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Population Genetics, Demography and Population Viability of Little Penguins (Eudyptula Minor) in Australia

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Population Genetics, Demography and Population Viability of Little Penguins (Eudyptula Minor) in Australia POPULATION GENETICS, DEMOGRAPHY AND POPULATION VIABILITY OF LITTLE PENGUINS (EUDYPTULA MINOR) IN AUSTRALIA A thesis submitted for the degree of Doctor of Philosophy By Sandra Vardeh School of Biological, Earth and Environmental Sciences, The University of New South Wales, Evolution and Ecology Research Centre April 2015 PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: First name: Other name/s: Abbreviation for degree as given in the University calendar: School: Faculty: Title: Abstract 350 words maximum: (PLEASE TYPE) Declaration relating to disposition of project thesis/dissertation I hereby grant to the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or in part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all property rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstracts International (this is applicable to doctoral theses only). …………………………………………………………… ……………………………………..……………… ……….……………………...…….…11/07/2016 Signature Witness Date The University recognises that there may be exceptional circumstances requiring restrictions on copying or conditions on use. Requests for restriction for a period of up to 2 years must be made in writing. Requests for a longer period of restriction may be considered in exceptional circumstances and require the approval of the Dean of Graduate Research. FOR OFFICE USE ONLY Date of completion of requirements for Award: THIS SHEET IS TO BE GLUED TO THE INSIDE FRONT COVER OF THE THESIS ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed …………………………………………….............. Date ……………………………………………..............11/07/2016 COPYRIGHT STATEMENT ‘I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstract International (this is applicable to doctoral theses only). I have either used no substantial portions of copyright material in my thesis or I have obtained permission to use copyright material; where permission has not been granted I have applied/will apply for a partial restriction of the digital copy of my thesis or dissertation.' Signed ……………………………………………........................... Date ……………………………………………..........11/07/2016 ................. AUTHENTICITY STATEMENT ‘I certify that the Library deposit digital copy is a direct equivalent of the final officially approved version of my thesis. No emendation of content has occurred and if there are any minor variations in formatting, they are the result of the conversion to digital format.’ Signed ……………………………………………........................... Date ……………………………………………..........11/07/2016 ................. POPULATION GENETICS, DEMOGRAPHY AND POPULATION VIABILITY OF LITTLE PENGUINS (EUDYPTULA MINOR) IN AUSTRALIA A thesis submitted for the degree of Doctor of Philosophy By Sandra Vardeh School of Biological, Earth and Environmental Sciences, The University of New South Wales, Evolution and Ecology Research Centre April 2015 Table of Contents List of Figures .............................................................................................................. VII List of Tables ................................................................................................................ XI Acknowledgements ..................................................................................................XVII Thesis abstract .............................................................................................................. 1 Chapter 1: Introduction / Review of the status of the Little Penguin (Eudyptula minor)........................................................................................ 3 1.1. Biology of the little penguin ........................................................................... 6 1.2. Penguin distribution and population trends in New South Wales ................. 7 1.3. Connectivity and dispersal ............................................................................ 11 1.4. Rationale of the study ................................................................................... 12 1.5. Thesis overview............................................................................................. 13 References ............................................................................................................... 17 Appendix 1 .................................................................................................................. 20 Chapter 2: Identifying a decline of flightless, burrow-nesting seabirds using non-invasive methods to replace mark-recapture approaches for estimating population size and survival rates .......................................... 35 Introduction ............................................................................................................ 39 Methods .................................................................................................................. 48 Results ..................................................................................................................... 65 Discussion ................................................................................................................ 77 Acknowledgements ................................................................................................. 82 References ............................................................................................................... 83 Appendix 2 ................................................................................................................... 88 Chapter 3: Population genetics of Little Penguins (Eudyptula minor) in Australia ... 89 Abstract ................................................................................................................... 91 Introduction ............................................................................................................ 93 Materials and Methods ........................................................................................... 98 Results ................................................................................................................... 107 Discussion .............................................................................................................. 120 Acknowledgements ............................................................................................... 124 Conflict of Interest ................................................................................................ 124 References ............................................................................................................. 125 Appendix 3 ................................................................................................................ 131 III Chapter 4: Patterns of Major Histocompatibility Complex diversity, parasitism and mate choice in Little Penguins (Eudyptula minor) ................................. 153 Introduction .......................................................................................................... 157 Materials and methods ......................................................................................... 162 Results ................................................................................................................... 173 Discussion .............................................................................................................. 184 Acknowledgements ............................................................................................... 189 References ............................................................................................................. 190 Appendix 4 ................................................................................................................ 196 Chapter 5: Viability of little penguin (Eudyptula minor) populations at their northern range edge ............................................................................... 201 Summary ..............................................................................................................
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