THE ENANTIOPHYLLUM CLADE OF DIOSCOREA IN AFRICA: SYSTEMATICS, DISTRIBUTION AND CONSERVATION ASSESSMENT Sina Morufu Omosowon A thesis submitted for the degree of Doctor of Philosophy from the Department of Life Sciences, Imperial College London March 2018 1 Copyright Statement The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution-Non-Commercial-No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or distribution, researchers must make clear to others the licence terms of this work. 2 ABSTRACT Yams belong to the Dioscorea L. which is by far the largest genus in Dioscoreaceae with over 600 species and the fourth most important tuber crop in economic terms after potatoes, cassava and sweet potatoes. Yams are important food plants in many parts of the world, especially in West Africa, which produces about 93% of the World production. Dioscorea cayennensis and D. rotundata, which are collectively referred to as Guinea yams, are the most important cultivated yams native to Africa. Guinea yams belong to the Enantiophyllum clade which contains species with stems twining to the right. Despite the importance of Guinea yams, their relationship within the clade is poorly understood. In order trace the wild ancestors of the Guinea yams, a phylogenetic analysis based on sequence data from six plastid genes using 46 accessions of Dioscorea containing 12 of the 21 species of Enantiophyllum in Africa was carried out. Results showed that D. baya, D. praehensilis and D. abyssinica are the closest wild relatives of the Guinea yams. I also reconstructed ancestral morphological characters states for the African Dioscorea in the Enantiophyllum clade to understand how characters have evolved over time. It was revealed that morphological character diversity is a product of evolutionary changes. The current and potential impacts of climate change on the habitat distribution of Dioscorea in Africa were also evaluated to establish the actual and potential areas of occurrence for proper conservation planning. Dioscorea cotinifolia, D. praehensilis and D. schimperiana are shown to likely be affected by climate change. An IUCN Red List assessment was also performed to know the threat status and population trend of the wild African Enantiophyllum species of Dioscorea to identify species that needs immediate conservation management. All assessed species are classified as Least Concern (LC). 3 ACKNOWLEDGEMENTS I give thanks to ALLAH (S.W.T) for His mercies in my life to complete yet another programme and for His provisions and protection. My profound gratitude goes to my supervisors, Dr. PAUL WILKIN, Prof. TIMOHTY BARRACLOUGH and Dr. FELIX FOREST for their supports and guidance throughout the course of this project, may God reward them abundantly. This project wouldn’t have been possible without your patience and enthusiasm which has always encouraged me even when I am down. I also appreciate the precious time you dedicated to me to make this thesis a reality. I am extremely lucky to be one of your trainees. Many thanks go JUAN VIRUEL, RICHARD ALLEN, DION DEVEY, LASZLO CSIBA and PENNY MALAKASI for their contributions, supports and encouragement throughout this course of this project. I’m immensely grateful to my guardian and confidant, Prof. A. A. JAYEOLA for his fatherly-love and support throughout the course of this programme, I pray that God spares his life to reap the fruit of his labour. In addition, my gratitude goes to my sweetheart and wife, Mrs. OMOSOWON FATHIA for her words of encouragement and prayer throughout the course of this work, may we live together forever in peace and harmony. I also thank my daughter INAAYA for being a source of inspiration since coming into my life. My sincere appreciation to the government of Nigeria for funding this project under the PRESSID scheme. I also give thanks to Global Relief Fund of Imperial College London for providing financial aid which makes me to be able to complete this thesis. I dedicate this thesis to my mother GBONJUBOLA ARIKE, though you have passed on but you have strongly prepared me ahead for challenges of life. Continue to rest in peace. 4 DECLARATION OF ORIGINALITY I hereby declare that this thesis is the result of my own work, it doesn’t include any work done in collaboration with or by others, except where specifically stated and this was appropriately referenced. In all cases, primary contributions, data analysis, interpretations and writing were performed by myself under the supervision of Prof. Timothy Barraclough, Dr. Paul Wilkin and Dr. Felix Forest. 5 Table of Contents Copyright Statement ................................................................................................................ 2 ABSTRACT ................................................................................................................................ 3 ACKNOWLEDGEMENTS ............................................................................................................ 4 DECLARATION OF ORIGINALITY ............................................................................................... 5 Table of Contents ..................................................................................................................... 6 LIST OF FIGURES ....................................................................................................................... 9 LIST OF TABLES ........................................................................................................................ 12 CHAPTER ONE:INTRODUCTION TO THE GENUS DIOSCOREA, FOCUSSING ON CULTIVATED TAXA AND THEIR WILD RELATIVES ............................................................... 13 Distribution and uses of the genus Dioscorea ................................................ 13 Dioscorea species as food sources ................................................................... 13 Yams as sources of toxins and medicines ........................................................ 16 Yam as sources of income ................................................................................ 17 Yam as sources of income in West Africa ....................................................... 18 Culture and yams ............................................................................................. 20 Cultivated yams ................................................................................................22 Systematic history of Dioscorea ....................................................................... 24 Infrageneric systematics of Dioscorea ............................................................. 27 Linnaean taxonomic origins ............................................................................. 27 Kunth (1850) ................................................................................................... 27 Harms and Uline (1898) ................................................................................... 28 Knuth (1924) .................................................................................................... 28 Prain and Burkill (1939, 1938) .......................................................................... 28 Huber (1998) .................................................................................................... 29 Wilkin et al. (2005) ........................................................................................... 29 Viruel et al. (2015) ........................................................................................... 30 The Enantiophyllum clade: Systematic review ................................................. 31 Concept of Crop Wild Relatives (CWRs)........................................................... 34 Importance of CWRs in the context of Dioscorea and cultivated yams ........... 36 Approaches to identifying CWR of important economic crops ....................... 37 6 DNA Sequence data ......................................................................................... 38 Aims and Objectives of thesis ........................................................................... 38 CHAPTER TWO: Phylogenetics of Guinea yams and their wild relatives .................................. 40 MATERIALS AND METHODS ............................................................................. 42 Taxon Sampling ................................................................................................ 42 DNA extraction, Amplification and Sequencing ............................................... 42 Phylogenetic analyses ...................................................................................... 47 Dating analyses ................................................................................................ 48 Hypothesizing the Gene pool concept ............................................................. 49 RESULTS............................................................................................................ 49 DISCUSSION ...................................................................................................... 54 Phylogenetic relationships ............................................................................... 54 Hypothesizing the Gene Pool concept on the Enantiophyllum clade ............... 56 CHAPTER THREE: Ancestral