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O Attribution — You Must Give Appropriate Credit, Provide a Link to the License, and Indicate If Changes Were Made COPYRIGHT AND CITATION CONSIDERATIONS FOR THIS THESIS/ DISSERTATION o Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. o NonCommercial — You may not use the material for commercial purposes. o ShareAlike — If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original. How to cite this thesis Surname, Initial(s). (2012) Title of the thesis or dissertation. PhD. (Chemistry)/ M.Sc. (Physics)/ M.A. (Philosophy)/M.Com. (Finance) etc. [Unpublished]: University of Johannesburg. Retrieved from: https://ujcontent.uj.ac.za/vital/access/manager/Index?site_name=Research%20Output (Accessed: Date). AN INTEGRATIVE APPROACH TOWARDS SETTING CONSERVATION PRIORITY FOR CYCAD SPECIES AT A GLOBAL SCALE BY RESPINAH TAFIREI Minor dissertation submitted in partial fulfilment of the requirements for the degree of MASTER OF SCIENCE IN ENVIRONMENTAL MANAGEMENT Faculty of Science UNIVERSITY OF JOHANNESBURG August 2016 SUPERVISOR Dr K. Yessoufou CO-SUPERVISOR Dr I.T. Rampedi DEDICATION This work is dedicated to my parents. iii ACKNOWLEDGEMENTS My entire family, mainly my beautiful children; Thabo, Ryan, Chloe, my nephew, Tinashe, as well as my husband: You were there for me throughout this journey. I am deeply appreciative and grateful for the support and rapport I received from my dear husband, Simon. Your patience did not go unnoticed. Thank you from the bottom of my heart. I am also very grateful for the support and scientific guidance I received from Dr. K. Yessoufou, who was the Supervisor of the Research Project. I am thankful for the insights and constructive feedback I received from you. My Co-Supervisor, Dr. I.T. Rampedi. You constantly encouraged me, guided me throughout the process and also reminded me of the deadlines. I acknowledge the input I received from the coursework modules you taught as well. God bless you all. iv ABSTRACT Prioritizing conservation efforts based on phylogenetic tools is gaining momentum globally. However, these efforts are almost exclusively focused on animals, and particularly vertebrate, with no equivalent efforts on plants. The main objective of the present study is to use phylogeny to inform conservation efforts of cycads, the most threatened group in plant kingdom. Specifically, four questions are investigated: 1) What is the geographic pattern of richness and evolutionary distinctiveness (ED) of cycads? 2) Would protecting elevated habitats (e.g. mountains) – traditionally thought to be refuges for ancient lineages – safeguard an ancient lineage like cycads? 3) Would protecting threatened cycads prevent the loss of high-ED species? 4) If not, how can ED and threat data be combined to inform prioritization efforts for cycads globally? Cycads have a tropical and subtropical distribution with the highest richness in Central America, eastern Southern Africa and eastern Australia. Tropical richness is traditionally attributed to a more rapid speciation and lower extinction rate in the tropics vs. temperate regions, but the restriction of cycads distribution to tropics in particular, could be the result of the tropics being a ‘‘hot spot’’ for ancient or relictual lineages. To assess this hypothesis, the first ever complete phylogeny of cycad taxa was reconstructed and used to calculate ED values for each species – an approximate measure of how ancient or unique a species is – and analyse their geographic patterns. High-ED species are likely to correspond to non-random phenotypes and uniquely divergent genomes, and habitats or regions rich in high-ED species therefore deserve particular attention. ED scores range from 10.587 million years (MY) (Cycas micronesica and Cycas zeylanica) to 98.762 MY (Microcycas calocoma) (SD = ±12.62). High average ED values are observed across all known biogeographic regions of cycads, particularly in America and Southern Africa, making America (New World) and Southern Africa priority regions for cycad conservation. There is, however, no relationship between ED and altitude, and this has also been reported recently for birds, indicating that elevated regions are not refuges for ancient cycad lineages. Nonetheless, geographic origin correlates strongly with ED, with cycad of American origin being the most evolutionarily distinct and therefore deserves much conservation efforts. There is, however, a trend towards high-ED species being highly threatened, suggesting that efforts to preserve cycads based on IUCN threat categories would also contribute to v preserving high-ED species. At the same time, there are several cases where threat-based prioritization would miss some high ED species. Threat level and ED were therefore combined to provide a more integrative option for conservation decision, using EDGE score (Evolutionary Distinctiveness and Globally Threatened) analysed within a biogeographic perspective. A complete ranking of cycad species based on EDGE score is provided. EDGE scores range from 2.497 (Cycas clivicola) to 7.375 (Microcycas calocoma) (SD = ± 1.06), making M. calocoma the one-of-the-kind cycad species to prioritize in conservation programme. The dominant genera in the top 50 EDGE species are Zamia (21 species) and Encephalartos (10 species), followed by Ceratozamia (8 species) and Cycas (6 species). From a biogeographic perspective, the cycads of the New World are dominant in the top EDGE ranking with 32 species in the top 50 EDGE species followed by the African cycads (Encephalartos; 10 species). These geographic regions (New World and Africa) therefore could be regarded as global “hot spots” of EDGE species. Several high-EDGE species are not found in protected areas, and this calls for global campaign to raise public awareness of this issue, train conservation officers on EDGE concept and design specific projects for high EDGE species. Further recommendations informed by EDGE species ranking are also provided. Keywords: Conservation prioritization, Evolutionarily Distinct and Globally Endangered species, Biogeography of cycad diversity, New World, Africa. vi TABLE OF CONTENTS DEDICATION ....................................................................................................................................ii ABSTRACT ......................................................................................................................................... v CHAPTER 1 ........................................................................................................................................ 1 INTRODUCTION AND RESEARCH CONTEXTUALISATION ........................................ 1 1.1 INTRODUCTION .......................................................................................................... 1 1.2 NEEDS FOR PRIORITIZING CONSERVATION EFFORTS ................................ 2 1.3. EDGE APPLICATIONS .............................................................................................. 5 1.4. RESEARCH PROBLEM ............................................................................................. 7 1.5. CYCAD TAXONOMIC GROUP ................................................................................ 8 1.5.1. Biogeography of Cycads ....................................................................................... 10 1.5.2 Species diversity and taxonomic changes in Cycads .......................................... 11 1.5.2.1. Family Cycadaceae .......................................................................................... 12 1.5.2.2. Family Stangeriaceae ...................................................................................... 12 1.5.2.3. Family Zamiaceae ............................................................................................ 13 1.6 RESEARCH OBJECTIVES ....................................................................................... 17 CHAPTER 2 ...................................................................................................................................... 18 METHODOLOGY .......................................................................................................................... 18 2.1 MATERIALS AND METHODS................................................................................. 18 2.1.1 Materials ................................................................................................................. 18 2.1.2 Research methodology .......................................................................................... 19 2.1.2.1 Assembling a complete phylogeny of Cycads ................................................... 19 2.1.2.2 Species distribution data and threat status ....................................................... 21 2.2 DATA ANALYSIS ....................................................................................................... 43 2.2.1 Species richness, ED, and EDGE maps ............................................................... 43 2.2.2 Statistical analysis .................................................................................................. 43 CHAPTER 3 ...................................................................................................................................... 45 RESULTS AND DISCUSSION .................................................................................................... 45 3.1. GEOGRAPHICAL
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