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University of Cape Town (UCT) in Terms of the Non-Exclusive License Granted to UCT by the Author 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 SYSTEMATIC STUDIES OF THE SOUTHERN AFRICAN PSORALEOID LEGUMES BY MESHACK NKOSINATHI DLUDLU University of Cape Town A DISSERTATION PRESENTED FOR THE DEGREE OF MASTER OF SCIENCE IN THE DEPARTMENT OF BOTANY, UNIVERSITY OF CAPE TOWN SEPTEMBER, 2010 DECLARATION STATEMENT I know the meaning of plagiarism and declare that all of the work in the document, save for that which is properly acknowledged, is my own. Signature:………………………………………………….. University of Cape Town i ACKNOWLEDGEMENTS Two years of working through this dissertation would have been very long and stressful if it were not for the wonderful support, friendly advice and positive criticism from my supervisors: Dr. A. M. Muasya and Dr. S. B. M. Chimphango, to whom I am very grateful. I am also grateful to Professor C. H. Stirton, who provided mentorship and intellectual guidance throughout this project. He was always willing to share his wealth of experience in the field, the herbarium and the laboratory. Special thanks to the technical officers of the Botany Department for assistance with research equipment and facilities. I would also like to thank the curators of the following Herbaria: BOL, NBG and PRE for allowing me access to their specimen collections. I also wish to thank Mr. S. C. Power for the assistance he rendered during the collection of soil samples and the analysis of their nutritional content. My family and friends provided moral support and upliftment during times when things seemed not to work out, and they were always there to say I can do it. Without them, I could not have reached this far. Research funds for this project came from the SANBI Threatened Species Programme (TSP) and the South African Biosytematics Initiative (SABI). Tuition and living costs were covered through funding from the UCT International Student Scholarship, a top up bursary from my supervisor: Dr. A. M. Muasya, the Dorothy Cameroon Scholarship, the Canon Collins Trust, and the University of Swaziland.University of Cape Town ii TABLE OF CONTENTS Page ABSTRACT……………………………………………………………………………………..1 CHAPTER 1: GENERAL INTRODUCTION AND LITERATURE REVIEW 1.0 Problem statement………………………………………………......................................3 1.1 Some economic uses and ecological functions of the Psoraleeae………………………..4 1.2 Taxonomic history and generic boundaries within the tribe Psoraleeae….………………5 1.3 Phylogenetic position of the tribe Psoraleeae…………………………………………….9 1.4 Sources of data for phylogenetic inference………………………………………………11 1.5 The Cape Floristic Region as a centre of diversity and endemism for the Psoraleeae ……………………………………………………………………………………...…....15 1.6 Testing speciation processes………………..…………………………………………...19 1.7 Species concepts and species delimitation in the southern African Psoraleeae….……..20 1.8 Aim and objectives of the study…...……...……………………………………………..23 CHAPTER 2: PHYLOGENETIC RELATIONSHIPS, MACROEVOLUTION AND ESTIMATION OF LINEAGE DIVERGENCE DATES IN THE PSORALEEAE 2.0 Introduction………………………………………………………………………….…...24 2.0.1 Phylogenetic position and taxonomic status of the tribe Psoraleeae……….....24 2.0.2 Phylogenetic relationships within the Psoraleeae…………..………………....24 2.0.3 EstimationUniversity of divergence dates of…………………………… Cape Town...…………………27 2.0.4 Objectives……………………………...………………………………………29 2.1 Materials and methods……………………………………..………………………….....29 2.1.1 Taxon sampling…………………………………..………………………….....29 2.1.2 Morphological, anatomical and phytochemical data scoring.…………….…..29 2.1.3 DNA extraction, amplification and sequencing…………………….……........34 2.1.4 Sequence alignment and phylogenetic analysis………………………………..39 2.1.5 Estimation of divergence dates………………………………………..………40 iii 2.2 Results…………………………………………………………………………………...42 2.2.1 Screening of molecular markers…………………………………...…………..42 2.2.2 Data matrices………………………………...………………………………...43 2.2.3 Models of evolution…………………………………………………...……….44 2.2.4 Phylogenetic reconstruction………………………….…………………..…….44 2.2.5 Divergence dates………………………………………………………………..53 2.3 Discussion………………...…………………………………...………………..……….55 2.3.1 Molecular markers……………………………………………………………..55 2.3.2 Monophyly of the tribe Psoraleeae…………………………………………….56 2.3.3 Generic relationships…………………………………...……………………...57 2.3.4 Ancestral state reconstructions………………………………..………………59 2.3.5 Divergence dates……………………………………………………………….60 2.4 Conclusions……………………………………………………………………………...61 CHAPTER 3: DISTRIBUTION PATTERNS IN THE SOUTHERN AFRICAN PSORALEEAE: EXPLORING THE ROLE OF EDAPHIC HETEROGENEITY 3.0 Introduction………………………………………………………………………………62 3.0.1 General distribution of Otholobium C.H. Stirt. and Psoralea L………………..62 3.0.2 Factors driving diversification in CFR lineages…………………………...