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The Ecology and Population Genetics of Introduced Deer Species

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The Ecology and Population Genetics of Introduced Deer Species The ecology and population genetics of introduced deer species Richard Guy Fautley Department of Life Sciences, Imperial College London A thesis submitted for the degree of Doctor of Philosophy June 2013 2 Abstract Deer have been introduced outside their native ranges numerous times worldwide, causing significant economic and environmental impacts. The scale of problems caused by some introduced deer species is expected to increase, while others are relatively harmless and may be important for conservation as their numbers decline in native regions. This thesis examines the factors promoting invasion in non- native deer, and investigates the population genetics of two deer species introduced to Great Britain. Factors hypothesised to predict invasion success were tested using a comparative analysis of the outcomes of introductions of non-native deer populations. Two modelling approaches were taken to account for confounding effects in species-level and population-level analyses, and different factors were found to explain success at different stages of the invasion process. Populations of roe deer expanding from refugia and reintroductions were examined, and differences in genetic diversity between core and peripheral populations, alongside a decline in diversity with rate of expansion from the core were found. High levels of differentiation between and among core and peripheral populations suggest that genetic drift is the major factor causing these patterns. Using a genome scan of British and European roe deer, loci potentially under selection were identified. Association between some of these loci and environmental variables suggests that climatic extremes may have a role in exerting selective pressures on roe populations. The Chinese water deer is severely declining in range and number in its native habitat, but rapidly expanding after being introduced to Great Britain. Relatively high levels of diversity in native Chinese populations, and significant differentiation between the Chinese and British populations were found. The source population of the British deer is likely to be extinct, and the level of genetic structuring indicates that conserving populations across both ranges is important to maintaining their diversity. 3 Declaration I confirm that the work presented in this thesis is my own with the following acknowledgements: A version of Chapter 2 has been published in Biological Invasions (Fautley, R., Coulson, T. and Savolainen, V. (2012) 'A comparative analysis of the factors promoting deer invasion', Biological Invasions, 14(11), 2271-2281). Vincent Savolainen and Tim Coulson participated in the study design and edited the manuscript. I participated in the study design, compiled datasets, generated DNA sequences, analysed the data and wrote the manuscript. Some of the data used in Chapters 4 and 5 were contributed by collaborators. Dr Massimo Scandura shared Italian roe deer tissue samples, and Dr Frank Zachos shared German roe deer DNA samples. Dr Min Chen and Prof.Endi Zhang from East China Normal University shared DNA sequence data on native Chinese water deer, and Christian Miquel sequenced samples from one British population. The use of any materials from other sources is acknowledged throughout this thesis. Richard Fautley Copyright Declaration The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work. 4 Acknowledgements Firstly, I would like to thank my supervisors Vincent Savolainen, Tim Coulson and Rory Putman for all their advice, insight and guidance over the past few years. This work was funded by the BBSRC and the British Deer Society. I am greatly indebted to the deer stalkers from the British Deer Society membership, the Forestry Commission and elsewhere who sent me roe deer tissue samples. I am also very grateful to Arnold Cooke for his insights into the Chinese water deer populations, and Paul Tinsley-Marshall, Richard Southwood and Nick Linsday who helped with my sample collection forays into the field. A special mention must go to Martyn Powell, who repeatedly went above and beyond the call of duty, from helping me get set up in the lab to running the sequencer at ungodly hours and much more besides. I would like to thank the members of the lab past and present: Jan, Alex, Haris, Helen, Silvana, Paul, Luis, Guillaume, Omar, Katya, Hanno, Zuzana, Andy, Adam, Andrew, Simon, Maria and Alan for all their lively discussions, unique senses of humour, valuable advice and support. Thanks also to the Silwood community for providing such a friendly and stimulating atmosphere in which to work, and Silwood Cricket Club for entertaining my attempts at batting. Many thanks go to Min Chen and Endi Zhang for their kind hospitality during my visit to Shanghai. Thanks also to Betty Lingshan Yu and Xueping Quan for translating documents and helping me set up the collaboration. Huge thanks to my housemates: Tim, Tariq, Pete, Chris, Coops, Ben and Jen at House 66, and to Tom H in Ealing for the many good times and helping maintain my sanity over the years. I hold Tom G in great esteem for his formatting wizardry. I am also especially grateful to my fellow journeymen Rob, Derek and Dom for sharing in my commiserations and showing me that the end was in sight. I am eternally grateful to my family for their continued love and support: my mother for encouraging me to follow my interests, and my sister for sharing a childhood which shaped my ambitions. Finally, I owe a huge debt of gratitude to my girlfriend Shuangzi for her unreserved kindness, keeping me going through the difficult times, and reminding me to focus on the future. 5 Table of Contents Abstract ............................................................................................................ 2 Declaration ....................................................................................................... 3 Acknowledgements ........................................................................................... 4 Table of Contents ............................................................................................. 5 List of Figures ................................................................................................. 10 List of Tables .................................................................................................. 11 Chapter 1: General introduction ................................................................... 12 1.1 Biological invasions ................................................................................................................ 12 1.1.1 Developments in invasion biology ..................................................................................... 13 1.1.2 Predicting invasive success ............................................................................................... 13 1.1.3 Features of biological invasions ....................................................................................... 14 1.1.4 Current trends in mammalian invasion biology ................................................................. 15 1.2 The genetics of introduced populations .................................................................................... 16 1.2.1 Colonisation ..................................................................................................................... 17 1.2.2 Range expansion............................................................................................................... 18 1.2.3 Adaptation ........................................................................................................................ 19 1.2.4 Conservation .................................................................................................................... 20 1.3 Deer as a study system ............................................................................................................ 20 1.3.1 Family Cervidae ............................................................................................................... 20 1.3.2 The European roe deer ..................................................................................................... 24 1.3.2 The roe deer of Great Britain ............................................................................................ 26 1.3.4 The Chinese water deer .................................................................................................... 27 1.4 Thesis aim and objectives ........................................................................................................ 32 1.5 Outline of thesis ...................................................................................................................... 33 6 Chapter 2: A comparative analysis of the factors promoting deer invasion34 Introduction .................................................................................................................................. 35 Materials and Methods .................................................................................................................. 40 Trait dataset .............................................................................................................................
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