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Pinus Caribaea Var. Bahamensis) in the Bahaman Archipelago

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Pinus Caribaea Var. Bahamensis) in the Bahaman Archipelago ORBIT - Online Repository of Birkbeck Institutional Theses Enabling Open Access to Birkbecks Research Degree output Conservation genetics and biogeography of the Caribbean pine (Pinus caribaea var. bahamensis) in the Bahaman archipelago http://bbktheses.da.ulcc.ac.uk/18/ Version: Full Version Citation: Sanchez, Michele (2012) Conservation genetics and biogeography of the Caribbean pine (Pinus caribaea var. bahamensis) in the Bahaman archipelago. PhD thesis, Birkbeck, University of London. c 2012 The Author(s) All material available through ORBIT is protected by intellectual property law, including copyright law. Any use made of the contents should comply with the relevant law. Deposit guide Contact: email Conservation genetics and biogeography of the Caribbean pine (Pinus caribaea var. bahamensis) in the Bahaman archipelago Thesis submitted by Michele Sanchez For the degree of Doctor of Philosophy School of Biological and Chemical Sciences Birkbeck, University of London and Genetics Section, Jodrell Laboratory Royal Botanic Gardens, Kew September, 2012 Declaration I hereby confirm that this thesis is my own work and the material from other sources used in this work has been appropriately and fully acknowledged. Michele Sanchez London, September 2012 2 “All past and present organic beings constitute one grand natural system…” (Darwin 1859) I would like to dedicate this work to my husband; whose support, encouragement and patience have been a constant throughout the years. 3 Abstract The Bahaman archipelago contains large expanses of pine forests, where the endemic Caribbean pine Pinus caribaea var. bahamensis is the dominant species. This pine forest ecosystem is rich in species and also a valuable resource for the local economy. Small areas of old-growth forest still remain in the Turks and Caicos islands (TCI) and in some of the islands in the Bahamas; despite on-going severe infestation by pine tortoise scale insect Toumeyella parvicornis and high pine mortality in the former and intensive past commercial logging activities in the latter. For the first time integrated research on the genetics, morphology, ecology and biogeography of this variety was carried out throughout its whole distribution range. Past and present forest areas were mapped using historical physical maps and modern satellite imagery, showing forest loss due to urbanisation, pests and storm surges and expansions resulting mainly from dry-season human induced fires. Population genetic analysis using plastid and nuclear microsatellites revealed high ancient gene flow and recent genetic distance between populations of the Bahamas and the TCI; in addition to genetic structure within regions. Morphological differences were also observed and discussed. The variety showed high individual genetic and morphological variance and high plasticity. Despite the observation of good forest regeneration in normal circumstances, stochastic events did cause severe reductions in forest area and effective population size. A predominantly random and outcrossing breeding system was also inferred from the data, despite detection of some inbreeding in the smaller populations. Suggestions for the future conservation and management of the species included fire management and the creation or extension of in-situ conservation areas and ex-situ collections. 4 Acknowledgements This research would not have been possible without the masterly guidance and support of my supervisors Dr. Martin Ingrouille and Dr. Mike Fay. I owe my deepest gratitude to my husband, colleague and field assistant Martin A. Hamilton for all his support throughout the years, sweat and hard work during fieldwork and encouragement during difficult times. Many thanks to my colleagues at Kew Gardens, whose valuable technical advice, time, flexibility and support contributed to the successful completion of this thesis, in particular Dr. Colin Clubbe, Robyn Cowan, Marcella Corcoran, Justin Moat, Susana Baena, Edith Kapinos, Dr. M. Dolores Lledó-Barrena, Sara Redstone, Noelia Alvarez and Kathleen Smith. I would also like to thank the valuable support from my parents, relatives, friends and PhD colleagues. I am fortunate to have had the financial support required to carry out this research, undertake fieldwork, laboratory analysis, participate in conferences and meetings, provide specialised training to partner institutions in the Bahamas and the TCI and be able to reduce working hours and dedicate more time to the PhD thanks to The Harold Hyam Wingate Foundation; Bentham-Moxon Trust; Kew Gardens Jodrell Laboratory, GIS Unit and UKOTs Programme; Birkbeck University of London and the Caicos Pine Recovery Project. Fieldwork could not have been carried out without the help and support received from the following: TCI Department of Environment and Coastal Resources (DECR), in particular Bryan Naqui Manco; Turks & Caicos National Trust (TCNT); Pine Cay Meridian Club; the Bahamas National Trust (BNT), especially Eric Carey, Tamica J. Rahming and David Knowles; Bahamas Department of Agriculture; Friends of the Environment, Abaco; and Bahamas Environment, Science and Technology Commission (BEST). Therefore, I offer my sincere gratitude to all of you who believed in me and my research and participated in some way to the completion of this work. 5 Table of Contents Declaration ........................................................................................................................ 2 Abstract ............................................................................................................................. 4 Acknowledgements ........................................................................................................... 5 Table of Contents .............................................................................................................. 6 Index of Tables .................................................................................................................. 9 Index of Figures .............................................................................................................. 11 Chapter 1 . Introduction .................................................................................................. 14 1.1. Pinus caribaea var. bahamensis ........................................................................... 15 1.1.1. Taxonomy ...................................................................................................... 15 1.1.2. Morphology ................................................................................................... 16 1.1.3. Varieties ......................................................................................................... 17 1.1.4. Distribution Range ......................................................................................... 19 1.2. The Bahaman archipelago .................................................................................... 20 1.2.1. Population and development .......................................................................... 20 1.2.2. Geology, soils and hydrology ........................................................................ 23 1.2.3. Climate ........................................................................................................... 26 1.2.4. Palaeoclimate and vegetation......................................................................... 29 1.3. Phylogenetics and ancient migration routes ......................................................... 33 1.4. Pine forest ecology ............................................................................................... 35 1.4.1. The pine forest ecosystem.............................................................................. 35 1.4.2. Forest regeneration and fire ........................................................................... 37 1.4.3. Seed and pollen dispersal ............................................................................... 38 1.5. Human Action ....................................................................................................... 39 1.5.1. Logging .......................................................................................................... 39 1.5.2. Human ignited uncontrolled fires .................................................................. 41 1.5.3. Agriculture and invasive species ................................................................... 42 1.5.4. Insect pests ..................................................................................................... 43 1.6. Plantations and other uses ..................................................................................... 45 1.7. Legislation and conservation areas ....................................................................... 46 1.8. Thesis outline ........................................................................................................ 48 Chapter 2 . Biogeography .............................................................................................. 49 2.1. Introduction .......................................................................................................... 49 6 2.2. Material and Methods ........................................................................................... 51 2.2.1. Bahamas ......................................................................................................... 51 2.2.1.1. Satellite imagery and Geographic Information System (Gis) ................. 51 2.2.1.2. Historical
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