Complex Hybridization in a Clade of Polytypic Salamanders (Plethodontidae: Desmognathus) Uncovered by Estimating Higher-Level Phylogenetic Networks.

This article focuses on the complex reticulate evolutionary history and ecomorphological hybrid speciation within the Pisgah clade of Desmognathus salamanders from the southern Appalachian Mountains, which includes seven genetically and phenotypically distinct lineages exhibiting two ancient, discrete phenotypes: aquatic shovel-nosed and semi-aquatic black-bellied forms. Using a novel heuristic method based on gene-tree concordance factors and supported by genomic data (genotype-by-sequencing and anchored hybrid enrichment), the authors infer a higher-level phylogenetic network with multiple overlapping hybridization events that traditional level-1 network methods cannot resolve. Their findings suggest that several lineages arose via hybridization between phenotypically differentiated parental species, with hybrid lineages maintaining distinct, non-intermediate phenotypes linked to a polygenic threshold trait, promoting ecological divergence and reproductive isolation through habitat specialization rather than intermediate or novel morphologies. This study highlights the challenges of reconstructing complex reticulate evolution and underscores the need for further genomic investigation to clarify the genetic basis and evolutionary origins of these ecomorphological traits.