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Relative Rates of Molecular Evolution in Rodents and Their Symbionts

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Relative Rates of Molecular Evolution in Rodents and Their Symbionts Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 1997 Relative Rates of Molecular Evolution in Rodents and Their yS mbionts. Theresa Ann Spradling Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Spradling, Theresa Ann, "Relative Rates of Molecular Evolution in Rodents and Their yS mbionts." (1997). LSU Historical Dissertations and Theses. 6527. https://digitalcommons.lsu.edu/gradschool_disstheses/6527 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 Historical Dissertations and Theses by an authorized administrator of LSU Digital Commons. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type o f computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely afreet reproduction. hi the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back o f the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6” x 9” black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. UMI A Bell & Howell Information Company 300 North Zeeb Road, Ann Arbor MI 48106-1346 USA 313/761*4700 800/521*0600 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. RELATIVE RATES OF MOLECULAR EVOLUTION IN RODENTS AND THEIR SYMBIONTS 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 Department of Zoology and Physiology ly Theresa Ann Spradling B.S., Emporia State University, 1988 M.S., University of North Texas, 1991 August 1997 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. UMI Number: 9808784 UMI Microform 9808784 Copyright 1997, by UMI Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. UMI 300 North Zeeb Road Ann Arbor, MI 48103 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Acknowledgments Many people have contributed to my graduate studies through their extreme generosity with their time and knowledge. I thank my major professor, Dr. Mark Hafner, for his patience and hard work in teaching me more about the process of science. As a graduate student of Dr. Hafner's, I never felt like a second-tier priority. My past and present committee members (Drs. C. F. Bryan, D. A. Good, D. Prowell, J. V. Remsen, F. H. Sheldon, R. M. Zink) also deserve special thanks. Dr. P. D. Sudman was instrumental in helping me get these research projects started; his advice and tutoring are greatly appreciated. Dr. D. W. Foltz also contributed to this research through discussions of population genetics and rates of evolution. Dr. X. Xia modified the Codrates program for use with mitochondrial DNA and assisted with data analysis. Dr. D. A. Good made available the MacSequence program and a program for calculating probabilities based on the binomial equation. People in the Museum of Natural Science and in the Systematics and Evolution group have helped in ways too numerous to mention. I especially thank B. S. Arbogast, A. L. Bass, J. M. Bates, P. O. Dunn, S. J. Hackett, C. A. Lehn, S. Meiers, D. A. McClellan, D. L. Reed, and L. A. Whittingham. Dr. J. W. Demastes was helpful in nearly every aspect of this project from beginning to end, assisting in specimen collection, providing advice on data analyses, and providing helpful criticisms of drafts of this manuscript. Several people at other institutions helped to make the research presented here possible. C. T. Beagley, It Okimoto, and D. R. ii Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Wolstenholme made available PCR primers for the amplification of mitochondrial DNA of both pocket gophers and chewing lice. B. J. Verts and L. N. Carraway took time to teach me how to catch the "big" gophers. Paul Sherman provided tissues of naked mole-rats from his collection, and the Museum of Southwestern Biology at the University of New Mexico provided tuco-tuco tissues. Drs. I. F. Greenbaum and E. Nevo made available tissues from the blind mole-rat. Finally, Dr. Roger Price was extremely helpful in confirming the identifications of many of the chewing lice included in this research. I appreciate financial support from the American Society of Mammalogists, the National Science Foundation Doctoral Dissertation Im provem ent Program (DEB-9321395), Sigma Xi, the NSF-Louisiana Education Quality Support Fund (ADP-02), the Theodore Roosevelt Memorial Fund of the American Museum of Natural History, and the Louisiana Board of Regents. Finally, I thank my parents, Cloyce and Bernadette Spradling, for their support. They fostered my earliest interest in rodents and genetics during my hamster-ranching days. iii Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Table of Contents Acknowledgments .......................................................................................ii List of Tables............................................................................................... v i List of Figures............................................................................................ v ii A bstract........................................................................................................ix C hapter 1 Introduction to the Study of Rates of Molecular E v olution ......................................................................................1 TYPES OF DNA SUBSTITUTIONS................................... 3 POSSIBLE CAUSES OF EVOLUTIONARY RATE HETEROGENEITY............................................................... 4 RELATIVE RATES OF EVOLUTION Tests Based on the Fossil Record ................................ 7 Tests Based on Cospedating Taxa ..............................9 Analyses Based on Relative-Rate Tests .................. 11 FOCUS OF THIS DISSERTATION.................................... 16 2 Phylogeny and Relative Rates of Evolution of R odents ....................................................................................... 18 MATERIALS AND METHODS........................................ 22 RESULTS AND DISCUSSION Phylogenetic Utility of Cytochrome b ..................... 26 Implications for the Evolutionary History of R odents ...................................................................... 34 Relative Evolutionary Rates Among Rodents 38 Selectionist and Neutralist Explanations of Rate Heterogeneity ....................................................49 Absolute Rates of Evolution in Rodents ................. 61 CONCLUSIONS.................................................................63 3 Historical Assodations of Pocket Gophers and Chewing Lice...............................................................................................68 POCKET GOPHERS AND CHEWING LICE................... 71 SPECIFIC AIMS OF THIS STUDY.................................... 73 MATERIALS AND METHODS Specimens Examined ................................................. 74 DNA Isolation, Cloning, and Sequencing ............... 76 iv Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Data Analysis .............................................................77 RESULTS AND DISCUSSION Phylogenetic Relationships of Chewing Lice ......... 80 Phylogenetic Relationships of Pocket Gophers 86 Historical Associations Between Hosts and Parasites .......................................................... 90 Relative Rates of Evolution Within Each G roup ........................................................................ 98 Do Chewing Lice Have a Higher Rate of E volution? ................................................................ 99 CONCLUSIONS...............................................................108 Literature Cited ........................................................................................ 110 Appendixes A .......................................................................................................
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