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