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.