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.