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Roseina Woods Phd Thesis Using ancient DNA to understand the evolution and biogeography of the Caribbean land mammal fauna A thesis submitted to Royal Holloway, University of London for the degree of DOCTOR OF PHILOSOPHY Roseina Woods Department of Biological Sciences September 2017 1 Declaration of Authorship I, Roseina Woods, hereby declare that this thesis and the work presented in it is entirely my own. Where I have consulted the work of others, this is clearly stated. Signed: Date: 2 Abstract The insular Caribbean is a prefect arena for the study of evolution and biogeography. One exceptional feature of the Caribbean islands is the colonisation of this archipelago by terrestrial mammal fauna. Historic changes in climate, colonisation of new species and the arrival of humans has greatly affected the endemic fauna of the Caribbean. Due to the extinction of much of the Late Quaternary Caribbean mammal fauna during the Holocene, many aspects of taxonomy in this group remains unresolved, preventing a complete study of evolutionary questions surrounding speciation, colonisation and extinction and critically, hindering the conservation of endangered species. This study has incorporated three groups of endemic Caribbean mammals: eulipotyphlan insectivores, rodents and primates, in order to investigate patterns in colonisation and evolutionary histories. Advanced techniques in extraction and sequencing of degraded or ancient DNA were utilised as part of this study in order to successfully able to extract and sequence DNA from museum and zooarchaeological specimens, despite the high degradation indicative of DNA from tropical regions. This study has found that whilst the Caribbean is home to ancient relic species, the islands are also hotspots for the generation of new species, as shown by the recent intra-island speciation of Hispaniolan Nesophontes species. This study has also been able to demonstrate patterns of insular evolution including accelerated evolution and the generation of unusual morphology, both exhibited by the Jamaican primate Xenothrix and extinct caviomorph rodents. Colonisation histories differ between groups, but both rodent and primate taxa looked at as part of this study colonised the Caribbean via over water dispersal during the mid-late Miocene, a period of low global sea level, when a riverine connection may have facilitated faunal movement between the Caribbean and South America. Previous taxonomy in many of the species looked as part of this study were based on morphology and needs to be re-assessed in light of the results of this molecular analysis. This is particularly important for the living Cuban hutia in the genera Capromys and Mesocapromys where the conservation of declining populations is vital for the continued survival of these unqiue taxa. 3 Acknowledgements First and formost I would like to thank my supervisors and advisors, Prof. Ian Barnes, Dr Sam Turvey, and Prof. Mark Brown, for their patience and support throughout my PhD. I would also like to thank Dr Sam Turvey for allowing me to sample from many of the specimens included in this thesis, and Prof. Ian Barnes for providing me with an environment that allowed me to work independently, but also being around for discussion and advice when I most needed it. A special mention must go to Dr Selina Brace who has been a massive influence on my PhD and whose advice, expertise and encouragement were indispensible to me throughout this project. This studentship was funded by the National Environment Research Council (NERC), I am very grateful for the opportunity this funding provided me with. I would also like to thank the many museums that allowed me to use their collections for this project including the Natural History Museum (NHM), Instituto de Ecología y Sistemática (IES), The University of Oriente, Museo d'historia natural tomas romay, Royal Albert Memorial Museum (RAMM), Peabody Museum Yale, and Florida Museum of Natural History (FLMNH). I would like to thank all the staff in the NHM Imaging and Analysis Centre (IAC) for their help with micro-CT scanning during this project. I would like to thank Roberto Miguez at the NHM for allowing me access to the collection. Additionally I would like to thank Holly Morgenroth at RAMM for taking the time to allow me to sample from Geocapromys thoracatus specimens for this thesis. I would particularly like to thank Prof. Ross MacPhee for providing me with samples for the Xenothrix chapter and allowing me access to his expertise. I would like to thank Prof. Pierre-Henri Fabre and Dr Nathan Upham for sharing their data, advice and expertise. A special thanks goes out to all my fellow postgraduates and friends at Royal Holloway particularly Kate and Lauren, at the Natural History Museum all of the occupants of PA417, Dr Tom Booth, Dr Sophy Charlton and especially Dr Melissa Marr who took the time to help me when ever I needed it, and Leila D’Souza for sharing in my island woes. My final thanks goes to my family for your continued support, which means so much to me. Charlie, Jay, Beagle and Calpyso, my Mum who first instilled in me my love of the natural world and Dave for technical support. 4 Contents Title page ............................................................................................................................ 1 Declaration of Authorship ................................................................................................. 2 Abstract ............................................................................................................................... 3 Acknowledgements ........................................................................................................... 4 List of figures and tables ................................................................................................ 12 Chapter 1. Introduction .................................................................................................... 17 1.1 Overview ................................................................................................................... 17 1.2 Island biogeography and evolution of insular species .............................................. 17 Introduction to island study ......................................................................................... 17 Island effects ............................................................................................................... 18 Mechanisms of speciation and adaptive and non-adaptive radiations ........................ 19 Colonisation and extinction ......................................................................................... 20 1.3 The Caribbean islands .............................................................................................. 21 Overview ..................................................................................................................... 22 A brief timeline of the formation of the Caribbean islands (Iturralde-Vinent, 2006) (Figure 2) ..................................................................................................................... 23 Climate in the wider Caribbean ................................................................................... 25 Cuba ............................................................................................................................ 26 The Cayman Islands and the Cayman trench ............................................................. 27 Hispaniola ................................................................................................................... 27 Puerto Rico ................................................................................................................. 28 Jamaica ....................................................................................................................... 28 1.4 The Caribbean land mammal fauna ......................................................................... 28 Rodentia ...................................................................................................................... 28 Lipotyphla .................................................................................................................... 29 Primates ...................................................................................................................... 29 Colonisation ................................................................................................................ 29 The Aves ridge and the GAAR-landia hypothesis ....................................................... 30 Over-water dispersal ................................................................................................... 30 Extinction ..................................................................................................................... 30 1.5 Conservation archaeogenomics ............................................................................... 31 1.6 Taxonomy of Caribbean land mammal species ....................................................... 32 5 1.7 Ancient DNA ............................................................................................................. 33 Ancient DNA degradation and preservation ................................................................ 33 Ancient DNA contamination ........................................................................................ 34 Ancient DNA in the tropics .......................................................................................... 35 Next
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