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Distribution, Abundance, Social and Genetic Structures of Indo-Pacific Bottlenose Dolphins (Tursiops Aduncus) in Perth Metropolitan Waters, Western Australia

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Distribution, Abundance, Social and Genetic Structures of Indo-Pacific Bottlenose Dolphins (Tursiops Aduncus) in Perth Metropolitan Waters, Western Australia Distribution, abundance, social and genetic structures of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Perth metropolitan waters, Western Australia Submitted by Delphine Brigitte Hélène Chabanne MSc (Montpellier, France) This thesis is presented for the degree of Doctor of Philosophy of Murdoch University School of Veterinary and Life Sciences 2017 Declaration I declare that this thesis is my own account of my research and contains as its main content work which has not previously been submitted for a degree at any tertiary education institution. .................................... Delphine B. H. Chabanne i ii Abstract In heterogeneous coastal and estuarine environments, dolphins are exposed to varying levels of human activities. Consequently, it is important to identify and characterise fine-scale population structuring based on ecological, social, spatial and genetic data to develop appropriate conservation and management strategies. This thesis focused on identifying subpopulations of Indo-Pacific bottlenose dolphins (Tursiops aduncus) inhabiting Perth waters, Western Australia (WA). Using spatial and social data collected over four years of boat-based photo-identification surveys, I: i) estimated abundances, survival and movement rates using a Multistate Closed Robust Design approach; and ii) examined the social structure and home range using social association and network analyses. I used microsatellite loci and mtDNA markers to investigate the genetic population structure of dolphins at metropolitan (Perth) and regional (c. 1000 km of coastline) scales. High capture probabilities, high survival and constant abundances described a subpopulation with high fidelity in an estuary. In contrast, low captures, emigration and fluctuating abundances suggested transient use and low fidelity in an open coastline region. Overall, dolphins formed four socially and geographically distinct, mixed-sex subpopulations that varied in association strength, site fidelity and residency patterns. Curiously, home range overlap and genetic relatedness did not affect the association patterns. In Perth metropolitan waters, a source-sink relationship was suggested between a subpopulation inhabiting a semi-enclosed embayment and three other subpopulations, including the estuarine subpopulation. On a broader scale, the Perth metapopulation was genetically distinct from other populations along the WA southwestern coastline, with little to no migration from and into other populations. The subpopulations present in Perth waters should each be regarded as a distinct management unit, with a particular focus on protecting the estuarine subpopulation, which is small, has limited connection with adjacent subpopulations and is more vulnerable because of the intensity and diversity of anthropogenic threats present in the estuary. iii iv Statement on the contribution of others Supervision Professor Lars Bejder, Doctor Hugh Finn, Professor William Bill Sherwin Project funding This research was made possible through the financial commitment of the Swan River Trust, with additional financial support from the Fremantle Harbour Ports and Murdoch University. Stipend Australian Postgraduate Award (APA) Murdoch Strategic Top-up Contribution to data chapters Chapter 2 – Applying the Multistate Capture-recapture Robust Design to assess metapopulation structure of a marine mammal: Delphine Chabanne collected and analysed the data and wrote the manuscript. Professor Kenneth Pollock advised on the analysis. Professor Kenneth Pollock, Doctor Hugh Finn and Professor Lars Bejder critically reviewed the manuscript. Chapter 3 – Identifying the relevant local population for environmental impact assessments of mobile marine fauna: Delphine Chabanne collected and analysed the data and wrote the manuscript. Professor Lars Bejder advised on the analysis. Doctor Hugh Finn and Professor Lars Bejder critically reviewed the manuscript. Chapter 4 – Genetic structure of socially and spatially discrete subpopulations of dolphins (Tursiops aduncus) in Perth, Western Australia: Delphine Chabanne collected and analysed the data and wrote the manuscript. Doctor Simon Allen contributed to the biopsy data collection. Delphine Chabanne, Doctor Celine Frère and Bethan Littleford-Colquhoun conducted the genetic laboratory work. Professor William Sherwin advised on the analysis. Professor William Sherwin, Doctor Hugh Finn and