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Molecular Evolutionary Analysis of the American Pika (Ochotona Princeps) Andrew Michael Rankin Northern Michigan University, [email protected]

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Molecular Evolutionary Analysis of the American Pika (Ochotona Princeps) Andrew Michael Rankin Northern Michigan University, Arankin@Nmu.Edu Northern Michigan University NMU Commons All NMU Master's Theses Student Works 5-2016 Molecular evolutionary analysis of the American pika (Ochotona princeps) Andrew Michael Rankin Northern Michigan University, [email protected] Follow this and additional works at: https://commons.nmu.edu/theses Part of the Genetics and Genomics Commons Recommended Citation Rankin, Andrew Michael, "Molecular evolutionary analysis of the American pika (Ochotona princeps)" (2016). All NMU Master's Theses. 89. https://commons.nmu.edu/theses/89 This Open Access is brought to you for free and open access by the Student Works at NMU Commons. It has been accepted for inclusion in All NMU Master's Theses by an authorized administrator of NMU Commons. For more information, please contact [email protected],[email protected]. MOLECULAR EVOLUTIONARY ANALYSIS OF THE AMERICAN PIKA (OCHOTONA PRINCEPS) By Andrew M. Rankin THESIS Submitted to Northern Michigan University In partial fulfillment of the requirements For the degree of MASTER OF SCIENCE Office of Graduate Education and Research May 2016 SIGNATURE APPROVAL FORM Title of Thesis: Molecular Evolutionary Analysis of the American Pika (Ochotona princeps) This thesis by Andrew M. Rankin is recommended for approval by the student’s Thesis Committee and Department Head in the Department of Biology and by the Assistant Provost of Graduate Education and Research. Committee Chair: Dr. Katherine Teeter Date First Reader: Dr. Kurt Galbreath Date Second Reader (if required): Dr. Alec Lindsay Date Department Head: Dr. John Rebers Date Dr. Robert J. Winn Date Interim Assistant Provost of Graduate Education and Research ABSTRACT MOLECULAR EVOLUTIONARY ANALYSIS OF THE AMERICAN PIKA (OCHOTONA PRINCEPS) By Andrew M. Rankin The American pika (Ochotona princeps) is a small winter-active mammal inhabiting alpine environments. For alpine mammals, metabolic heat production and cellular mechanisms to cope with hypoxia are critical for survival and reproduction. Thus, because of the pikas’ long association with alpine environments, they may have genetically adapted to alpine conditions. Here, I present evidence for positive selection acting at three loci within the Ochotona princeps genome. These loci were identified by first assembling a list of 54 candidate genes and extracting sequence data from two O. princeps draft genomes available from public databases. I then tested the possibility that positive selection acted on the Ochotona lineage, relative to other species in the super order Euarchontoglires, using the CODEML program in the PAML package. These analyses indicated positive selection at four loci. I then investigated rates of synonymous and nonsynonymous substitutions within the conserved domain of each of the four genes, which indicated an increased rate of nonsynonymous substitutions within pikas when compared to other mammals. To test this assumption further, I collected DNA sequence data from the four genes of interest in multiple individuals from a broad geographic range. I used the Ewens-Watterson homozygosity test, and Tajima’s D and Fu’s Fs statistics to test the resulting sequence data for patterns of non-neutral evolution. These tests have provided additional support for positive selection acting on three of the four genes sequences i Copyright by ANDREW M. RANKIN 2016 ii ACKNOWLEDGMENTS Before I begin, I owe a debt of gratitude to my advisors and mentors whom supported me throughout my academic career. Specifically, I would like to mention my undergraduate mentor Dr. Chris Floyd and graduate mentor Dr. Katherine Teeter, both of whom have influenced me greatly. I am also compelled to acknowledge Dr. Kurt Galbreath for his overwhelming encouragement, and Dr. Alec Lindsay for the reassurance he offers to NMU biology graduate students. I would also like to thank my funding sources, the American Society of Mammalogists, the Sigma Xi Research Society, and the Excellence in Education Grant, Spooner Grant, and the NMU Biology Department Developmental Fund. This thesis follows the format of The Journal of Mammalogy. iii TABLE OF CONTENTS List of Tables ......................................................................................................................v List of Figures ................................................................................................................... vii Introduction ..........................................................................................................................1 Chapter One: Literature Review Natural History of American Pika .......................................................................................4 Genetic Diversity in Natural Populations of American Pika ...............................................6 Pika Adaptation ....................................................................................................................8 Future Direction .................................................................................................................14 Chapter Two: Mining the American Pika (Ochotona princeps) Genome for Putatively Adaptive Loci Introduction ........................................................................................................................16 Materials and Methods .......................................................................................................18 Results ................................................................................................................................23 Discussion ..........................................................................................................................52 Chapter Three: Using Nuclear Loci to Detect Selective Sweeps in the American Pika (Ochotona princeps) genome Introduction ........................................................................................................................56 Materials and Methods .......................................................................................................58 Results ................................................................................................................................69 Discussion ........................................................................................................................105 Conclusion .......................................................................................................................112 Summary and Conclusion ................................................................................................113 Works Cited .....................................................................................................................115 Appendix A ......................................................................................................................125 Appendix B ......................................................................................................................126 iv LIST OF TABLES Table 2.1. Comparison of pairwise alignments between two pika sequences originating from the OchPri3 and OchPri2 draft genomes ...................................................................30 Table 2.2. Using the 28 polymorphic sequences between OchPri3 and OchPri2, I calculated (1) the number of nonsynonymous substitutions/number of nonsynonymous sites (Nonsynonymous Divergence) and (2) rate of nonsynonymous substitutions/rate of synonymous substitutions (dN/dS) .....................................................................................31 Table 2.3. Results of the CODEML branch-specific and branch-site analyses implemented for the IGF1 alignment ................................................................................33 Table 2.4. Ratio of synonymous (dS) and nonsynonymous (dN) substitutions between pairwise comparisons of five mammals for the IGF1 conserved domain .........................34 Table 2.5. The observed number of amino acid differences between IGF1 of five mammals: naa = 68, L = 5 ..................................................................................................36 Table 2.6. The estimated numbers of substitutions within the IGF1 conserved domain for five mammals ..................................................................................................36 Table 2.7. Results of the CODEML branch-specific and branch-site analyses implemented for the EHHADH alignment .........................................................................38 Table 2.8. Ratio of synonymous (dS) and nonsynonymous (dN) substitutions between pairwise comparisons of five mammals for the EHHADH conserved domain .................39 Table 2.9. The observed number of amino acid differences between EHHADH of five mammals: naa = 184, L = 5 ................................................................................................41 Table 2.10. The estimated numbers of substitutions within the EHHADH conserved domain for five mammals ..................................................................................................41 Table 2.11. Results of the CODEML branch-specific and branch-site analyses implemented for the NOS2 alignment................................................................................43 Table 2.12. Ratio of synonymous (dS) and nonsynonymous (dN) substitutions between pairwise comparisons of five mammals for the NOS2 conserved domain ........................44 Table 2.13. The observed number of amino acid differences between NOS2 of five mammals: naa = 412, L = 5 ................................................................................................46
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