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.

Gopherus polyphemus populations are diminishing throughout their range due to urbanization, fragmentation, and poor management of habitats. Increased population densities, poor habitat quality, and lack of fire may influence disease transmission. Parasite roles within wild tortoise populations are largely unknown, despite evidence these pathogens may pose health risks. This study provides a baseline of gopher tortoise endoparasites across South Florida and reports on how varying environmental and tortoise characteristics may affect endoparasite species prevalence, approximate loads, and overall distributions. Tortoise fecal samples were taken from five differing SF habitats. Seven species of intestinal parasites were discovered from 123 tortoises. Identified parasites include endo-helminths such as cyathostomes, pinworms, ascarids, flukes, and protozoans including Eimeria, Cryptosporidium, and Amoeba species. Significant differences in parasite prevalence and loads were seen between sampling years, seasons, size classes, and sites, however, overall parasite distributions suggest parasitism remains relatively ubiquitous throughout most host and site characteristics. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2017. / FAU Electronic Theses and Dissertations Collection

Gopherus polyphemus, commonly known as the Gopher Tortoise, is a dryland reptile native to the southeastern United States. It is commonly a resident of longleaf pine and dry oak sand hill habitats. It is considered a keystone species because they dig deep burrows that provide shelter to them as well as many other animals. Habitat loss, fragmentation, and disease are major threats and have caused this species to be federally listed as a threatened species under the Endangered Species Act (ESA). Disease is a major threat to the gopher tortoise’s survival, and with declining populations, the need to investigate pathogens is crucial. Herpesvirus, is known to contribute to upper respiratory tract diseases (URTD) in G. polyphemus and is the primary focus of this project. Due to high mutation rates in the virus, a modified version of PCR, nested PCR, was conducted on eye and nose swabs and blood samples obtained from G. polyphemus to detect the presence of the alpha herpesvirus pathogen. The positive samples were then sent for genetic sequencing to confirm the occurrence of the pathogen. The detectability of Herpesvirus in eye and nose swabs was compared to blood and lymph samples and statistical tests concluded that both sample types had the same detectability.

Gopher tortoise (Gopherus polyphemus; hereinafter, tortoise) is listed as threatened under the Endangered Species Act in the western portion of its range. Across the species’ range, approximately 70 % of potential habitat is privately owned, and these properties are often managed primarily for timber production. However, tortoise ecology on private, working forest landscapes remains poorly understood. To provide a better understanding of tortoise response to active forest management, I evaluated population demographics, movement ecology, and habitat selection of two tortoise populations: former Ben’s Creek Wildlife Management Area (BC) in Washington Parish, Louisiana and Perry County Gopher Tortoise Management Unit (PCGTMU) in Perry County, Mississippi. At BC, tortoises were generally clustered along utility rights-of- way and roadways. At PCGTMU, tortoises were clustered within forest stands with high quality soils. Low recruitment has been documented at BC for the last 25 years. However, PCGTMU appears to have a stable population with active recruitment.

This thesis evaluates the interaction between four habitat factors vital to the gopher tortoise in Florida. Federally and state listed as threatened throughout its entire range, the gopher tortoise is vital to protect, not only for itself individually but its burrows provide an essential habitat to over 300 species making it a key stone species within its environment. Historic habitat modeling methods are reviewed for the gopher tortoise to highlight the gap on this topic. This research expanded on the methods utilized by Baskaran et al. (2006) evaluating the soil, landcover, percentage of canopy cover and the depth to water table habitat factors key to the gopher tortoise. Statistical analysis was used to establish the interactions using a regression type analysis of the presence/absence data relative to the four factors. A probability map for the study site was then computed from the results. The Analysis of Deviance results for the statistical model with land cover type as an independent variable and a 3-way interaction term for the other factors found that the land cover term was significant as an independent variable and the 3-way interaction of the other 3 habitat factors was significant. This result demonstrates that there is in fact an interaction between the habitat factors influencing the location of gopher tortoises. This finding is significant in future gopher tortoise research as it indicates that habitat factors evaluated individually may not be as important as the interactions between the factors. By understanding the interactions between the habitat factors, the FWC can work alongside other agencies to ‘increase and improve’ these key habitat areas preventing them from destruction. The map results also help pinpoint those fragmented potential habitat sites which are most at risk from full destruction and loss allowing agencies the work on protecting and expanding the suitable habitat landscape in order to ‘enhance and restore’ the gopher tortoise populations residing there, helping them to ‘maintain the gopher tortoise’s function as a keystone species’

Species-species and species-habitat interactions have been demonstrated to be important in influencing diversity across a variety of ecosystems. Despite generalities in the importance of these interactions, appropriate mechanisms to explain them are absent in many systems. In sandhill systems of the southeast U.S., gopher tortoises have been hypothesized to be a crucial species in the maintenance of diversity and function. However, the mechanisms and magnitude in which they influence their communities and habitats have rarely been empirically quantified. I examined how habitat structure influences tortoise abandonment of burrows and how tortoise densities influence nonvolant vertebrate community diversity. Tortoise burrow abandonment is directly influenced by canopy closure, with each percent increase in canopy cover relating to a ~2% increase in the probability of burrow abandonment. In addition, tortoise burrow density was positively correlated with diversity and evenness, but not species richness. This influence was directly proportional to burrow density, supporting a dominance role for this species and rejecting the commonly asserted keystone species mechanism. I also quantified the influence of tortoises in influencing diversity relative to other environmental and habitat variables. Through this research, I have demonstrated that disturbance and habitat structure are important, but diversity responds most to density of burrows in the habitat. These findings demonstrate the intricate relationships interacting to maintaining diversity in sandhill systems. In particular, habitat change leading to declines of gopher tortoises may have drastic negative impacts on vertebrate species diversity.