryptic species. However, these biogeographical barriers may not be permanent, and secondary contact between previously independently evolving populations can result in hybridization and introgression. In this study, we used genome-wide single nucleotide polymorphism data to re-examine a classic example of cryptic species in the Appalachian Mountains: the slimy salamander (Plethodon glutinosus) species complex. This group of morphologically similar terrestrial salamanders includes 14 species with parapatric distributions across the eastern USA. We focused on the Chattahoochee slimy salamander (P. chattahoochee) in northern Georgia and used a series of complementary phylogenomic and population genomic analyses to evaluate spatial genetic structure within this species and admixture with at least four other species of parapatric woodland salamanders. Our results highlight the utility of genomic data in clarifying species boundaries and underline the difficulty of species delimitation in organisms with complex evolutionary histories.