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

Effect of Ingestion by Alligator Snapping Turtles (Macrochelys Temminckii) on Seeds of Riparian Vegetation

The alligator snapping turtle (Macrochelys temminckii) is a large freshwater turtle that inhabits many lotic water bodies in the Southeastern United States. The species consumes primarily fish but also consumes large amounts of vegetation including seeds of common persimmon (Diospyros virginiana), tupelos (Nyssa sp.), willow oak (Quercus phellos), and pecan (Carya illinoensis). Captive specimens of M. temminckii were fed samples of the above-mentioned seeds to assess how the species affects ingested seeds in order to evaluate the potential role this species may play as a seed disperser. The proportion of seeds defecated intact varied with species (57−99 %), was lowest in D. virginiana, and highest in N. aquatica. Ingestion reduced the percentage of seeds that germinated in comparison to uneaten controls in all species except Q. phellos where ingestion increased germination percent. Germination percent also decreased the longer seeds remained inside turtles. Ingestion reduced the germination rates of D. virginiana and N. aquatica seeds but increased germination rates for seeds of Q. phellos in comparison to uneaten controls. Due to fungal contamination, conclusions could not be drawn regarding the effect of ingestion on germination percent or rate of C. illinoensis seeds. This study suggests M. temminckii could potentially play some role as a disperser of Q. phellos and N. aquatica but is less likely for D. virginiana. Information regarding post-dispersal fates of seeds ingested by M. temminckii and other freshwater turtles is needed to evaluate the importance of freshwater turtles as dispersers of riparian and wetland vegetation

Landscape genomics of a widely distributed snake, Dolichophis caspius (Gmelin, 1789) across Eastern Europe and Western Asia

Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius

Climate control of terrestrial carbon exchange across biomes and continents

Peer reviewe

The Major Histocompatibility Complex of Old World Camels—A Synopsis

This study brings new information on major histocompatibility complex (MHC) class III sub-region genes in Old World camels and integrates current knowledge of the MHC region into a comprehensive overview for Old World camels. Out of the MHC class III genes characterized, TNFA and the LY6 gene family showed high levels of conservation, characteristic for MHC class III loci in general. For comparison, an MHC class II gene TAP1, not coding for antigen presenting molecules but functionally related to MHC antigen presenting functions was studied. TAP1 had many SNPs, even higher than the MHC class I and II genes encoding antigen presenting molecules. Based on this knowledge and using new camel genomic resources, we constructed an improved genomic map of the entire MHC region of Old World camels. The MHC class III sub-region shows a standard organization similar to that of pig or cattle. The overall genomic structure of the camel MHC is more similar to pig MHC than to cattle MHC. This conclusion is supported by differences in the organization of the MHC class II sub-region, absence of functional DY genes, different organization of MIC genes in the MHC class I sub-region, and generally closer evolutionary relationships of camel and porcine MHC gene sequences analyzed so far

Effects of long-term oral testosterone undecanoate therapy on urinary symptoms: data from a 1-year, placebo-controlled, dose-ranging trial in aging men with symptomatic hypogonadism

Background: There has been a longstanding question as to whether testosterone therapy could precipitate or worsen urinary symptoms in aging men. We investigated the effects of 1-year oral testosterone undecanoate (TU) therapy on urinary symptoms in aging, hypogonadal men. Methods: A total of 322 men 50 years with symptomatic testosterone deficiency participated in a 1-year, randomized, multicenter, double-blind trial. Patients received placebo or oral TU 80mg/day, 160mg/day, or 240mg/day. Results and limitations: Compared with placebo, treatment with oral TU at doses of 80mg/day and 160mg/day resulted in no significant change in IPSS urinary symptoms or quality of life (QoL) scores. Treatment with oral TU 240mg/day led to a statistically significant, but clinically insignificant, improvement in IPSS total score and a significant improvement in IPSS QoL score. None of the TU doses tested had a significant effect on PSA or PV. Conclusions: Long-term oral TU therapy had no deleterious effects on IPSS total score and did not change PV and PSA in aging, hypogonadal men. Oral TU therapy at a dose of 240mg/day may even improve IPSS QoL score