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Phd-Thesis Version 7 EFFECTS OF HABITAT OVERLAP ON HELMINTH TRANSMISSION BETWEEN SYMPATRIC BABOONS, VERVET MONKEYS AND UNGULATES IN AMBOSELI ECOSYSTEM, KENYA A thesis submitted to the University of Nairobi in fulfillment of Doctor of Philosophy degree in Applied Veterinary Parasitology. Vincent Onyango Obanda Department of Veterinary Pathology, Microbiology and Parasitology Faculty of Veterinary Medicine, University of Nairobi 2015 ii DEDICATION This thesis is for the honour of two special people; My wife, Alexia and son, Mich iii ACKNOWLEDGEMENT I am sincerely grateful to my employer Kenya Wildlife Service for giving me the opportunity to carry out this study in wildlife. The supervision of this work required a lot of dedication for which I thank my supervisors Prof N. Maingi, Dr. G. Muchemi, Dr. N. Chege and Prof. Elizabeth Archie. Their supervision was exceptionally excellent! I am deeply indebted to Prof. Elizabeth Archie for funding this study. My appreciation also goes to Dr. Sheila Ommeh and Dr. Patrick Chiyo for their assistance in genetic analysis and statistical inference. This study relied heavily on mapping and the guidance from Laura Grieneisen was great and for that I appreciate all her contributions. The help I received from the Amboseli Baboon Research team during field sample collection was unparalleled and went beyond the call of duty and for that reason I humbly appreciate them. I would like to salute Tegi, Rebecca and Gabriel for your incessant support and helping me fulfil my dream! If you have read this thesis and realize that you gave me assistance and your names is not mentioned, kindly know that your contribution was worthy and led to this success and pat yourself on the back for me. iv TABLE OF CONTENTS DECLARATION .............................................Error! Bookmark not defined. DEDICATION ............................................................................................. iii ACKNOWLEDGEMENT .......................................................................... iv TABLE OF CONTENTS .............................................................................. v LIST OF TABLES ....................................................................................... xi LIST OF FIGURES ................................................................................... xiv LIST OF ABBREVIATIONS .................................................................. xvii ABSTRACT .............................................................................................. xviii CHAPTER ONE: GENERAL INTRODUCTION ..................................... 1 1.1 Introduction ............................................................................................................... 1 1.2. Research Questions .................................................................................................. 5 1.3 Objectives .................................................................................................................. 5 1.3.1 Overall objective ........................................................................................................ 5 1.3.2 Specific objectives ..................................................................................................... 5 1.4 Justification ............................................................................................................... 7 CHAPTER TWO: LITERATURE REVIEW ............................................ 8 2.1 Host ecology of study animals .................................................................................. 8 2.1.1 Baboons...................................................................................................................... 8 2.1.2 Vervet Monkeys ....................................................................................................... 11 2.1.3 Impala ...................................................................................................................... 12 2.1.4 Grant’s Gazelles ....................................................................................................... 14 2.1.5 Thomson’s Gazelles ................................................................................................. 15 2.1.6 Wildebeests .............................................................................................................. 16 2.1.7 Cattle ........................................................................................................................ 17 2.1.8: Goats ....................................................................................................................... 18 2.1.9: Sheep ....................................................................................................................... 19 2.2 Helminth infection in hosts ..................................................................................... 20 2.2.1: Helminths in baboon ............................................................................................... 20 v 2.2.2: Helminths in Vervet Monkeys ................................................................................ 22 2.2.3: Helminths in Impala................................................................................................ 22 2.2.4: Helminths in Grant’s gazelles ................................................................................. 23 2.2.5: Helminths in Thomson’s Gazelles .......................................................................... 24 2.2.6: Helminths in Wildebeests ....................................................................................... 24 2.2.7: Helminths in Cattle ................................................................................................. 24 2.2.7: Helminths in Goats ................................................................................................. 25 2.2.9: Helminths in Sheep ................................................................................................. 26 2.3: Helminth Ecology and Epidemiological parameters.............................................. 26 2.3.1 Parasite Prevalence .................................................................................................. 26 2.3.2 Abundance ............................................................................................................... 27 2.3.3 Parasite Species Richness ........................................................................................ 28 2.4 Methods of helminth identification ......................................................................... 28 2.5 Genetic techniques for identification of helminths ................................................. 30 2.6 Habitat range overlap .............................................................................................. 33 2.7 Indices for animal presence and population estimation .......................................... 34 2.7.1 Direct sampling method ........................................................................................... 35 2.7.2 Indirect sampling methods ....................................................................................... 36 2.8 Effects of habitat overlap on helminth transmission ............................................... 37 CHAPTER THREE: DEGREE OF HABITAT OVERLAPS AMONG BABOON GROUPS AND BETWEEN BABOON AND ALTERNATIVE HOSTS IN AMBOSELI ECOSYSTEM, KENYA .....39 3.1 Introduction ............................................................................................................. 39 3.2 Material and Methods.............................................................................................. 41 3.2.1 Study area................................................................................................................. 41 3.2.2 Study population ...................................................................................................... 45 3.2.2.1 Non human primates .................................................................................. 45 3.2.2.2 Wild ungulates ........................................................................................... 45 3.2.2.3 Domestic ungulates .................................................................................... 45 3.2.3 Determination of the degree of habitat overlap among baboon social groups ........ 47 vi 3.2.4 Determination of the degree of habitat overlap between baboons and other alternative hosts ................................................................................................................ 48 3.3 Results ..................................................................................................................... 50 3.3.1 Degree of habitat overlap among baboon groups .................................................... 50 3.3.2 Degree of overlap between baboons and alternative host species ........................... 54 3.3.2.1 Dung piles as an index of overlap .............................................................. 54 3.3.2.2 Frequency of alternative hosts sightings as an index of overlap ............... 57 3.4 Discussion ............................................................................................................... 62 3.4.1 Degree of habitat overlap among baboons social groups ........................................ 62 3.4.2 Degree of habitat overlap between baboons and alternative host species ............... 65 3.4.2.1 Degree of habitat overlap based on dung pile counts ................................ 65 3.4.2.2 Degree
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