Plethodontid salamanders are renowned for their morphological conservatism despite extensive phylogeographic divergence. We illustrate this approach here with Seal Salamanders (Desmognathus monticola) and introduce a new unsupervised machine-learning approach for species delimitation. Integrative taxonomy can therefore reflect an understanding of how each axis of variation relates to underlying speciation processes, with nomenclature for distinct evolutionary lineages. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly large datasets. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases a hypothesis that must therefore be falsified under an explicit evolutionary model. Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early‐diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. Using phylogenetic and population‐clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding (i) species‐level diversity, (ii) hybridization and admixture, and (iii) misleading phylogenetic inference. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering‐based species delimitation. Previous studies also suggest a complex history of hybridization between these lineages. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Abstract Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species.
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