Discordance between phylogenomic methods in near Eastern mountain newts (Neurergus, Salamandridae).

Target enrichment by sequence capture allows researchers to collect genome-wide sequence data, suitable to re-evaluate complex systematic and taxonomic cases. The family Salamandridae is rife with rapid, successive speciation events, introgression and incomplete lineage sorting: factors that complicate the inferring of phylogenetic relationships and species boundaries. Phylogenetic relationships among, and the (sub)species status of, the taxa comprising the newt genus Neurergus are not fully resolved. We perform target enrichment by sequence capture to obtain ca. 7 k nuclear DNA markers, and conduct concatenated analysis with RAxML, gene-tree summary analysis in ASTRAL, and species tree estimation in SNAPPER, and investigate admixture between populations and genetic introgression with ADMIXTURE and Dsuite. We observe discordance between analyses pertaining to the placement of N. crocatus. We consider the placement of N. crocatus as sister to N. derjugini sensu lato in SNAPPER, instead of to N. kaiseri + N. derjugini sensu lato as in RAxML and ASTRAL, to be an artifact of introgression, as backed up by our Dsuite analysis. We show that N. strauchii barani and N. strauchii munzurensis, often treated as distinct species, are deeply nested within N. strauchii sensu stricto and should not be treated as species. Keeping them as subspecies would render the nominotypical subspecies as polyphyletic. Furthermore, we confirm that N. derjugini microspilotus should not be considered a distinct species, but as a subspecies of N. derjugini sensu lato. We consistently recover the northern and southern lineages of N. kaiseri as distinct genetic groups with geographically restricted admixture and recommend that these are treated as two distinct species. Our study highlights the strength of target enrichment by sequence capture in resolving systematic and taxonomic questions in taxa with a history of genetic admixture and introgression.