REPRODUCTIVE BIOLOGY AND POPULATION ECOLOGY OF Senegalia senegal (L.) BRITTON WITHIN LAKE BARINGO WOODLAND ECOSYSTEM, KENYA By STEPHEN FREDRICK OMONDI (MPHIL.) REG. I80/92661/2013 A thesis submitted in fulfillment of the requirement for award of the degree of Doctor of Philosophy (PhD) in Plant Ecology of the University of Nairobi 2016 DECLARATION CANDIDATE I hereby declare that this thesis is entirely my original work and has not been submitted for a degree award in any other University. Signature: ……………………………………… Date: ……………………………… STEPHEN FREDRICK OMONDI SUPERVISORS We confirm that the work reported in this thesis was carried out by the candidate under our supervision and has been submitted for examination with our approval. 1) Dr. George O. Ongamo, School of Biological Sciences, University of Nairobi, P. O. Box 30197, 00100, Nairobi. Signature: ………………………………...... Date: ………………………………. 2) Dr. James I. Kanya, School of Biological Sciences, University of Nairobi, P. O. Box 30197, 00100, Nairobi. Signature : ………………………….............. Date: ………………………………. 3) Dr. David W. Odee, Kenya Forestry Research Institute, P.O. Box 20412, 00200, Nairobi. Signature: Date: 03/08/2016 4) Prof. Damase P. Khasa, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Sainte-Foy, Québec, Canada G1V 0A6 Signature: Date: 03/08/2016 ii DEDICATION I dedicate this work to my wife Eunice and children Adrian, Xavier and Victoria in appreciation of their sacrifices, patience and support during the study. Their support gave me the much needed strength and encouragement to accomplish this study. iii ACKNOWLEDGEMENT I wish to sincerely express my gratitude to my supervisors (Dr. George Ongamo, Dr. James Kanya both of the School of Biological Sciences, University of Nairobi, Dr. David Odee of Kenya Forestry Research Institute and Professor Damase P. Khasa of Univaseté Laval, Canada), for spending their valuable time shaping my research activities in the field and laboratory, preparing manuscripts and finally, this thesis. Without their support I would have not managed to finish this study on time. My special regards go to Professor Damase for having spared his valuable time and resources to regularly visit me in Nairobi from Canada for discussions that shaped this study. I thank him also for having seen the value of my research and secured funding from Natural Sciences and Engineering Research Council of Canada (NSERC) for purchasing portable weather stations that were used to gather weather data for this study. I also thank Kenya Forestry Research Institute (KEFRI) and International Foundation for Science (IFS) for providing research funds. I appreciate the work of KEFRI staff like Mr. Peter Koech who braved the harsh weather conditions of the study area to assist in various ways during the study including establishment of sampling plots, field sampling and assessments. Special thanks to the headmaster of Mesori primary school, Lake Bogoria National Reserve authorities, specifically Mr. Raphael Kimosop and Ms Sophia for allowing me to use their premises for installing weather stations. Equally, I am also grateful to KEFRI biotechnology laboratory and biostatistics staff whose involvements were valuable during samples preparation, data analysis and storage. Special thanks go to my wife and children who continually gave me moral support that kept me going during the study period. I also can’t forget the deserved prayers and support from my parents that kept me strong during this study. My revered appreciation to the Almighty God for giving me good health and sufficient strength to finish the study. To all, I say thank you and God bless. iv TABLE OF CONTENTS DECLARATION ............................................................................................................................ I DEDICATION ............................................................................................................................. III ACKNOWLEDGEMENT .......................................................................................................... IV TABLE OF CONTENTS .............................................................................................................. V LIST OF TABLES ....................................................................................................................... XI LIST OF FIGURES .................................................................................................................. XIII LIST OF ABBREVIATIONS AND ACRONAMES ............................................................. XIV ABSTRACT .............................................................................................................................. XVI CHAPTER ONE ............................................................................................................................. 1 1.0 GENERAL INTRODUCTION ............................................................................................... 1 1.1 Background information ............................................................................................................. 1 1.2 Problem statement and justification ........................................................................................... 3 1.3 Research hypothesis ................................................................................................................... 4 1.4 Main objective ............................................................................................................................ 4 1.4.1 Specific objectives .................................................................................................................. 4 1.5 Relevance of the study ................................................................................................................ 5 1.6 Thesis structure ........................................................................................................................... 5 CHAPTER TWO ............................................................................................................................ 6 2.0 LITERATURE REVIEW ........................................................................................................ 6 2.1 Taxonomy of Senegalia senegal (L.) Britton (Syn. Acacia Senegal (L.) Willd.) ...................... 6 2.2 Ecological distribution of S. senegal in arid and semi-arid lands (ASALs) ............................... 7 2.3 Socio-economic importance of S. senegal .................................................................................. 9 v 2.4 Breeding systems in S. senegal ................................................................................................ 11 2.5 Natural regeneration ................................................................................................................. 13 2.5.1 Plant regeneration dynamics ................................................................................................. 14 2.6 Plant demographic studies ........................................................................................................ 15 2.7 Plant genetic diversity .............................................................................................................. 15 2.7.1 Effects of anthropogenic disturbances on plant genetic diversity ........................................ 17 2.8 Genetic markers ........................................................................................................................ 19 CHAPTER THREE ...................................................................................................................... 23 3.0 GENERAL MATERIALS AND METHODS ...................................................................... 23 3.1 Description of the study area .................................................................................................... 23 3.2 Degradation and fragmentation history of the study area......................................................... 25 3.3 Development of population disturbance index (PDI) ............................................................... 26 3.4 DNA isolation and Polymerase Chain Reaction (PCR) analyses ............................................. 27 CHAPTER FOUR ........................................................................................................................ 30 4.0 GENETIC DIVERSITY AND POPULATION STRUCTURE OF Senegalia senegal WITHIN LAKE BARINGO WOODLAND ECOSYSTEM ............................................. 30 4.1 Introduction .............................................................................................................................. 30 4.2 Materials and methods .............................................................................................................. 31 4 .2.1 Samples collection ............................................................................................................... 31 4.2.2 DNA analysis ........................................................................................................................ 32 4.3 Results ...................................................................................................................................... 35 4.3.1 Population disturbance index (PDI) ..................................................................................... 35 vi 4.3.2 Population genetic diversity measures ................................................................................