Plethodontid salamanders of the Ensatina eschscholtzii complex have received special attention from evolutionary biologists because they represent one of the very few examples of a ring species, a case where two reproductively isolated forms are connected by a chain of intergrading populations surrounding a central geographic barrier. Ensatina has become a textbook example of speciation, yet there still remain fundamental gaps in our knowledge of this fascinating system. In this study, consisting of three components, I extend previous work on the Ensatina complex in new directions.
In Chapter 1, I conducted a fine-scale genetic analysis of a hybrid zone between the geographically terminal forms of the ring using Bayesian methods for hybrid identification and classification in combination with mathematical cline analyses. F1s and pure parentals dominated the sample. Cline widths were concordant and narrow with respect to dispersal, but there is cytonuclear discordance, both in terms of introgression and the geographic position of mitochondrial versus nuclear clines. Nearly all hybrids possess mitochondrial DNA from one parental type (klauberi suggesting isolation is asymmetrical. Selection against hybrids is inferred to be strong (~21%), but whether this selection is endogenous (genetically-based) or exogenous (environmentally-based) remains to be tested.
In Chapter 2, I investigated the role of late Quaternary climate change on phylogeographic patterns within the Large-blotched Ensatina (Ensatina eschscholtzii klauberi). Intersecting species distribution models constructed under current climatic conditions, as well as two different historical time periods (Last Glacial Maximum, 21 ka and mid-Holocene, 6 ka), predicted stable refugial areas where the species may have persisted throughout climatic fluctuations. Significant phylogeographic structure exists, but geographic structuring of genetic variation by refugia was not supported. Results suggest that populations in putative refugia have not been isolated for very long, or that gene flow may have masked any earlier periods of divergence in allopatry.
In Chapter 3, I conducted a multilocus phylogeographic analysis of the entire Ensatina eschscholtzii complex to reexamine previous phylogenetic hypotheses based on mitochondrial DNA alone. A concatenation approach was used in addition to newer methods that model the relationship between the species tree and the gene trees embedded within them. The concatenated tree was similar to previous mitochondrial trees, identifying well-supported coastal and inland clades, and recovering oregonensis and platensis as paraphyletic. The concatenated tree was not well resolved at the base. Basal relationships recovered by the species tree were well resolved, but most relationships were not well supported compared to the concatenated tree. Results are generally consistent with previous efforts based on mtDNA, but provide further resolution to the Ensatina phylogeny, while highlighting the difficult nature of inferring species trees from samples of closely related populations that are experiencing gene flow.