Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2016 Immune Gene Variation and Susceptibility to Upper Respiratory Tract Disease in Gopher Tortoises Jean Pierre Elbers Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Environmental Sciences Commons Recommended Citation Elbers, Jean Pierre, "Immune Gene Variation and Susceptibility to Upper Respiratory Tract Disease in Gopher Tortoises" (2016). LSU Doctoral Dissertations. 4245. https://digitalcommons.lsu.edu/gradschool_dissertations/4245 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. IMMUNE GENE VARIATION AND SUSCEPTIBILTY TO UPPER RESPIRATORY TRACT DISEASE IN GOPHER TORTOISES A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The School of Renewable Natural Resources by Jean Pierre Elbers B.S., Southeastern Louisiana University, 2008 M.S., Missouri State University, 2010 December 2016 ACKNOWLEDGEMENTS Let me begin by first thanking my wonderful advisor, Sabrina Taylor. She has shown interest and care in not only my dissertation project but also my development as person, researcher, and scientist. I have been truly thankful to work under her tutelage and guidance: thank you so much Sabrina! Next I would like to thank the Lucius Wilmot Gilbert Foundation for Forestry Research, which provided funding for not only my research projects but also for my research assistantship at Louisiana State University. I am also thankful for financial and logistical support from the Louisiana State University AgCenter. My graduate committee has been especially helpful during my dissertation project; many thanks go Drs. Chris Austin, Javier Nevarez, and Phil Stouffer. I am especially grateful to Dr. Javier Nevarez who generously gave of his time to instruct me on drawing blood from gopher tortoises. Chapters 4 and 6 of this dissertation would not have been possible without the help of one my coauthors Dr. Rachel W. Clostio. She charitably donated hundreds of gopher tortoise DNA and blood samples that she collected as part of her dissertation research. For this I am truly grateful and appreciative. I am thankful to Richard Carmouche of Pennington Biomedical Research Center’s Genomics Core who performed next-generation sequencing lab work for Chapters 6 and 7. Another one of my coauthors, Dr. Mary Brown, provided blood samples from clinical and non-clinical gopher tortoises for chapter seven for which I am very grateful. The Louisiana State University community was instrumental in completing this dissertation project, especially students and faculty of the School of Renewable Natural Resources. I am very grateful to past and current members of the Taylor lab for their support and ii friendship: Andrea Bonisoli Alquati, Kristin Brzeski, Christy Bergeon Burns, Blain Cerame, Rob Ford, Anna Perez-Umphrey, Andrew Rodriguez, Amie Settlecowski, Kelcee Smith, Allie Snider, and Stef Woltmann. I am also grateful to Drs. Michael Kaller for advice on statistical analysis, Bret Collier for introducing me to R and LaTex, Maheshi Dassanayake and Brant Faircloth for advice on genomics and bioinformatics, and Eric Achberger for guidance on molecular cloning. I am very appreciative of the help received from the Louisiana Department of Wildlife and Fisheries, especially gopher tortoise biologists Keri Landry and Beau Gregory. I received assistance conducing field work on Chapter 3 from Christy Bergeon-Burns, Maria Bianco, Leah Delahoussaye, Anna Evans, Caitlin Glymph, Kaitlin Kuylen, Jaclyn Shanley, Charleston Shirley, and Bonnie Slaton. Charleston was especially helpful and served as an excellent field technician throughout the hot field season in summer and autumn of 2013. Last but not least, I wish to thank my family: my brother Don Paul Elbers, sister Heidi Elbers, aunt Brenda Lege, grandmother Mary Rose Elbers, mother Cheryl Elbers, and father Don Elbers. They have been with me the entire dissertation progress and have been supportive and understanding during this journey. I do not know if I would have been able to finish my dissertation without them by my side. iii TABLE OF CONTENTS ACKNOWLEDGEMENTS.................................................................................................ii ABSTRACT.......................................................................................................................vi CHAPTER 1: GENERAL INTRODUCTION....................................................................1 IMMUNE SYSTEM................................................................................................1 CONSERVATION GENETICS..............................................................................3 STUDY SYSTEM AND OBJECTIVES.................................................................4 LITERATURE CITED............................................................................................6 CHAPTER 2: MAJOR HISTOCOMPATIBILITY COMPLEX POLYMORPHISM IN REPTILE CONSERVATION...........................................................................................11 INTRODUCTION.................................................................................................11 MHC POLYMORPHISM, PARASITE RESISTANCE, AND MATE CHOICE IN REPTILE POPULATIONS..............................................................................14 DISCUSSION........................................................................................................22 CONCLUSIONS...................................................................................................27 LITERATURE CITED..........................................................................................27 CHAPTER 3: SEASONAL BUT NO SEX EFFECTS IN GOPHER TORTOISE (GOPHERUS POLYPHEMUS) INNATE IMMUNE RESPONSE...................................39 INTRODUCTION.................................................................................................39 METHODS............................................................................................................42 RESULTS..............................................................................................................46 DISCUSSION........................................................................................................49 LITERATURE CITED..........................................................................................54 CHAPTER 4: NEUTRAL GENETIC PROCESSES INFLUENCE MHC EVOLUTION IN A THREATENED TORTOISE (GOPHERUS POLYPHEMUS)................................59 INTRODUCTION.................................................................................................59 METHODS............................................................................................................62 RESULTS..............................................................................................................69 DISCUSSION........................................................................................................89 LITERATURE CITED..........................................................................................99 CHAPTER 5: GO2TR: A GENE ONTOLOGY-BASED WORKFLOW TO GENERATE TARGET REGIONS FOR TARGET ENRICHMENT EXPERIMENTS......................110 INTRODUCTION...............................................................................................110 GO2TR.................................................................................................................111 TO USE GO2TR..................................................................................................114 PROOF OF CONCEPT.......................................................................................114 iv RECOMMENDATIONS.....................................................................................123 OTHER USEFUL TOOLS TO USE IN CONJUNCTION WITH GO2TR.......124 LITERATURE CITED........................................................................................125 CHAPTER 6: POPULATION GENETIC INFERENCES USING IMMUNE GENE SNPS MIRROR PATTERNS INFERRED BY MICROSATELLITES.........................130 INTRODUCTION...............................................................................................130 METHODS..........................................................................................................133 RESULTS............................................................................................................140 DISCUSSION......................................................................................................153 CONCLUSION…................................................................................................157 LITERATURE CITED........................................................................................158 CHAPTER 7: TORTOISE IMMUNOMES SHED LIGHT ON GENETIC VARIATION UNDERLYING INFECTIOUS DISEASE.....................................................................166 INTRODUCTION...............................................................................................166 METHODS..........................................................................................................168