Diversification of genes, populations, and species: Evolutionary genetics of real and virtual pocket gophers

Pocket gophers (Thomomys)---subterranean rodents found throughout western and southern North America---are among the most taxonomically diverse mammals. As a result, they have received a great deal of attention by evolutionary biologists. The first chapter of this dissertation explores the use of pocket gophers as a model system to address a broad range of evolutionary issues involving the spatial distribution of genetic variation. Clearly, constraints of subterranean existence have been key factors molding pocket gopher evolution. One consequence of these constraints is that individual territories and populations are discrete and spatially distinct. These factors lend to the tractability of studying pocket gopher populations both in the field and by simulation modeling. Chapter two uses a spatially-explicit, individual-based simulation model based on pocket gopher biology (hence, "virtual pocket gophers") to explore the power of genetic markers to infer current population parameters (such as dispersal rates) for threatened or fragmented species. The simulations show that this approach can produce seriously misleading results unless equilibrium conditions prevail. Unfortunately, in these times of rampant habitat destruction, population dynamics are often far from stable, suggesting that conditions will not typically be at equilibrium. The third chapter focuses on a threatened complex of the Pacific northwestern Mazama pocket gopher ( Thomomys mazama) in Washington state. Phylogenies of the mitochondrial gene cytochrome b are used to evaluate taxonomic designations and to explore phylogeographic hypotheses on the origins of Washington taxa. In addition to suggesting the need for taxonomic revisions, this study reveals that a disjunct subspecies endemic to a narrow subalpine region of the Olympic mountains is likely a pre-Pleistocene relict, having apparently survived local glaciation. The fourth and final chapter describes an interesting molecular phenomenon detected during the mitochondrial DNA analysis, namely that the cytochrome b gene occurs in multiple copies in the nuclear genomes of T. mazama and its congener T. talpoides . Phylogenetic analyses suggest that a single mitochondrial to nuclear translocation event occurred sometime before T. mazama and T. talpoides split into separate lineages, and that the multiple pseudogenes detected are the result of duplications of the translocated gene.