….64 3.0.3 Scope of this study………………………………...………………………….67 3.0.4 Objectives……………………………..………………….…………………...68 3.1 Materials and methods.…………………………………………………..……………...68 3.1.1 Determination of soil types and post-fire regeneration strategy…………….68 3.1.2 Soil sampling and nutritional analysis…………………………….………...69 3.1.3 DataUniversity analysis…………………………………… of Cape Town..………………..………....69 3.2 Results………………………………………...…………………………………………70 3.2.1 Proportions of species on the various soil types……………………..………70 3.2.2 Soil nutrients in the different sites……...…………………..……………….72 3.2.3 Soil nutrients in relation to species’ phylogenetic relationships…………….75 3.3 Discussion………………………………………………………………...……………...79 3.3.1 Soil types…………………………………………………………………..….79 3.3.2 Regeneration strategy……………………………….………………..............79 3.3.3 Soil nutrients in relation to species’ phylogenetic relationships……………..80 3.4 Conclusions………………………………………………………………………………81 iv CHAPTER 4: MORPHOMETRIC STUDIES OF THE PSORALEA APHYLLA AND P. PINNATA COMPLEXES 4.0 Introduction………………………………………………………………………………82 4.0.1 Psoralea aphylla L. complex……………………………...………………….83 4.0.2 Psoralea pinnata L. complex………...…………………………………...…..85 4.1 Materials and methods………………………………………………...………………...86 4.1.1 Field collections, morphometric measurements and data sets………………..86 4.1.2 Characters studied…………………………………………………………….86 4.1.3 Statistical analyses………………………..………………………………….87 4.2 Results…………………………………………………………………………………...90 4.2.1 Psoralea aphylla L. complex………………………………………...……….90 4.2.2 Psoralea pinnata L. complex………………………………………………….95 4.3 Discussions and conclusions…………………………………………………………...100 4.3.1 Psoralea aphylla L. complex………………………………………………..100 4.3.2 Psoralea pinnata L. complex………………………..………………....……103 4.4 Taxonomic treatment………………………………………..…………….…………...105 4.4.1 Psoralea aphylla L. complex……………………………………..……….….105 4.4.2 Psoralea pinnata L. complex…………………………………………………130 CHAPTER 5: SUMMARY AND SYNTHESIS…………………..…………………………144 REFERENCES………………………………………………………………………………...147 University of Cape Town v LIST OF FIGURES No. Title l.l Structure of the ribosomal anay 2.1 Phylogenetic relationships between the North American Psoraleeae according to Egan & Crandall (2008) 2.2 Phylogenetic relationships within the Psoraleeae according to Grimes (1990) 2.3 Phylogeny of the Psoraleeae infelTed from DNA sequence data 2.4 Phylogeny of Otholobium C.H. Stirt. and Psoralea L. inferred from morphological data 2.5 Phylogeny of the southern African Psoraleeae infetTed from DNA and morphological data 2.6 Ancestral state reconstruction for presence of cupulum 2.7 Ancestral state reconstruction for loss of leaves 2.8 Ancestral state reconstruction for leaf type 2.9 Ancestral state reconstruction for the occunence of recurved mucronate leaf apices 2.10. Ancestral state reconstruction for the occunence of flowers in triplets subtended by a single bract 2.11 BEAST tree showing date estimates for the Psoraleeae 3.1 Distribution map for Otholobium 3.2 Distribution map for Psoralea 3.3 PropOltions of Psoralea species across various soil types in the CFR of South Africa 3.4 PropOltions of Otholobium species across various soil types in the CFR of South Africa 3.5 umbers of seeders and resprouter species in Otholobium and Psoralea 3.6 Ordination ofreseeders and resprouters from the PCA of the soil nutrient data 4.1 Illustrations of some of the characters measured for the Psoralea aphylla and P. pinnata complexes 4.2 Plots of the Mean±SE for some of the characters studied in the Psoralea aphylla complex 4.3 Phenogram of the Psoralea aphylla L. complex 4.4 Ordination of the P. aphylla complex specimens on the ftrst and second CVs of the discriminant function analysis 4.5 Plots of the Mean±SE for some of the characters studied in the Psoralea pinnata complex 4.6 Phenogram of the Psoralea pinnata L. complex 4.7 Ordination of the P. pinnata complex specimens on the ftrst and second CVs of the discriminant function analysis 4.8 Distribution map for Psoralea aphylla subsp. aphylla. 4.9 Distribution map for Psoralea aphylla subsp. usitata 4.10. Distribution map for Psoraleafilifolia Eckl. & Zeyh. 4.11 Distribution map for Psoralea peratica C .H. Stirt. 4.12 Distribution map for Psoraleajleta C.H. Stitt. ined. 4.13 Distribution map for Psoralea pullata C.H. Stitt. ined. 4.14 Distribution mapUniversity for Psoralea rigidula C.H. Stitt. ined.of Cape Town 4.15 Distribution map for Psoralea gigantea M . Dludlu, A.M. Muasya & c.H.
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