Taxonomy and evolutionary studies on the genus Psoralea L. (Psoraleeae, Fabaceae) Abubakar Bello Thesis presented for the degree of Doctor of Philosophy in the Department of Biological Sciences, University of Cape Town Supervisors: A. Prof A. Muthama Muasya and Dr Samson B.M. Chimphango University of Cape Town December, 2015 The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town DEDICATION This study is dedicated to my late father, Alhaji Muhammadu Bello Sule who answered the call of his Lord on the cold morning of Tuesday, 2nd June, 2014 for his patience especially during his trying times on his sick bed when he was extremely in need of my presence but could not be with him as a result of this study. My Lord! Bestow on him Your Mercy as he did bring me up when I was young. Page | ii DECLARATION I Abubakar Bello, hereby declare that the work on which this thesis is based is my original work (except where acknowledgements indicate otherwise) and that neither the whole nor any part of it has been, is being, or is to be submitted for another degree in this or any other university. I authorise the University of Cape Town to reproduce for the purpose of research either the whole or a portion of the content in any manner whatsoever. This thesis includes three publications that were published in collaboration with my supervisors and research associates. My supervisors testified that I made substantial contributions to the conceptualisation and design of the papers; that I independently ran experiments and wrote the manuscripts (the first two manuscripts below), with their support in the form of comments and suggestions (see Appendix D). The published papers: - Bello A., Daru B.H, Stirton C.H., Chimphango S.B.M, van der Bank M., Maurin O., and Muasya A.M. (2015). DNA barcodes reveal microevolutionary signals in fire response trait in two legume genera. AoB PLANTS, 7: plv124; doi:10.1093/aobpla/plv124. (Chapter 3). - Bello A., Stirton C.H., Chimphango S.B.M., Muasya A.M. (2015). Psoralea diturnerae and P. vanberkelae (Psoraleeae, Fabaceae): two new species restricted to the Core Cape Region of South Africa. PhytoKeys, 44: 97–107. doi: 10.3897/ phytokeys.44.8999. (Part of Chapter 4). - Stirton C.H., Stajsic V., Bello A. (2015). Naturalised species of Psoralea (Fabaceae: Psoraleeae) in Australia. Muelleria, 33: 97−107. (Part of Chapter 4). Page | i ACKNOWLEDGEMENTS All thanks and glorifications are due to Allah (SWT) Who sustain my life to this day and endowed me with the strength and the ability to accomplish this study. I thank Prof. A. Muthama Muasya for taking the risk of accepting me as a candidate for this study at a time when everyone is curious as to whom to employ as a good research candidate in a highly competitive academic arena. I also thank my Co-Supervisor Dr. S.B.M. Chimphango for his fatherly advice and critical challenges on my work, making sure that I did things in a right and orderly manner. I would also like to express my sincere gratitude to my external supervisor, Prof Charles H. Stirton for his mentorship, guidance, contributions and training both in the field, lab and in the write up. The tuition and upkeep for this study were funded by Nigeria Tertiary Education Trust Fund (NTETF) and Umaru Musa Yarádua University Katsina, Nigeria and a top up from the J. W. Jagger Centenary Gift Scholarship from the University of Cape Town. The study was supported by grants from the South African National Research Foundation (NRF; AMM). Without the income provided by these funds, this study would not have been possible. This thesis has had mentorship and various forms of support from numerous outstanding individuals both from within UCT and outside. I extend my heartfelt gratitude to these individuals for without them, this thesis would not have been completed. These individuals include: Dr Barnabas H. Daru, Meshack M. Dludlu, Jack Viljoen, Dr Tracey Nowell, Hassan Sadiq (UCT Statistics), Dr Benny Lemaire, Prof Michelle Van der Bank and Dr Olivier Maurin. I also thank Dr Ashley N. Egan for her tremendous help in the edit of the phylogeny chapter. The fieldwork for this research was permitted by Cape Nature (permit 0028-AAA008-00035) and the Eastern Cape Department of Economic Development, Environmental Affairs and Tourism (No CRO. 153/13CR). I am indebted to the superb hospitality of Di and Bill Turner, over a number of visits, of the Outramps Group of the Custodians of Rare and Endangered Wild Flowers (CREW) from George, and Nicky van Berkel, without whose efforts, two of my new species might not have been discovered. Page | iii I thank the Curators and Staff of BOL, NBG and PRE herbaria particularly Terry Trinder- Smith, Dr Cornelia Klak, Dr Anthony R. Magee and Dr Dee Snijman. I also thank the Department of Biological Sciences of UCT and my fellow students for their company and support. I thank the staff and members of CREW (Custodians of Rare and Endangered Wildflowers (CREW) Programme, especially Mr. Ismail Ibrahim and Vathiswa Zikishe for field trip opportunities and friendship. I want to truly express my sincere appreciation and gratitude to my parents, for my upbringing and prayers. There are no words to convey how much I love them. I would like to thank my wife, Mrs. Maryam Abdulkadir, for her patience, love and strength in taking over all the house activities and the training of the kids while I am undertaking this study for almost four years Away from home in Nigeria. For my kids, Fadila, Ahmad and Hafsat, I thank you very much for pressurising me to come back. This really gingered me towards putting more efforts and working harder to accomplish the mission. I thank my friend Buhari Yusuf Shinkafi for taking most of my responsibilities while I am away. There are no words to express my appreciations to him. I pray for Allah’s guidance and assistance on your PhD journey. Lastly to all those who helped in one way or the other whose names were not mentioned here due to shortage of space and time, I say a big thank you to all of you. Page | iv TABLE OF CONTENTS PAGE DECLARATION ......................................................................................................................... i DEDICATION ........................................................................................................................... ii ACKNOWLEDGEMENTS ...................................................................................................... iii TABLE OF CONTENTS ............................................................................................................ v LIST OF APPENDICES ......................................................................................................... viii LIST OF ACRONYMS AND ABBREVIATIONS .................................................................. ix THESIS SUMMARY ................................................................................................................ xi CHAPTER ONE: GENERAL INTRODUCTION AND OBJECTIVES 1.1 Introduction. .......................................................................................................................... 1 1.2 Evolution and biogeography of legumes .............................................................................. 1 1.3 Psoraleeae in the Greater Cape Floristic Region .................................................................. 2 1.4 DNA barcoding and its applications ..................................................................................... 3 1.5 The genus Psoralea L. ......................................................................................................... 4 1.6 Statement of the problem ...................................................................................................... 5 1.7 Aim and objectives of the thesis ........................................................................................... 5 1.8 Structure of the thesis ............................................................................................................. 6 CHAPTER TWO: PHYLOGENY, BIOGEOGRAPHY AND CHARACTER EVOLUTION IN PSORALEEAE (FABACEAE) Abstract ...................................................................................................................................... 7 2.1 Introduction ........................................................................................................................... 8 2.2 Materials and methods ........................................................................................................ 12 2.2.1 Taxon sampling ................................................................................................................ 12 2.2.3 DNA extraction, amplification and sequencing ............................................................... 13 2.2.4 Sequence assembling, alignment and phylogenetic analyses .......................................... 14 2.2.5 Ancestral state reconstructions ....................................................................................... 15 2.2.6 Estimation of divergence dates ........................................................................................ 16 2.2.7 Dating the tree .................................................................................................................