Immune Gene Variation and Susceptibility to Upper Respiratory Tract Disease in Gopher Tortoises

The immune system defends the host from bacteria, fungi, parasites, and viruses. The immune system is partially under genetic control through immune response genes, such as those of the major histocompatibility complex (MHC) whose nucleotide variation influences the host’s ability to recognize foreign pathogens and can influence disease susceptibility. Populations of threatened species generally possess low levels of genetic variation, and genetically depauperate hosts may be at greater risk of infectious disease contributing to extirpations because they also possess low immunogenetic variation. My dissertation examines the relationship between immunogenetic variation and disease susceptibility and the factors that influence innate immune responses in threatened gopher tortoises (Gopherus polyphemus), which are susceptible to an infectious and occasionally fatal upper respiratory tract disease primarily associated with infection by Mycoplasma bacteria. I reviewed available reptile MHC literature in Chapter 2 and found that MHC polymorphism appears to be extensive in reptile populations, and current evidence suggests MHC polymorphism may influence parasite resistance and mate choice as in other vertebrates. I found that season but not sex influenced the innate immune responses of free-ranging Louisiana gopher tortoises in Chapter 3. In Chapter 4, although I found evidence of natural selection acting on a MHC class II locus in a range-wide sample of gopher tortoises, MHC and microsatellite variation were correlated suggesting that generally small effective population sizes of gopher tortoises also allow neutral genetic processes to influence MHC evolution. I developed a software workflow that filters annotated genomes by desired gene functions in Chapter 5, and I used this workflow to filter the western painted turtle genome by all known immune response genes (i.e., immunome). I used the western painted turtle’s immunome to develop reagents to sequence the immunomes from gopher tortoises from four populations from Louisiana to Florida in Chapter 6 and found that population genetic inferences derived from gopher tortoise immunomes mirrored inferences from microsatellites further suggesting neutral genetic processes are influencing immune response gene evolution. Next, I analyzed immunomes from Florida gopher tortoises that were URTD-clinical or -non-clinical in Chapter 7 and found several single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) that were top-ranking variants with possible roles in Mycoplasmal-immunity. These variants were not statistically associated with Mycoplasmal-URTD susceptibility after corrections for multiple tests; however, this is a common outcome of genome wide association tests where the large number of tests typically precludes statistical significance of any genetic variant. Nonetheless, researchers pursue top-ranking variants for future research, which has yielded important results for understanding the genetic basis of disease in agricultural crops, humans, and model organisms. If further experimental studies and more careful examination of these genes show a causal relationship, managers may wish to translocate tortoises from appropriate donor to at risk populations to bolster genetic variation at these loci