Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

Dusky Salamanders (genus Desmognathus) currently comprise only 22
described, extant species. However, recent mitochondrial and nuclear
estimates indicate the presence of up to 49 candidate species based on
ecogeographic sampling. Previous studies also suggest a complex history of
hybridization between these lineages. Studies in other groups suggest that
disregarding admixture may affect both phylogenetic inference and
clustering-based species-delimitation. 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. 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.
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. We
find strong support for both recent admixture between terminal lineages
and ancient hybridization across internal branches. 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. 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. --