Understanding worldwide declines in reptiles due to factors such as habitat loss and emerging infectious disease has become an increasingly important focus in conservation biology. Here, I use novel approaches from the field of landscape genetics to combine spatial genetic data with landscape data at both regional and local spatial scales to explore natural and anthropogenic landscape features that shape population structure and gene flow in a federally threatened reptile, Gopherus polyphemus. I also utilize approaches from the field of spatial epidemiology to examine the extent to which environmental variables can be used to predict the seroprevalence of an associated pathogen Mycoplasma agassizzi in gopher tortoise populations. Using mitochondrial data, I find evidence of a historical barrier to gene flow that appears to coincide with the Apalachicola River. I also discover low genetic diversity and evidence of population bottlenecks in the western portion of the range. My evaluation at the regional scale shows that dispersal is limited by geographic distance, areas of low elevation and major roads ways. A finescale study reveals no evidence of spatial genetic structure within a 14 x 35 km area. However, soil type is significantly correlated with pairwise genetic distances between individuals, suggesting that this variable influences fine-scale population structure in the gopher tortoise. In addition to soil, high density canopy cover is an important factor impeding gene flow at the local level for females, while land cover type explains some of the genetic variance between males. Finally, temperature and precipitation appear to be important predictors of the seroprevalence of the pathogen Mycoplasma agassizii in gopher tortoises. The probability of an individual testing seropositive for exposure to this disease increased with high temperature and low precipitation values. The methods presented in this dissertation evaluate novel approaches for assessing the influence of environmental variables on population structure, dispersal and disease occurrence and could be applied in future studies of other threatened and endangered taxa.

Upper Respiratory Tract Disease (URTD), caused by the pathogens Mycoplasma agassizii and M. testudineum, has been documented in the desert tortoise (Gopherus agassizii). Although URTD was identified as a putative agent that led to federal listing of the Mojave population of the desert tortoise, little is known about this disease in the Sonoran population of the desert tortoise. The purpose of this study was to determine: 1) the prevalence of URTD across an urban gradient in Greater Tucson, Arizona, 2) the relationship between URTD and captive and free-ranging tortoises in Mohave, Maricopa, and Pima counties in Arizona, and 3) the effects of URTD on desert tortoise home range size and winter temperature selection.