Conclusions
Mechanisms including isolation by adaptation, barrier, environment,
hierarchy, and resistance can lead to local genetic diversity and the
accumulation of deeply divergent phylogeographic lineages within
species. If divergent ecological selection acts to enhance population
divergence along any number of axes such as phenotype, microhabitat, or
behavior to reduce migration and increase reproductive isolation, then
speciation is the natural and expected outcome. In contrast, multiple
processes may counter this, enhancing rates of migration and gene flow
and limiting ecomorphological diversification despite the accumulation
of geographic genetic lineages. This may lead to long-term prevalence of
population structure within species that is not necessarily tied to
incipient, incomplete, or ongoing speciation, but is instead a stable or
persistent endpoint held in check by migration. We demonstrate one such
example here in Seepage Salamanders, Desmognathus aeneus.Geographic lineages dating back to the mid-Pleistocene are nonetheless
unified by high levels of migration through time, while stabilizing
ecomorphological selection arising from extreme microhabitat specificity
apparently limits potential ecological speciation. This conclusion is
reinforced by the limited but non-zero genomic signature of correlated
genetic and phenotypic divergence along axes of temperature and
precipitation between montane and lowland regions. The framework
presented here clarifies many of the theoretical expectations and offers
potential empirical tests for the previously ambiguous definition of
structure versus speciation in the quantification of phylogeographic
lineage diversity.