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Population differentiation in the dingo: biogeography and molecular ecology of the Australian Native Dog using maternal, paternal and autosomal genetic markers Kylie Mae Cairns A thesis submitted for the degree of Doctor of Philosophy in the Faculty of Science School of Biotechnology and Biomolecular Sciences The University of New South Wales, Sydney, Australia 2014 I would like to dedicate this thesis in memory of A/Prof Alan Wilton for inspiring my interest in and appreciation of dingoes. Originality 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 authorize 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.’ Kylie Mae Cairns 28 August, 2014 Copyright Statement ‘I hereby declare that this submission is my own work, and to the best of my knowledge contains no materials previously published or written by other persons, 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 this research by others with whom I have worked at UNSW or elsewhere is explicitly acknowledged in the thesis. I also declare that all 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.’ Kylie Mae Cairns 28 August 2014 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.’ Kylie Mae Cairns 28 August, 2014 Abstract Dingoes are an essential feature of the Australian landscape, a trophic regulator and apex carnivore. As an ancient dog they may also hold the key to investigating the evolution, history and origin of domestic dogs. Conservation efforts are hampered by a lack of consistency in federal and state legislation. In the wild dingoes are threatened by hybridisation with domestic dogs. Conservation groups have posited that different ecotypes of dingo exist, however little biogeographical data has been collected. This thesis explores the phylogeny, biogeography and genetic identity of the dingo using maternal, paternal, autosomal and whole genome genetic markers. Previous genetic studies lacked a broad geographic sample inhibiting the observation of broad biogeographical patterns. Thus, for this research, dingoes from five broad geographic populations across the entire Australian continent were interrogated; The Kimberley (Western Australia), The Gibson Desert (Western Australia), The Simpson Desert (Northern Territory), Fraser Island (Queensland) and The Australian Alpine region (New South Wales/Victoria/Australian Capital Territory). New Guinea Singing Dogs, the wild dog of Papua New Guinea, were also incorporated as the closest genetic relative to the dingo. The main finding of this thesis research is that there are at least three genetically distinct geographically subdivided populations of dingo; southeastern, Fraser Island and northwestern. Genetic data suggests that the dingo lineages diverged outside Australia. Mitochondrial and Y chromosome evidence further suggests that these populations may I be the result of multiple introductions into Australia. The New Guinea Singing Dog was observed to have shared ancestry with the dingo. Paternal introgression from domestic dogs was observed, particularly in southeastern Australia. Additionally strong inbreeding was observed in the Fraser Island dingo population. These findings have significant implications for the management and conservation of dingoes. First, the three distinct dingo populations should be managed separately, with limited mixing in captivity and restricted human-mediated translocations in the wild. Second, hybridisation with domestic dogs is a particular threat to the southeastern dingo population and lethal control methods may be increasing male biased introgression into dingoes. Third, inbreeding possibly compromises Fraser Island dingoes; further genetic surveys are imperative and current management strategies may be unsustainable. II Acknowledgements Writing a thesis, particularly a doctorate, is a long journey. Like raising a child, “it takes a village”. I would like to thank the various people who have helped me through this journey from both my professional and personal life. I would not be the scientist (or person) I am today without you. Firstly, I must acknowledge the thoughtful guidance and support of my supervisor Bill Ballard. I thank you for your scientific tutelage and advice, you have taught me many valuable lessons about science and academia. Thank you for encouraging me to take on a PhD and guiding me through it. To my co-supervisor A/Professor Alan Wilton, who sadly passed away in 2011 during my candidature. Thank you for teaching me all that you could about dingoes, dogs and genetics. You are greatly missed by friends, family and colleagues. To my co-supervisor Dr Paul Waters, who kindly stepped in to fill a void in 2012 following A/Prof Wilton’s passing. I am indebted to you for your excellent continued help, advice and kindness during the end of my tenure. To my thesis committee, Professor Mike Archer and Dr Mike Letnic at UNSW, I thank you for your thoughtful and useful input into my research project. Many thanks for always making the time for me. III To my dear friend Dr. Barbara Zangerl, I wish we had met under happier circumstances. Thank you for the guidance regarding microsatellites, SNP genotyping, canine genetics and science in general. I am indebted to you as well for reading various drafts of my thesis and giving valuable constructive criticism. To all the members of the Ballard Lab throughout my candidature: the post-docs Nadia Urosevic, Louise Puslednik, Richard Melvin, Jonci Wolff, Nicolas Pichaud and Martin Horan; the graduate students Theodore Orfanos, Olaf Bressel, Eric Ngo, Michael Nafisinia, Marie Messmer, Melina Chok, Wen Aw, Rijan Bajracharya , Mihi Hwang and Cha Yeon Lee and to the lab assistants Preetha Sujit, Lize Toman, Mikey Amiezer and Jason Wang. Thank you for being such a friendly, helpful and welcoming crowd. Especially for the many times you offered me advice concerning wet lab work, listened to lab presentations about dingoes or read my paper drafts. Particularly to Mart and Jonci thank you for teaching me about PCR – troubleshooting, numts, hot start etc, it was invaluable. It was a pleasure to interact with each and every one of you. I wish to give special acknowledgement to Pann Pann Chung and Carolina Correa, we started our PhDs ‘together’ and now we have all ‘finished’. Thank you both for the continued support, willingness to help with editing, reading, commenting on my work, discussions about women in science and most importantly friendship. To my family, Mom, Dad, and my siblings Hilary, Alastair and Tim. Thank you for supporting me through this journey and willingly listening to endless conversations about dingoes. Thanks must especially go to my Father, Iver, for countless discussions IV about academia, science and peer-review. My mother Ann, sister Hilary and mother-in- law Janine; without your assistance in caring for Casper I could not have finished, thank you. To my husband Nathan, I must thank you for the unfailing support and positivity. You’ve been with me every step of this journey; listening to endless talks about dingoes, science, grant writing and offering advice with patience. Thank you for putting up with my absentmindedness, passion for science and supporting me to undertake a career that will never be 9-5. To my son Casper, you make it all worthwhile. It is hard spending time away from you, even harder given you are so young, however I had to do this. I hope you are proud of me when you are older and the sacrifice was worth it. In addition, I would like to acknowledge the contributions of the various dingo trappers, scientists, National Parks rangers, citizens and conservation groups whom have sent Dr. Alan Wilton (and myself) dingo samples. In particular I must thank Dr. Danielle Stephens whom kindly offered me the use of dingo samples from her PhD research and was always available to discuss the intricacies of dingo genetics. Without these contributed samples this research would not have been possible. V Academic Acknowledgements Chapter 1 The authors would like to acknowledge the Ballard/Wilton laboratory group and Michelle Potter at the University of New South Wales for comments on the manuscript. We thank Dr. Denise Donlon (University of Sydney) for providing permission to reproduce the photograph in Figure 1-1 and providing access to the J. L. Shellshear Museum archives (University of Sydney). We thank H.C. Cairns for permission to reproduce the photographs in Figure 1-2 from his book, co-authored with Bill Yidumduma Harney, Dark Sparklers and providing insight into Indigenous Australian culture and spiritualism concerning the dingo. The dingo 454 sequence reads were generated at Pennsylvania State University by Stephan Schuster.

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