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Genetic Analysis of Mitochondrial Dna in Cercopithecus

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Genetic Analysis of Mitochondrial Dna in Cercopithecus GENETIC ANALYSIS OF MITOCHONDRIAL DNA IN CERCOPITHECUS MITIS POPULATIONS FROM KIBALE NATIONAL PARK, UGANDA by Narcissus D. Smith A Thesis Submitted to the Faculty of Charles E. Schmidt College of Science In Partial Fulfillment of the Requirements for the Degree of Master of Science Florida Atlantic University Boca Raton, FL December 2018 Copyright 2018 by Narcissus D. Smith ii GENETIC ANALYSIS OF MITOCHONDRIAL DNA IN CERCOPITHECUS MITIS POPULATIONS FROM KIBALE NATIONAL PARK, UGANDA by Narcissus D. Smith This thesis was prepared under the direction of the candidate's thesis advisor, Dr. John D. Baldwin, Department of Biological Sciences, and has been approved by all members of the supervisory committee. It was submitted to the faculty of the Charles E. Schmidt College of Science and was accepted in partial fulfillment of the requirements for the degree of Master of Science. SUPERVISORY COMMITTEE: t?~ . Baldwin, Ph.D. es~visor Colin~~ Hughes, Ph.D. j(a:> /)vi ~J (,...._... Kate M. Detwiler, h.D. hey, Ph.D. Chair, Department of Bi ~__::;§ae ~Ph.D~ Dean, Charles E. Schmidt College of Science ~__5~L:. JO.nvo.ry ~4, 20\~ Khaled Sobhan, Ph.D. Date Interim Dean, Graduate College iii ACKNOWLEDGEMENTS To the individuals which I dedicated this study, I am beyond grateful for having you all as my support system. You encouraged me to never quit and push through all obstacles. I also thank you for providing me with the comfort and luxuries that I needed to complete this thesis study. My graduate career would have been unimaginable and impossible without your love and support. Thank you to my graduate committee Dr. John D. Baldwin, Dr. Kate M. Detwiler, and Dr. Colin Hughes for all their help, patience, and collaboration towards this thesis study. I am most thankful to my thesis advisor Dr. John D. Baldwin for supporting me as a Master of Science graduate student. He has been an exceptional advisor and an even better leader. His guidance and leadership have allowed me a tremendous amount of academic and personal growth. He has taught me fundamental lessons; that I believe have helped me build the character and the necessary tools that I need to move forward in my academic career. Dr. Baldwin’s direction has allowed me to make my own academic choices and structure my graduate career as I desired. I thank Dr. Colin Hughes he made his lab space, lab equipment, and additional resources available for my utilization, as necessary. He was always accessible by multiple means. Dr. Hughes assisted me significantly in the scientific process during my thesis benchwork. He pointed out my mistakes when I did not realize them my-self, aiding me in learning from my own errors. Dr. Hughes provided me with insightful and iv invaluable information, which I can carry on in my future endeavors; both academic and non-academic. I thank Dr. Kate Detwiler and Dr. Michelle Brown at the University of California for entrusting me with original monkey samples and the aptitude to complete this thesis. I would like to thank Dr. Detwiler for allowing me to contribute to her ongoing research of over two decades and by adding this chapter. I also thank her for her guidance and instructions over the last two years, including making trips down to the Davie campus to assist me when she could. She helped incorporate me into the South Florida Primatology Conferences and held phylogenetic workshops to aid in future research tasks. I thank the members of Dr. Detwiler’s FAU Anthropology lab for their assistance and support. A special thank you to Sandra Almanza for providing me with data and suggesting phylogenetic tests to perform; used for the analysis in this thesis. I acknowledge Dr. Nwadiuto Esiobu at Florida Atlantic University and Dr. Santana at Cornell University in Venezuela, South America, for their insight about DNA extraction utilizing invasive samples. I thank and acknowledge to Dr. Marina Cords at Columbia University for sending me her published chapter about the Kakamega Forest (Kenya) as well as her feedback about my research. To my peer Estevao Santos, I am grateful to have met you! I sincerely thank you for conducting research with me for months on end, to help design and create parameters for testing the success of DNA extractions via the Polymerase Chain Reaction. I sincerely thank my peers Dr. Saheed Oseni, Karim Dawkins, and Alain Brutas for their ongoing support and aid. They also helped me with meaningful revisions when they were starting their own businesses or working on their own graduate studies at FAU’s College of v Science. Dr. Oseni was an excellent mentor who provided me with additional tools and knowledge about development and progression throughout the