Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 10-3-2016 Profiling Populations Using Neutral Markers, Major Histocompatibility Complex Genes and Volatile Organic Compounds as Modeled in Equus caballus Linnaeus Ketaki Deshpande Florida International University, [email protected] DOI: 10.25148/etd.FIDC001190 Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Animal Studies Commons, Genetics Commons, Hormones, Hormone Substitutes, and Hormone Antagonists Commons, Immunology and Infectious Disease Commons, Laboratory and Basic Science Research Commons, and the Molecular Genetics Commons Recommended Citation Deshpande, Ketaki, "Profiling Populations Using Neutral Markers, Major Histocompatibility Complex Genes and Volatile Organic Compounds as Modeled in Equus caballus Linnaeus" (2016). FIU Electronic Theses and Dissertations. 3044. https://digitalcommons.fiu.edu/etd/3044 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida PROFILING POPULATIONS USING NEUTRAL MARKERS, MAJOR HISTOCOMPATIBILITY COMPLEX GENES AND VOLATILE ORGANIC COMPOUNDS AS MODELED IN EQUUS CABALLUS LINNAEUS A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOLOGY by Ketaki Deshpande 2016 To: Dean Michael R. Heithaus College of Arts, Sciences and Education This dissertation, written by Ketaki Deshpande, and entitled, Profiling Populations Using Neutral Markers, Major Histocompatibility Complex Genes and Volatile Organic Compounds as Modeled in Equus Caballus Linnaeus having been approved in respect to style and intellectual content, is referred to you for judgment. We have read this dissertation and recommend that it be approved. ______________________________________ Kenneth Furton ______________________________________ Robert Lickliter ______________________________________ Jeffrey Wells ______________________________________ Eric von Wettberg ______________________________________ DeEtta Mills, Major Professor Date of Defense: October 3, 2016 The dissertation of Ketaki Deshpande is approved. _______________________________________ Dean Michael R. Heithaus College of Arts, Sciences and Education _______________________________________ Andrés G. Gil Vice President for Research and Economic Development and Dean of the University Graduate School Florida International University, 2016 ii © Copyright 2016 by Ketaki Deshpande All rights reserved. iii DEDICATION I dedicate this dissertation to my parents Dr. Vijay Deshpande and Dr. Urmila Deshpande as well as my late grandmother Padmaja Deshpande. You will forever be my inspiration and strength. I will always strive to make you proud. iv ACKNOWLEDGMENTS This dissertation could not have been completed without the help and support from my committee members, colleagues, friends and family. It is my great pleasure to acknowledge people who have given me guidance, help and encouragement throughout my journey as a PhD student. I would like to thank my PhD advisor, Dr. DeEtta Mills, whose support, guidance and encouragement cannot be overstated. I am grateful to her for her patience, motivation, and immense knowledge. Her guidance helped me in all the time of research and writing of this dissertation. The joy and enthusiasm she has for research was contagious and motivational for me, even during tough times in the Ph.D. pursuit. I am also thankful for the excellent example she has provided as a successful mentor and professor. Besides my advisor, I would like to thank the rest of my advisory committee members Dr. Kenneth Furton, Dr. Jeffrey Wells, Dr. Robert Lickliter, and Dr. Eric vonWettberg for their important suggestions and remarks in this research, but also for the hard questions, which incentivized me to widen my research from various perspectives. I thank them for their time and effort in service on my doctoral committee despite their already heavy loads of responsibility. I would like to thank the Department of Biology for providing me teaching assistantship for five years. I would like to gratefully acknowledge the Conservation Genetics Resources Journal for allowing me to reprint a publication as Chapter 2 of this dissertation. A good support system is important to surviving and staying sane in grad school. My time at Florida International University was made enjoyable in large part due to my friends and colleagues that became a part of my life. My lab mates have contributed v immensely to my personal and professional time at Florida International University. I thank Beatrice Kallifatidis, Dr. Natalie Damaso, Lauren Martin, Evelyn Perez, Melissa Villareal, Ivy Cheung, Julian Mendel and Christina Burns for their stimulating discussions, friendships as well as good advice and especially for your consideration during the last few months by allowing me unlimited use of lab equipment so I may finish my experiments on time. My special appreciation goes to all the friends (too many to list here but you know who you are!) for their invaluable assistance, support and friendship that I needed during the period of completing my PhD. I am enormously indebted to Dr. Priyanka Kushwaha, and Dr. Deepthi Nori who have offered me great help both psychologically and physically during the rough periods of graduate school. These two friends formed the core of my research time at Florida International University and I am glad that they will remain an integral part of my life forever. Finally, my deepest gratitude to my parents, my brother and sister-in-law, whose support and constant encouragement helped me through the hard times of this program. My sincere appreciation is expressed to them for their patience, warm support, love, understanding, and inspiration. Without their blessings and encouragement, I would not have been able to finish this work. vi ABSTRACT OF THE DISSERTATION PROFILING POPULATIONS USING NEUTRAL MARKERS, MAJOR HISTOCOMPATIBILITY COMPLEX GENES AND VOLATILE ORGANIC COMPOUNDS AS MODELED IN EQUUS CABALLUS LINNAEUS by Ketaki Deshpande Florida International University, 2016 Miami, Florida Professor DeEtta Mills, Major Professor Assessing the genetics of wild animal populations aims to understand selective pressures, and factors whether it be inbreeding or adaptation, that affect the genome. Although numerous techniques are available for assessing population structure, a major obstacle in studying wild populations is obtaining samples from the animals without having to capture them, which can lead to undue distress and injury. Therefore, biologists often use non-invasive sampling methods (i.e., collection of feces, hair) to extract host DNA. In this study, new DNA extraction protocols were developed that improved the quality and quantity of DNA obtained from fecal matter. Fecal samples aged up to Day 6 as well as field samples with unknown days since defecation were successful in individualization of the contributors using microsatellites and were further used to demonstrate kinship. Neutral markers such as short tandem repeat, and mitochondrial D- loop sequences are used for assessing relatedness and evolutionary relationships and can mutate without detrimental effects on the organism. Loci, such as the major histocompatibility complex (MHC), adapt more rapidly under selective pressure such as vii parasite load, or resistance to diseases and support natural selection processes. Analysis of the neutral microsatellites in Big Summit feral horse population demonstrated a population lacking diversity and trending towards being an inbred population. However, examination of the MHC genes showed maintenance of greater variation that may be the result of selection pressures. The MHC similarity and lower genetic demarcation between geographically separated horse populations further indicated effect of selection pressures in preserving diversity at the MHC genes. Although such molecular markers are used in profiling populations, the current study was also successful in demonstrating the use of individual odor profiles as an additional profiling tool. Volatile organic compounds (VOC) obtained from hair of domestic horses were able to individualize horses as well as differentiate between horse breeds and display kinship. The relation of genetics to odor phenotype is of interest as the inherent polymorphic nature of MHC genes has the potential to generate unique combinations of genotypes that presumably produce distinct odor phenotypes. Subsequently, this study was able to show a significant correlation between MHC genotypes and VOC odor profiles in horses. Understanding the relationship between MHC and odor using domestic horses with known relatedness provides evidence that these same correlations may be applicable to wild equids and dictates their harem hierarchal social structure. viii TABLE OF CONTENTS CHAPTER .................................................................................................................. PAGE 1. INTRODUCTION .......................................................................................................... 1 1.1. Conservation genetics .............................................................................................. 1 1.1.1.