The Phylogeography of Rare Central Tennessee Glade Endemics Trifolium calcaricum and Viola egglestonii

Endemic species are range-restricted to a particular type of habitat and generally occur in a few small populations. Often endemic species are threatened or endangered due to their geographic isolation and limited habitat breadth. Despite the fact that understanding factors that may have shaped the evolutionary history of a species with a narrow distribution can provide important insights for their management and conservation, little is known about the historical forces that gave rise to many endemic species. Endemic species can arise because of factors such as variation in climate, geographic barriers, and habitat specificity, or the combination of several of these factors. One geographical area with high endemism is the cedar glades of the Central Tennessee Basin, which is home to 29 endemic species that occupy open sites characterized by exposed limestone bedrock with shallow soil and little to no shade. The historical factors that led to the evolution of the species endemic to these rocky outcrops are unknown.In this dissertation, I first conducted an extensive review of biogeographic and phylo- geographic studies of Eastern North American species to understand the progress achieved in the literature since the publication of a seminal paper, Soltis et al. (2006), which outlined phylogeographic patterns in eastern North America corresponding to hypothesized biogeographical boundaries. Since the study was published, many advances in molecular and analytical technological have been made, potentially allowing an improved understanding of the historical factors shaping species diversity and distributions in eastern North America. I reassessed the support for previously identified phylogeographical discontinuities, analyzed support for new discontinuities, and analyzed the adoption of technologies for analyzing phylogeographical patterns and conducting phylogeographical hypothesis testing over the last 15 years. Few phylogeographical studies in the region have utilized technologies that improve the resolution and hypothesis testing ability, limiting our ability to assess the strength of support for phylogeographical discontinuities. Improved taxonomic diversity is necessary to broaden our inference of the generality of the forces shaping the geographical patterns of genetic variation across species. In the next two chapters, I investigated the historical factors giving rise two endemic species of the Central Tennessee Basin cedar glades, Trifolium calcaricum and Viola egglestonii. First, I tested hypotheses about the origin of a disjunction in the range of Trifolium calcaricum between populations occurring in the Central Tennessee Basin and western Virginia. Our results most strongly support the hypothesis that a climate-related vicariance at the close of the Pleistocene during the LGM gave rise to the disjunction in the range of T. calcaricum, possibly due to populations occupying two refugia during the Pleistocene, leading to geographic isolation and genetic differentiation between the two groups of populations within the species. I next tested several hypotheses about the historical factors leading to the origin of the cedar glade endemic species, Viola egglestonii. Our results also support the hypothesis that physical or climate-related barriers that occurred during the Pleistocene gave rise to the divergence between V. egglestonii and its sister species, V. palmate. This work provides an important initial test to elucidate the historical factors that potentially gave rise to the endemic species that occur in the CTB and indicates that the Pleistocene was likely an important epoch shaping the evolutionary history of the species in the region