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An Investigation Into Factors Affecting Breeding Success in The An investigation into factors affecting breeding success in the Tasmanian devil (Sarcophilus harrisii) Tracey Catherine Russell Faculty of Science School of Life and Environmental Science The University of Sydney Australia A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy 2018 Faculty of Science The University of Sydney Table of Contents Table of Figures ............................................................................................................ viii Table of Tables ................................................................................................................. x Acknowledgements .........................................................................................................xi Chapter Acknowledgements .......................................................................................... xii Abbreviations ................................................................................................................. xv An investigation into factors affecting breeding success in the Tasmanian devil (Sarcophilus harrisii) .................................................................................................. xvii Abstract ....................................................................................................................... xvii 1 Chapter One: Introduction and literature review .............................................. 1 1.1 Devil Life History .................................................................................................... 4 1.2 Devil Facial Tumour Disease (DFTD) .................................................................... 7 1.3 The impact of DFTD on the Tasmanian ecosystem .............................................. 12 1.4 Captive breeding, a measure to save endangered species ...................................... 12 1.5 Captive breeding and genetic diversity .................................................................. 13 1.6 Thesis chapters ....................................................................................................... 14 1.6.1 Animal Husbandry and captive breeding in confined enclosures – chapter 2 ... 14 1.7 Devil reproduction ................................................................................................. 16 1.7.1 Polyandry in a wild devil population – chapter 3 .............................................. 16 1.7.2 The major histocompatibility complex (MHC) and mate choice in captive devils i Faculty of Science The University of Sydney – chapter 4 ...................................................................................................................... 17 1.7.3 Investigations into devil endocrinology – chapter 5 .......................................... 19 1.8 References .............................................................................................................. 23 2 Chapter Two: An examination of factors associated with breeding success of Tasmanian devils in captivity (2006 to 2012) ............................................................. 44 2.1 Abstract .................................................................................................................. 44 2.2 Introduction ............................................................................................................ 45 2.3 Methods ................................................................................................................. 49 2.3.1 Insurance Population Establishment .................................................................. 49 2.3.2 Insurance Population Breeding Success 2006-2012 .......................................... 50 2.3.3 Founder Evaluation ............................................................................................ 51 2.3.4 Studbook Evaluation .......................................................................................... 52 2.3.5 Housing .............................................................................................................. 53 2.3.6 Statistical Analysis ............................................................................................. 53 2.4 Results.................................................................................................................... 54 2.4.1 Insurance Population Breeding Success 2006-2012 .......................................... 54 2.4.2 Founder Evaluation ............................................................................................ 57 2.4.3 Housing .............................................................................................................. 59 2.5 Discussion .............................................................................................................. 61 2.5.1 Breeding success ................................................................................................ 62 2.5.2 Founder evaluation ............................................................................................. 66 ii Faculty of Science The University of Sydney 2.5.3 Housing and stress ............................................................................................. 67 2.5.4 Acknowledgements ............................................................................................ 71 2.6 References .............................................................................................................. 72 3 Chapter Three: Multiple paternity and precocial breeding in wild Tasmanian devils (Sarcophilus harrisii) .......................................................................................... 81 3.1 Abstract .................................................................................................................. 81 3.2 Introduction ............................................................................................................ 82 3.3 Materials and methods ........................................................................................... 84 3.3.1 Genetic analyses ................................................................................................. 84 3.3.2 Allele frequency, heterozygosity and linkage disequilibrium ........................... 85 3.4 Results.................................................................................................................... 86 3.4.1 Genetic analyses ................................................................................................. 86 3.4.2 Paternity analyses ............................................................................................... 89 3.4.3 Age ..................................................................................................................... 90 3.5 Discussion .............................................................................................................. 91 3.6 Conclusion ............................................................................................................. 95 3.7 Acknowledgements ................................................................................................ 96 3.8 References .............................................................................................................. 97 4 Chapter four: MHC diversity and female age underpin reproductive success in an Australian icon; the Tasmanian Devil ............................................................ 107 4.1 Abstract ................................................................................................................ 108 4.2 Introduction .......................................................................................................... 109 iii Faculty of Science The University of Sydney 4.3 Material and methods ............................................................................................. 110 4.2.1 Study animals ................................................................................................... 110 4.2.2 Genetic analyses ............................................................................................... 111 4.2.3 Estimates of allele frequency, heterozygosity and linkage disequilibrium ...... 111 4.2.4 Statistical analyses ........................................................................................... 111 4.3 Results.................................................................................................................. 112 4.4 Discussion ............................................................................................................ 117 4.5 Conclusion ........................................................................................................... 118 4.6 References ............................................................................................................ 120 4.7 Acknowledgements .............................................................................................. 127 4.8 Author Contributions ........................................................................................... 127 5 Chapter Five: Exploring the role of endocrinology and behaviour in relation to the reproductive success of captive Tasmanian devils ........................................ 128 5.1 Abstract ................................................................................................................ 128 5.2 Introduction .......................................................................................................... 128 5.3 Materials and
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