The limits of the metapopulation: Lineage fragmentation in a widespread terrestrial salamander (Plethodon cinereus)

In vicariant species formation, divergence results primarily from periods
of allopatry and restricted gene flow. Widespread species harboring
differentiated, geographically distinct sublineages offer a window into
what may be a common mode of species formation, whereby a species
originates, spreads across the landscape, then fragments into multiple
units. However, incipient lineages usually lack reproductive barriers that
prevent their fusion upon secondary contact, blurring the boundaries
between a single, large metapopulation-level lineage and multiple
independent species. Here we explore this model of species formation in
the Eastern Red-backed Salamander (Plethodon cinereus), a widespread
terrestrial vertebrate with at least six divergent mitochondrial clades
throughout its range. Using anchored hybrid enrichment data, we applied
phylogenomic and population genomic approaches to investigate patterns of
divergence, gene flow, and secondary contact. Genomic data broadly match
most mitochondrial groups but reveal mitochondrial introgression and
extensive admixture at several contact zones. While species delimitation
analyses in BPP supported five lineages of P. cinereus, genealogical
divergence indices (gdi) were highly sensitive to the inclusion of admixed
samples and the geographic representation of candidate species, with
increasing support for multiple species when removing admixed samples or
limiting sampling to a single locality per group. An analysis of
morphometric data revealed differences in body size and limb proportions
among groups, with a reduction of forelimb length among warmer and drier
localities consistent with increased fossoriality. We conclude that P.
cinereus is a single species, but one with highly structured component
lineages of various degrees of independence.