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Diversity and Phylogenetic Analyses in Parmelioid Lichens in Kenya

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Diversity and Phylogenetic Analyses in Parmelioid Lichens in Kenya i DIVERSITY AND MOLECULAR PHYLOGENETIC ANALYSES OF PARMELIOID LICHENS (PARMELIACEAE, ASCOMYCOTA) IN KENYA Kirika, Paul Muigai (M.Sc.) Reg. No.: I84/23317/2012 A Thesis Submitted in Partial Fulfillment of the Requirements for the Award of the Degree of Doctor of Philosophy (Plant Taxonomy) in the School of Pure and Applied Sciences of Kenyatta University NOVEMBER 2017 i DECLARATION This thesis is my original work and has not been presented for a degree in any other university or for any other award. Name: Kirika, Paul Muigai Reg. No.: I84/23317/2012 Signature: ________________________________Date_______________________________ School of Pure and Applied Sciences, Department of Plant Sciences, Kenyatta University, Kenya DECLARATION BY SUPERVISORS We confirm that the work reported in this thesis was carried out by the candidate under our supervision. Dr. Grace W. Gatheri Signature: _______________________Date____________________________________ Department of Plant Sciences, Kenyatta University, Kenya Dr. George K. Mugambi Signature: ___ __________Date___________________________________ Department of Biological Sciences, Meru University of Science and Technology, Kenya Prof. Pradeep K. Divakar Signature: _______________________Date____________________________________ Department of Plant Biology II, Faculty of Pharmacy, Complutense University of Madrid, Spain Dr. Thorsten Lumbsch Signature: ____ _______Date___________________________________ Integrative Research Center, The Field Museum of Natural History, Chicago, USA ii DEDICATION I dedicate this work to my family for their love and unwavering support; my wife Jennifer Muigai and our daughters Wambui, Wairimu and Mumbi. You have always been the source of my inspiration and have always given me the reason to push on. iii ACKNOWLEDGEMENTS Firstly, I thank my supervisors; Dr. Grace W. Gatheri - Kenyatta University (Kenya), Prof. Pradeep K. Divakar - Complutense University of Madrid (Spain), Dr. Thorsten Lumbsch - The Field Museum of Natural History, Chicago (USA) and Dr. George Mugambi of Meru University of Science and Technology (Kenya) who have always offered their invaluable support, advice and being available whenever I needed their assistance. I am grateful to the National Museum of Kenya (NMK) for the support accorded to me during my studies and to all my colleagues at the Botany Department for their continued moral support and encouragement. I am also grateful to Dr. Steven Leavitt and the entire lichen team at the Field Museum, all the members of Pritzker Laboratory for Molecular Systematics and Evolution and all the members of the lichen team at the Molecular Laboratory in the Department of Biology, faculty of pharmacy, Computense University of Madrid for their assistance. All of who greatly helped me with my laboratory work. My thanks also go to the Directors of the Kenya Wildlife Service (KWS), Kenya Forests Service (KFS), National Environmental Management Authority (NEMA) and National Commission for Science, Technology and Innovation (NACOSTI) for granting me the necessary research permits. Finally, I acknowledge the generous financial support I received from The Field Museum/IDP Foundation and the Spanish Ministerio de Ciencia e Innovación (CGL2013-42498-P) without which this work could not have been accomplished. iv TABLE OF CONTENTS DECLARATION................................................................................................................ i DEDICATION................................................................................................................... ii ACKNOWLEDGEMENTS ............................................................................................ iii LIST OF TABLES ......................................................................................................... viii LIST OF FIGURES ......................................................................................................... ix LIST OF PLATES ............................................................................................................ x ABBREVIATIONS AND ACRONYMS ....................................................................... xii ABSTRACT .................................................................................................................... xiv CHAPTER 1 ...................................................................................................................... 1 INTRODUCTION............................................................................................................. 1 1.1 BACKGROUND INFORMATION ................................................................................... 1 1.2.1 STATEMENT OF THE PROBLEM .............................................................................. 5 1.2.2 JUSTIFICATION ....................................................................................................... 6 1.3 HYPOTHESES ............................................................................................................. 7 1.4 RESEARCH QUESTIONS .............................................................................................. 8 1.5 OBJECTIVES .............................................................................................................. 8 1. 5.1 General Objective .............................................................................................. 8 1.5.2 Specific Objectives .............................................................................................. 8 1.6 SIGNIFICANCE AND EXPECTED OUTPUTS ................................................................. 9 CHAPTER 2 ................................................................................................................... 10 LITERATURE REVIEW .............................................................................................. 10 v 2.1 MOLECULAR PHYLOGENETIC RELATIONSHIPS OF PARMELIACEAE .................... 10 2.2.1 Bulborrhizina Kurok. ....................................................................................... 15 2.2.2 Bulbothrix Hale................................................................................................. 16 2.2.3 Canoparmelia Elix & Hale ............................................................................... 18 2.2.4. Hypotrachyna subgenus Everniastrum (Hale ex Sipman) Divakar et al......... 20 2.2.5. Parmelinella Elix & Hale ................................................................................ 22 2.2.6. Relicina (Hale & Kurok.) and Relicinopsis Elix & Verdon ............................ 23 CHAPTER 3 .................................................................................................................... 25 MATERIALS AND METHODS ................................................................................... 25 3.1 SPECIMENS AND DNA SEQUENCES SAMPLED. ........................................................ 25 3.2 MORPHOLOGICAL AND CHEMICAL STUDIES ......................................................... 27 3.3 DNA EXTRACTION AND PCR AMPLIFICATION ..................................................... 27 3.4 SAMPLES USED IN THE PHYLOGENETIC ANALYSIS OF GENERA .............................. 29 3.4.1 Samples used in the phylogenetic analysis of Bulborrhizina. .......................... 29 3.4.2. Samples used in the phylogenetic analysis of Bulbothrix. ............................... 29 3.4.3 Samples used in the phylogenetic analysis of Canopamelia. ........................... 30 3.4.4. Samples used in the phylogenetic analysis of Hypotrachyna. ......................... 30 3.4.5 Samples used in the phylogenetic analysis of Parmelinella. ............................ 30 3.4.6 Samples used in the phylogenetic analysis of Relicina and Relicinopsis. ........ 31 3.5 SEQUENCE EDITING AND ALIGNMENT ................................................................... 31 3.6 PHYOGENETIC ANALYSIS ....................................................................................... 32 3.7 ALTERNATIVE HYPOTHESIS TESTING ..................................................................... 33 CHAPTER 4 .................................................................................................................... 34 vi RESULTS AND DISCUSSIONS ................................................................................... 34 4.1 PHYLOGENETIC RECONSTRUCTION IN BULBORRHIZINA ........................................ 34 4.2 PHYLOGENETIC RECONSTRUCTION IN BULBOTHRIX ............................................. 37 4.2.1. Taxonomic treatment ....................................................................................... 46 4.2.2. New species...................................................................................................... 46 4.2.3 New combination .............................................................................................. 49 4.3. PHYLOGENETIC RECONSTRUCTION IN CANOPARMELIA ........................................ 49 4.3.1 Taxonomic treatment ........................................................................................ 55 4.3.2 New subgenus ................................................................................................... 55 4.3.3 New combinations............................................................................................. 56 4.4 PHYLOGENETIC RECONSTRUCTION IN HYPOTRACHYNA SUBGEN EVERNIASTRUM 56 4.4.1. Taxonomic treatment ......................................................................................
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