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Systematic Studies of the South African Campanulaceae Sensu Stricto with an Emphasis on Generic Delimitations

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Town The copyright of this thesis rests with the University of Cape Town. No quotation from it or information derivedCape from it is to be published without full acknowledgement of theof source. The thesis is to be used for private study or non-commercial research purposes only. University Systematic studies of the South African Campanulaceae sensu stricto with an emphasis on generic delimitations Christopher Nelson Cupido Thesis presented for the degree of DOCTOR OF PHILOSOPHY in the Department of Botany Town UNIVERSITY OF CAPECape TOWN of September 2009 University Roella incurva Merciera eckloniana Microcodon glomeratus Prismatocarpus diffusus Town Wahlenbergia rubioides Cape of Wahlenbergia paniculata (blue), W. annularis (white) Siphocodon spartioides University Rhigiophyllum squarrosum Wahlenbergia procumbens Representatives of Campanulaceae diversity in South Africa ii Town Dedicated to Ursula, Denroy, Danielle and my parents Cape of University iii Town DECLARATION Cape I confirm that this is my ownof work and the use of all material from other sources has been properly and fully acknowledged. University Christopher N Cupido Cape Town, September 2009 iv Systematic studies of the South African Campanulaceae sensu stricto with an emphasis on generic delimitations Christopher Nelson Cupido September 2009 ABSTRACT The South African Campanulaceae sensu stricto, comprising 10 genera, represent the most diverse lineage of the family in the southern hemisphere. In this study two phylogenies are reconstructed using parsimony and Bayesian methods. A family-level phylogeny was estimated to test the monophyly and time of divergence of the South African lineage. This analysis, based on a published ITS phylogeny and an additional ten South African taxa, showed a strongly supported South African clade sister to the campanuloids. Assessment of divergence times using a secondary calibration point suggests that this clade started to diversify during the OligoceneTown (28 mya), which coincided with global climatic changes from hot wet to cold dry conditions. A phylogenetic analysis of the South African lineage was undertaken based on morphological and DNA sequence data from the chloroplast trnL-F and the nuclear ITS regions. These data sets were analyzed separately and in combination. The phylogenetic hypothesis was used to re-assess the questionableCape generic boundaries in the family. The ITS data produced poor resolution under parsimony and poor support under Bayesian methods. The resulting phylogenies show fiveof species assemblages that contradict traditional generic circumscriptions, which have primarily been based on the mode of capsule dehiscence. The date estimated for the South African clade was used as calibration point to estimate the age of the clades revealed by the molecular data. Radiation of the Campanulaceae in southern Africa seems to correlate with dramatic climatic and topographical changes such as aridification and continental uplift on the subcontinent that started during the Oligocene. The phylogenetic hypothesis was also used to trace the evolution of nine characters considered important in the circumscription of genera. An uncontradicted synapomorphy was found for the Rhigiophyllum- Siphocodon clade.University The fruit character was found to be taxonomically unreliable at the generic level. The phylogeny of the South African clade was further used to focus on the closely related genera, Roella, Merciera and Prismatocarpus – a group forming a well supported clade in most analyses. The total evidence analysis was used to evaluate the status of each of these genera. Several options were explored to translate the phylogeny into a classification. This process was guided by the primary criterion of monophyly followed by stability in nomenclature, strong statistical support for the taxon, maximum phylogenetic information and ease of identification of the taxon. The results favour retaining of Roella, Prismatocarpus and Merciera as separate genera. A synopsis of these three is provided. v ACKNOWLEDGEMENTS I would like to extend my gratitude and appreciation to the following individuals and institutions for their contribution towards the completion of this thesis. My supervisor, Prof. Terry Hedderson for his guidance and with his kind positive manner kept me motivated. Dr. Gail Reeves initially supervised the molecular component of the projects. My colleagues at the Compton Herbarium for their interest, support, encouragement and collecting of numerous species. The endless help with laboratory techniques, software, reagents, and fruitful discussions of the Leslie Hill Molecular Lab staff and students (Amelia, Angeline, Annika, Ferozah, Tracey and Krystal, Margaret) created a great working environment. Dr. Felix Forest tirelessly helped with numerous technical aspects of the project. The South African National BiodiversityTown Institute (SANBI), my employer, provided financial support and the infra-structure. The various Nature Conservation Authorities in South Africa granted collecting permits and the National Herbarium (PRE) kindly provided specimensCape on loan. Dr. Bill Eddie, my Campanulaceae mentor and friend for always sharing his vast knowledge on the family with me. My steppy gang friends/colleaguesof (Barry, Fatima, Leschelle, Beryl, Shaun, Ismail, Judy A, Barney, Lee-anne, Caitlin) for the much-needed outlet and humour that kept me sane during these long years of many challenges. To my family for their patience, understanding and prayers that propelled me towards the completion of the project. University vi TABLE OF CONTENTS DECLARATION .................................................................................................. IV ABSTRACT .......................................................................................................... V ACKNOWLEDGEMENTS .................................................................................... VI LIST OF FIGURES ............................................................................................... XI CHAPTER 1 - GENERAL INTRODUCTION ......................................................... 16 CHAPTER 2 - SOUTH AFRICAN CAMPANULACEAE: A TEST OF MONOPHYLY AND AN ESTIMATE OF DIVERGENCE TIME ....................................................Town 32 2.1. Introduction ..........................................................................................................................................32 2.2. Materials and methods .........................................................................................................................37 2.2.1. Data sampling .................................................................................................................................37 2.2.2. Data set construction .......................................................................................................................37 2.2.3. Phylogenetic Analyses ....................................................................................................................Cape 38 2.2.4. Dating of the South African lineage ...............................................................................................39 2.2.5. Estimation of per-lineage diversification rateof ................................................................................. 40 2.3. Results....................................................................................................................................................40 2.3.1. Maximum Parsimony ......................................................................................................................41 2.3.2. Bayesian Analysis ...........................................................................................................................43 2.3.3. Estimates of divergence time ..........................................................................................................44 2.4. Discussion ..............................................................................................................................................47 2.4.1. Monophyly of the South African Campanulaceae ..........................................................................47 2.4.2. Age of the South African clade .......................................................................................................49 2.4.3. The positionUniversity of W. hederacea ......................................................................................................... 51 CHAPTER 3 - MOLECULAR PHYLOGENETICS OF THE SOUTHERN AFRICAN CLADE ................................................................................................................ 53 3.1. Introduction ..........................................................................................................................................53 3.2. Materials and Methods ........................................................................................................................57 3.2.1. Taxon sampling ..............................................................................................................................57 3.2.2. Outgroup choice ..............................................................................................................................58 3.2.3. DNA Extraction and Amplification ................................................................................................58 3.2.4. Sequencing and Alignment .............................................................................................................60
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