Data and code from Pierson et al. "Revisiting a cryptic species complex: interspecific gene flow among woodland salamanders in the Blue Ridge Mountains of northern Georgia"

<p>ABSTRACT</p> <p>The complex topography of mountainous landscapes can create biogeographic barriers and promote allopatric speciation&mdash;even among morphologically cryptic species. However, these biogeographic barriers are rarely permanent, and secondary contact between previously independently evolving populations may result in hybridization and introgression. Here, we use genome-wide SNP data to reexamine a classic example of cryptic species in the Appalachian Mountains: the slimy salamander (<em>Plethodon glutinosus</em>) species complex. This group of morphologically similar terrestrial salamanders includes 14 species with parapatric distributions across the eastern United States. In this study, we focused on the Chattahoochee Slimy Salamander in northern Georgia and used a series of complementary phylogenomic and population genomic analyses to evaluate spatial genetic structure within this species and demonstrate admixture with at least four other species of parapatric woodland salamanders. Our results highlight the utility of genomic data in clarifying species boundaries and underscore the difficulty of species delimitation in organisms with complex evolutionary histories.</p>