HISTORICAL BIOGEOGRAPHY OF ENDEMIC PLANTS IN THE CARIBBEAN AND PODOCARPUS AS A CASE STUDY By © María Esther Nieto-Blázquez A dissertation submitted to the School of Graduate Studies In partial fulfillment of the requirements for the degree of Doctor of Philosophy Biology Department, Faculty of Science Memorial University of Newfoundland July 2019 St. John’s, Newfoundland and Labrador Abstract Despite numerous floristic studies of the Caribbean region, the large-scale evolutionary origins of its diversity remain relatively under-explored. Here, I add to the empirical knowledge of the origin and assembly of the Caribbean flora by large-scale molecular analysis of the biogeography and phylogenetics of its constituent genera, with special emphasis on the conifer genus Podocarpus L’Hér. ex Pers. and its endemic species in the Antillean island chains. Connection of the Greater Antilles to northern South America by a late Eocene / early Oligocene land bridge, GAARlandia, has been hypothesized to facilitate colonization of the Caribbean islands. Well-calibrated estimates from molecular data of the ages of extant Caribbean endemic plant genera show a combination of relatively recent (late Oligocene / early Miocene) and older (late Paleocene / early Eocene) lineages, such that the GAARlandia hypothesis is not necessary to explain floral colonization of the Caribbean. Ancestors of most endemic genera included in my study were of Antillean origin. I show that diversity in Caribbean Podocarpus is paraphyletic, the result of a single colonization of the Greater Antilles from South America in the late Oligocene, species diversification leading to endemism beginning in the early Miocene, and dispersal to the Lesser Antilles from a Greater Antillean ancestor later in the early Miocene. Detailed examination of the phylogeography of the two endemic species on Hispaniola, P. buchii and P. hispaniolensis, shows an initial colonization to the southern palaeo-island of Hispaniola by a P. buchii ancestor. Subsequent northward stepping-stone migration is evident in the localization of genetic clusters across the main cordillera systems. P. hispaniolensis arose by progenitor-derivative speciation in the Central ii Cordillera. The assembly of Caribbean flora has been complex, and geology, vicariance, dispersal, and in situ speciation, together shaped the biotic assembly of the islands. “Abunda la tierra aspera del Cibao (de Ciba, piedra) de pinos mui altos que no llevan piñas, por tal orden compuestos por naturaleza, que parecen azeytunos del Axarafe de Sevilla” C. Columbus iii Acknowledgments There are many people I want to thank and who have been involved in one way or the other in the process of this PhD thesis. I would like to start thanking my supervisor, Dr. Julissa Roncal for her support and guidance through this project. Thanks Julissa for being always available to help and helping me believe in my project when I had doubts about it. Also, thanks for your help with personal matters outside work, I will always be grateful for your mentorship and your help. Thanks to my co-supervisor Dr. Alex Antonelli for his help during this thesis and for hosting me at University of Gothenburg during the summer of 2015. I would also like to thank my committee members, Dr. Dawn Marshal and Dr. Steve Carr for their valuable input during meetings and discussions. Your knowledge greatly improved my research. I thank my funding sources, NSERC‐Discovery grant to Julissa Roncal and MUN's President's Doctoral Student Investment Fund. Thanks to Compute Canada for their assistance, in particular, thanks to Dr. Oliver Stueker for his advice and help on the use of the cluster. Thanks to the Royal Botanic Garden Edinburgh, Royal Botanic Gardens Kew and Montgomery Botanical Center for supplying Podocarpaceae samples for my research. Many thanks to colleagues from the Caribbean. Thanks to Francisco Jimenez for hosting me at Jardín Botánico Nacional Dr. Rafael Ma. Moscoso and providing everything I needed for my collections. Special thanks go to Teodoro Clase for the help during fieldwork and locating the podocarps in the field. Also thanks to Pedro, Angel and Yuley iv for the assistance during fieldwork and at the Herbarium. In Cuba, I should sincerely thank Ramona Oviedo for helping me organizing the logistics of my trip to Guantanamo. I sure enjoyed your deep knowledge of the Cuban flora and your vitality. Thanks to Gerardo Begué from Unidad Provincial de Servicios Ambientales (UPSA) for his help during fieldwork in Ojito de Agua, Guantanamo. Thanks to Dr. Paula Quiroga for sharing Podocarpus samples and helpful comments and thoughts during this thesis. I would like to thank each of my present and past lab mates: Hugo Morales, Zobayer Alam, Fritz Pichardo, Sander