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This Thesis Has Been Submitted in Fulfilment of the Requirements for a Postgraduate Degree (E.G This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. The biogeographic affinities of the Sri Lankan flora A thesis submitted for the degree of Doctor of Philosophy Lakmini Darshika Kumarage Institute of Molecular Plant Sciences, University of Edinburgh Royal Botanic Gardens, Edinburgh January 2016 Abstract The island of Sri Lanka’s exceptional biodiversity and enigmatic biogeography begs investigation, as the island is key in understanding the evolution of the Asian tropical flora. Since the Jurassic, Sri Lanka has been subjected to remarkable tectonic changes, thus its flora could have been influenced by that of a number of nearby landmasses, as well giving Sri Lanka the potential to have played a wider role in the assemblage of floras elsewhere. Firstly, as Sri Lanka originated as a fragment of the supercontinent Gondwana, part of its flora may contain Gondwanan relict lineages. There is also the potential for immigration from Laurasia after the Deccan Plate collided with it 45-50 Mya. Further, Sri Lanka may harbour floristic elements from nearby land masses such as Africa and Southeast Asia as a result of long distance dispersals, and in situ speciation has the potential to have played an important role in enhancing the endemic Sri Lankan flora. I tested the relative contributions of the above hypotheses for the possible origins of the Sri Lankan flora using three representative families, Begoniaceae, Sapotaceae and Zingiberaceae. These families represent both herbaceous and woody elements, and have high diversity across the tropics. Dated molecular phylogenies were constructed for each family. I used recent analytical developments in geographic range evolution modelling and ancestral area reconstruction, incorporating a parameter J to test for founder event speciation. A fine scale area coding was used in order to obtain a better picture of the biogeography of continental Asia. Amongst all the models compared, a dispersal-extinction cladogenesis model incorporating founder event speciation proved to be the best fit for the data for all three families. The dates of origin for Sri Lankan lineages considerably post-date the Gondwanan break up, instead suggesting a geologically more recent entry followed by diversification of endemics within the island. The majority of Sri Lankan lineages have an origin in the Sunda Shelf (53%). Persistence of warm temperate and perhumid climate conditions in southwestern Sri Lanka resembling those of Peninsular Malaysia and Sumatra could have facilitated suitable habitats for these massive dispersals from the Sunda Shelf region. Some trans-oceanic long distance dispersals from Africa (11%) are also evidenced, again these are too young to accept a hypothesis of dispersal during i the Deccan Plate’s migration close to the African coast during the late Cretaceous, but occurred later during the Miocene. Further, some lineages of Laurasian origin (20%) are evidenced in the Zingiberaceae with ancestral areas of China and Indochina, which is congruent with a post collision invasion. Among the families tested, dispersals have occurred stochastically, one during the Eocene, six during the Oligocene, seven during the Miocene, two during the Pliocene and one during the Pleistocene. The highest number of dispersals occurred during the Miocene when a warm climate was prevailing during the Miocene thermal maximum. My results confirm that in situ speciation is an important contributor to the Sri Lankan flora. More rapid radiation of endemics has occurred during Pliocene-Pleistocene; two endemics in Begoniaceae, ten endemics in Sapotaceae and ten endemics in Zingiberaceae have evolved in situ during this period. Sri Lanka will have been subjected to expansion and contraction of climatic and vegetation zones within the island during glacial and interglacial periods, potentially resulting in allopatric speciation. As a conclusion, long distance dispersals have played a prominent role in the evolution of the Sri Lankan flora. The young ages challenge the vicariant paradigm for the origin and current disjunct distributions of the world’s tropical lineages and provide strong evidence for a youthful tropics at the species level. The thesis contains six chapters; first two are introductory chapters, then there are three analytical chapters, one for each family, and finally a summary chapter is provided. Each analytical chapter is written as a stand-alone scientific publication, thus there is some repetition of relevant content in each. ii iii Acknowledgements Firtslty I would like to give my sincere thanks and gratitude to Dr Mark Hughes, Dr James Richardson and Dr Richard Milne for their immense support and advices throughout my project from the beginning to the end. They were always very helpful and have always made the time to discuss my ideas, to answer my questions. A special thank goes to Dr Mark Hughes who was with me in my ups and downs, helping me to face difficult situations and finding solutions. He kept me on trackevery time, encouraged me and was so kind to visit Sri Lanka twice to help me in the thesis work. Without his huge support and guidance this would not have been possible. Also I like to thank Dr Sumudu Rubasinghe, University of Peradeniya, Sri Lanka for helping me in applying for permits in palnt collections in Sri Lanka. Funding for this research came from the Darwin Trust of Edinburgh which covered my tuition fee, lab costs and living expenses. I am immensely grateful to the founder of the schoralship late Prof Kenneth Murray and interview panel for selecting me to offer the shoclarship which provided opportunity for me to pursue a PhD in University of Edinburgh. Funding for field work in Sri Lanka was facilitated by the Davis expedition fund, I am thankful to them to offering me the funds to carry out the field work successfully. Also a big thanks goes to the forest Department and the wildlife department of Sri Lanka for giving the permission to collect plant specimens and Upali, Tharanga, Indika and many other people who helped me in the field. A special thank you goes to Royal Botanic Gardens, Edinburgh which provided me the opportunity to join the Tropical Group and working space in the molecular biology laboratories. Also I am grateful to all members at RBGE for their kindness, smiles, and support throughout the period. More specially, Dr Michelle Hart, Dr Laura Forrest, Ruth Hollands for their help and advice in lab and always willingness to help and Deborah Vaile for her support in the library. I am grateful to everyone who has helped with the collection of plant material, provided silica dried samples, DNA isolations and sequence data during the course of my research. Notable mentions go to Dr Daniel Thomas, Dr Jane Droop for providing the DNA sequence alignments and Dr Mark Newman for his support in Zingiberaceae iv specimen identification and sharing his expertise. Also I am thankful to Dr Sangeetha Rajbhandary, Dr Ching-I-Peng and Koh Nakamura for providing me the Himalayan Begonia DNA samples. Further, I am grateful to all the academic and non academic staff members of the Open University of Sri Lanka for their support in various forms for me to carry out my research very well. Thanks also go to all my collegues and my fellow PhD students for their moral support and humour and for making the PhD room more pleasant. I am thankful to all my family members for their immense support and encouragement in all my achievements. And last but not least I am grateful to Ayon, being so good, allowing me to work freely and Kumari for looking after him very well.More specially thanks goes to Sahan, who looked after Ayon very well giving freedom for me to work on my research. Without his love, encouragement, understanding and support, none of this would have been possible. v TABLE OF CONTENTS CHAPTER 1: Introduction to Biogeography………………..…………….. 1 What is Biogeography?................................................................................................. 1 1.2 The early history of biogeography as a discipline………………………….………..…………. 1 1.3 A review of historical biogeographic methods………………………………………….………. 3 1.3.1 Paradigm shifts key to historical biogeographic analysis………………..…………. 3 1.3.2 The beginnings of a modern synthesis of analytical historical biogeography 8 1.3.3 Approaches to analytical historical biogeography……………………………………. 9 1.4 The current state of the field…………………………………………………………………………….. 15 1.5 Summary…………………………………………………………………………………………………………… 15 CHAPTER 2: Introduction to Sri Lankan biogeography………………. 17 2.1 Current Geology and climate of Sri Lanka………………………….………………………………. 17 2.2 Palaeoclimate, geological changes………………………………….…………………………………. 19 2.3 Flora of Sri Lanka…………………………………………………………………………………..………….
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