completion of graduate school. He also gave me “one- on -one” guidance, which significantly helped me through my writing process. I acknowledge and thank my aunts and uncle- Sharrette Adolphus, Mr. and Mrs. Adrien D. and Kimberly Y. Smith for their never ending, encouragement, support, and excitement for my academic studies. vi ABSTRACT Author: Narcissus D. Smith Title: Genetic Analysis of Mitochondrial DNA in Cercopithecus mitis populations from Kibale National Park, Uganda Institution: Florida Atlantic University Thesis Advisor: Dr. John D. Baldwin Degree: Master of Science Year: 2018 Past sightings of red-tailed (Cercopithecus ascanius) x blue monkey (Cercopithecus mitis) hybrids in Uganda indicates the potential for hybridization between C. ascanius and C. mitis individuals. Apart from Gombe Stream National Park, there is no of evidence suggestive of C. ascanius x C. mitis monkey hybridization at investigated East African locations. Phylogenetic analysis was examined using Mitochondrial DNA (mtDNA) sequence data of twelve C. mitis stuhlmanni samples (from two populations) in Kibale National Park (KNP), Uganda to test for any evidence of hybridization. Strict mono- phylogeny among two new C. mitis haplotypes were detected. Genetic diversity measurements support neither interspecific or intraspecific hybridization among C. mitis individuals from populations within Kibale National Park. To intensify the implications of this study further examination should include an increase in sample size(s), mtDNA comparison of C. mitis subspecies from additional populations at East African locations, and assessment of nuclear and genomic DNA. vii DEDICATION I dedicate this thesis to Mr. and Mrs. James K. Smith, Sharetta D. Smith, Alma C. Smith and the late George E. and Michael D. Smith To my mother who came from Belize over forty years ago in search for a better life for her-self and her children and to my father who has been by my side every day of my life since I began attending school, I will never be able express how thankful I am for all of the sacrifices you’ve made for my sister and me. Your unconditional love, support and infrastructure, that your blissful thirty-two-year marriage has brought to our family dynamic is what has allowed me to achieve the accomplishments I have thus far in my life. To my little sister, I thank you for being my best friend above all else, providing me with motivation, encouragement and love, most sisters would only dream of. To my grandmother, my late grandfather, and my late uncle, some of the earliest educators in our family and in our African American community, thank you for embedding me with educational skills and knowledge. Most of all, thank you all for teaching me to finish all tasks to completion and that anything is possible. I love you all! GENETIC ANALYSIS OF MITOCHONDRIAL DNA IN CERCOPITHECUS MITIS POPULATIONS FROM KIBALE NATIONAL PARK, UGANDA LIST OF TABLES ................................................................................................................... xi LIST OF FIGURES ................................................................................................................ xii INTRODUCTION .................................................................................................................... 1 BACKGROUND ...................................................................................................................... 5 Study Species: Red-tailed (Cercopithecus ascanius) Monkeys and Blue (Cercopithecus mitis) Monkeys .......................................................................................... 5 The History of Red-tailed (Cercopithecus ascanius) and Blue (Cercopithecus mitis) Hybrid Monkey Sightings ................................................................................................... 5 Research Questions ............................................................................................................. 6 METHODS AND MATERIALS .............................................................................................. 8 Study Site and Sample Collections ..................................................................................... 8 DNA Extraction, Amplification, and Sequencing ............................................................ 10 Sequence Preparation and Analysis .................................................................................. 11 Phylogenetic Tree Reconstruction and Genetic Diversity Measurements ........................ 14 DATA ANALYSIS AND RESULTS ....................................................................................... 16 Taxonomy and Diversity of Cercopithecus mitis Samples from Kibale, National Park, Uganda ....................................................................................................................
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