Boisen and Nicolas Peñafiel, for many great moments in the lab and outside the lab. We sure have laughed a lot and those memories are priceless. Particular thanks to my dear friend Fritz, who was always happy to help me with technicalities when I had troubles, and with whom I shared many conversations about plants, herbaria and, “against my will”, Linux and computing gibberish. Thanks to all my St. John’s friends for making my time in Newfoundland much more enjoyable and special. I want to deeply thank my family for their support and encouragement not just during this dissertation. Thanks to my parents for their love and support throughout my life, and for teaching me the sense of determination. Finally, thanks to Natalia, for her love, companion, patience, support and a huge of understanding during low times I had along the process. Sorry I tricked you to come here, but thanks for joining me in the Newfoundland adventure. v Table of Contents ABSTRACT .................................................................................................................................................. II ACKNOWLEDGMENTS ........................................................................................................................... IV LIST OF TABLES ....................................................................................................................................... IX LIST OF FIGURES ..................................................................................................................................... XI LIST OF ABBREVIATIONS AND SYMBOLS .................................................................................... XIII LIST OF APPENDICES ........................................................................................................................... XV CHAPTER 1 - INTRODUCTION AND THESIS OVERVIEW ............................................................. 17 1.1 INTRODUCTION ................................................................................................................................. 18 1.1.1. HISTORICAL BIOGEOGRAPHY .............................................................................................. 18 1.1.2. TESTING BIOGEOGRAPHIC HYPOTHESES ......................................................................... 20 1.1.3. MOLECULAR PHYLOGENETICS AND NEXT GENERATION SEQUENCING IN BIOGEOGRAPHY ......................................................................................................................................... 21 1.1.4. ISLAND BIOGEOGRAPHY ...................................................................................................... 25 1.1.5. STUDY REGION ....................................................................................................................... 27 1.1.6. PODOCARPACEAE: A KEY TAXON IN BIOGEOGRAPHY ................................................... 30 1.2. THESIS OVERVIEW .......................................................................................................................... 32 1.3. REFERENCES ..................................................................................................................................... 34 CO-AUTHORSHIP STATEMENT ........................................................................................................... 44 CHAPTER 2 - HISTORICAL BIOGEOGRAPHY OF ENDEMIC SEED PLANT GENERA IN THE CARIBBEAN: DID GAARLANDIA PLAY A ROLE? ........................................................................... 46 2.1. ABSTRACT ………………………………………………………………………………………….. 47 2.2. INTRODUCTION ................................................................................................................................ 48 2.3. MATERIAL AND METHODS ........................................................................................................... 53 2.3.1. TAXON SAMPLING SELECTION ............................................................................................ 53 2.3.2. DNA SEQUENCE SELECTION AND ALIGNMENT ................................................................ 53 2.3.3. PHYLOGENETIC RECONSTRUCTION AND DATING .......................................................... 54 2.3.4. ANCESTRAL AREA ESTIMATION ........................................................................................... 55 2.3.5. A COMPILATION OF INDEPENDENT EVOLUTIONARY AND BIOGEOGRAPHIC STUDIES ON A SUBSET OF CARIBBEAN ENDEMIC GENERA ................................................................................ 59 2.4. RESULTS .............................................................................................................................................. 60 2.4.1. PHYLOGENETIC RECONSTRUCTION AND MOLECULAR DATING