The effects of climate and habitat change on the distribution and genetic diversity of chipmunks in the Sierra Nevada, California

Historical changes in climate have affected the diversity and distribution of species across the globe. Recent and rapid human-induced climate change is expected to have extreme consequences for biodiversity and ecosystem integrity. Documented species' responses to recent climate change include adaptation, distributional shifts and extinctions. There is an urgent need for scientists to improve understanding of how climate change will affect not only species distribution and abundance but also genetic diversity, which is the basis for evolutionary potential and thus critical to long-term persistence. Here I investigate the effects of climate change on the diversification, distribution and genetics of chipmunks in Sierra Nevada, California. First, I examine the role of late Pleistocene climate fluctuations on the divergence of the endemic Alpine Chipmunk (Tamias alpinus) from its sister taxa, western populations of the Least Chipmunk (T. minimus). I use one mitochondrial gene (cytochrome b) and 14 microsatellite loci to examine the evolutionary relationship between these co-distributed species. Mitochondrial sequence data revealed that that T. alpinus and T. minimus populations share mitochondrial haplotypes with no overall geneaological separation, and that diversity at this locus is better explained by geography than by species' boundaries. In contrast, the microsatellite analysis showed that although highly differentiated populations within species exist, populations of the same species are more similar to each other than they are to members of the other species. This result suggests that the two species are distinct and there is no contemporary introgression along their parapatric boundary. Coalescent analysis of the divergence history indicated a late Pleistocene splitting time (~450ka) and subsequent, though limited, gene flow between the two lineages. The divergence of T. alpinus during this time period provides more evidence that Pleistocene glacial cycles played an important role in diversification of species in the Sierra Nevada and North America in general.Second, I used small mammal surveys repeated over a century to assess accuracy of species distribution models in predicting known changes in chipmunk distributions, and to identify the main environmental drivers of these shifts. Historical (1900-1940) climate, vegetation and species occurrence data were used to develop single-species and multi-species multivariate adaptive regression spline (MARS) distribution models for three species of chipmunk. Models were projected onto the current (1980-2007) environmental surface and then tested against modern field resurveys of each species. I evaluated models both within and between time periods and found that even with the inclusion of biotic predictors, climate alone is the dominant predictor explaining the distribution of the study species within a time period. However, climate was not consistently an adequate predictor of the distributional change observed in all three species across time. For T. alpinus, climate alone showed the best predictive performance, strongly suggesting this species has retracted its range up in elevation due warming over the past 100 years. Modeling results showed that both climate and vegetation were factors in the collapse of T. senex populations in the study area and my modeling approach failed to predict the stability of the distribution over time observed in T. speciosus.Third, I investigated how the climate-induced range contraction observed in T. alpinus over the past century has affected the species' overall diversity and population genetic structure in Yosemite National Park. I used one mitochondrial and seven microsatellite loci, amplified from both historical and modern specimens, to compare genetic structure of T. alpinus with that of T. speciosus, whose distribution remained stable over time. I found a decline in overall genetic diversity and a reduction of gene flow between local populations over time in T. alpinus, as expected from spatial modeling of distributions. As predicted given its relative stability through time, there were no significant genetic changes seen in T. speciosus. Overall, my dissertation contributes to existing research on the diversification, climate change impacts, and conservation genetics of small mammals. Most importantly, this work exemplifies the value of natural history museums, and the use of historically collected data in contemporary biodiversity research