Phylogenomics of the woodland salamanders (Plethodon): Reticulate evolution and indistinct species boundaries

Rapid species formation, cryptic species, and interspecific hybridization present serious analytical challenges for systematists, yet are important processes in the diversification of many taxa. We estimated the phylogenomic history of the woodland salamanders (Plethodon), a genus with many morphologically cryptic species and unresolved phylogenetic relationships. Hybridization between many contemporary species is well-established, but its effect on species tree topology has not yet been addressed in a phylogenetic framework using genomic data. Using anchored hybrid enrichment data from 194 samples across all 57 recognized species of Plethodon, we estimated species relationships and tested for gene flow using clustering analyses (DAPC), hybrid detection statistics (HyDe), and species networks (SNaQ). Relationships within most major clades were well-supported, with some hybridization events corresponding to low node support or discordance across tree-based methods. Cryptic phylogeographic structure was recovered in many species, highlighting novel lineages in need of targeted species delimitation studies. However, the "glutinosus group," which includes half of all described species, exhibited extensive hybridization and many instances of clustering assignments discordant with the current taxonomy. Phylogenetic network analyses revealed that a combination of reticulate evolution, species-level polyphyly, and taxonomic over-splitting caused the phylogenetic discordance. Our results suggest that hybridization has played an important role in the history of Plethodon, and that species-level taxonomy, particularly in the glutinosus group, should be revisited.