Speciation hypotheses from phylogeographic delimitation yield an integrative taxonomy for Seal Salamanders (Desmognathus monticola)

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.
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. We
can now test speciation hypotheses linking trait differentiation to
specific mechanisms of divergence with increasingly large datasets.
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 illustrate this
approach here with Seal Salamanders (Desmognathus monticola) and introduce
a new unsupervised machine-learning approach for species delimitation.
Plethodontid salamanders are renowned for their morphological conservatism
despite extensive phylogeographic divergence. We discover two geographic
genetic clusters, for which demographic and spatial models of ecology and
gene flow provide robust support for ecogeographic speciation despite
limited phenotypic divergence. These data are integrated under
evolutionary mechanisms (e.g., spatially localized gene flow with reduced
migration) and reflected in emergent properties expected under models of
reinforcement (e.g., ethological isolation and selection against hybrids).
Their genetic divergence is prima facie evidence for species-level
distinctiveness, supported by speciation models and divergence along axes
such as behavior, geography, and climate that suggest an ecological basis
with subsequent reinforcement through prezygotic isolation. As datasets
grow more comprehensive, species delimitation models can be tested,
rejected, or corroborated as explicit speciation hypotheses, providing for
reciprocal illumination of evolutionary processes and integrative
taxonomies.