Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders

Hybridization can leave genealogical signatures in an organism's genome, originating from the parental lineages and persisting over time. This potentially confounds phylogenetic inference methods that aim to represent evolution as a strictly bifurcating tree. We apply phylotranscriptomic approach study evolutionary history of, test for inter-lineage introgression Salamandridae, Holarctic salamanders group of interest studies toxicity aposematism, courtship behavior, molecular evolution. Although relationships between 21 currently recognized salamandrid genera have been subject numerous studies, some branches remained controversial sometimes affected by discordances mitochondrial vs. nuclear trees. To resolve phylogeny this family, understand source mito-nuclear discordance, we generated new transcriptomic (RNAseq) data 20 salamandrids used these along with published data, including 28 genomes, obtain comprehensive perspective on Our final set included 5455 gene alignments 40 species representing 17 genera. Using concatenation species-tree methods, find (1) Salamandrina sister clade “True Salamanders” (consisting Chioglossa, Mertensiella, Lyciasalamandra, Salamandra), (2) Ichthyosaura Near Eastern Neurergus Ommatotriton, (3) Triturus Lissotriton, (4) Cynops paraphyletic respect Paramesotriton Pachytriton. Combining tests networks, evidence among taxa within clades “Modern Asian Newts” European Newts”. However, could not unambiguously identify number, position, direction introgressive events. analysis observed discordances, hypothesize scenario hybridization capture ancestral Lissotriton into Calotriton, plus genes Lissotriton. Furthermore, both may occurred assigned Cynops. More genomic will, future, allow testing against alternative scenarios involving other, extinct newts.