Professor Lars Bejder critically reviewed the manuscript. v Chapter 5 – Population genetic structure and effective population sizes in Indo- Pacific bottlenose dolphin (Tursiops aduncus) in southwestern Australia: Delphine Chabanne analysed the data and wrote the manuscript. Doctor Simon Allen, Anna Sellas, and Dee McElligot contributed to the biopsy data collection. Claire Daniel and Doctor Oliver Manlik conducted the genetic laboratory work. Doctor Oliver Manlik and Professor William Sherwin advised on the analysis. Doctor Oliver Manlik, Professor William Sherwin, Doctor Hugh Finn and Professor Lars Bejder critically reviewed the manuscript. This thesis is presented as a series of four manuscripts in journal format, in addition to a general introduction and general discussion. Ethics statement This study was carried out with approval from the Murdoch University Animal Ethics Committee (W2342/10 and R2649/14) and was licensed by the Department of Parks and Wildlife (SF008067, SF008682, SF009286 and SF009874). Biopsy sampling for molecular analyses were carried out as a part of broader study, with data collected in accordance with the Murdoch University Animal Ethics Committee approval (W2076/07; W2307/10; W2342/10 and R2649/14), and collected under research permits (SF005997; SF006538; SF007046; SF007596; SF008480; SF009119: SF009734; SF010223) licensed by Department of Parks and Wildlife. vi Acknowledgements The completion of this PhD marks the end of a long and eventful journey and could not have been possible without the guidance and support from many people, especially during the last few months. I have met so many people throughout this journey: some that were around from the beginning to the end and others that I briefly met along the way. To everyone, thank you so much for your contribution, big or small, it has significantly helped me to get through it. I would like to thank Lars Bejder and Hugh Finn for not giving up on me when I was about to embark on a different adventure. Your guidance and suggestions during the planning and writing up of the thesis were invaluable and helped me improve my critical thinking and scientific writing (well, I hope so!). I’m particularly grateful to both of you for your understanding and encouragement during my chaotic last few months. To Lars, thank you for trusting me for many years and giving me the opportunity to be part of the team (again). To Hugh, thank you for sharing so many of your anecdotes with me. Our discussions have always helped me to find the right direction and given me more confidence. Sincere thanks to Bill Sherwin, for accepting to be my genetic mentor and making me part of his team. Bill, I have learnt so much over our Skype conversations and the weekly lab meetings with your students. Also, thanks go to Oliver Manlik for taking the time to discuss genetic data and provide some advice. To Celine Frère, thank you for introducing me to the genetic world. You welcomed me in your lab where I had the privilege to experience the genetic lab work, learn how to process and analyse data and have brainstorming sessions where your expertise was much appreciated. A special thanks to Kenneth Pollock for teaching me what I know about mark- recapture. It has been a privilege to work with you, Ken. Our discussions on multistate mark-recapture and your enthusiasm for my research have inspired me. I wish you all the best in your retirement. vii I am particularly grateful to Holly Raudino for giving me the opportunity to assist her during her PhD in Bunbury (WA). You taught me the essentials I needed to pursue my own project. You helped me to step up in my goals by trusting me and letting me lead the fieldwork when you were writing up your thesis. You took me under your wing and always made sure that I was OK and still do. Your ongoing support means a lot to me. In that learning process, I’m also very much thankful to Simon Allen for taking the time to teach me how to biopsy a dolphin and for sharing many of your fieldwork experiences. I will forever thank you for caring, listening and giving me advice when unexpected things occurred. My fieldwork would not have been possible without the dedicated help from many assistants and interns. Thank you all for keeping the motivation up and countless hours collecting and processing data. In alphabetical order, thank you to: Ana Carolina Andrade, Emmeline Audic, Rebecca Bakker, Bronte Bates, Maree Bekkers, Anna Bendz, Martin Binet, Lisa Binks, Alex Brown, Jacklyn Buchanan, Dennis Buffart, Joanna Burgar, Anita Byrone, Rene Byrskov, Elizabeth Chabanne, Sharon Chan, Manon Chautard, Elisa Chillingworth, Lucie Chovrelat, Ana Costa, Alicia day, Aurelien Delume, Brechtje de Schipper, Georgie Dicks, Gwenael Duclos, Vivienne Foroughirad, Julia Friese, Hayley Gamble, Beatriz Gemez, Kate Greenfeld, Olivia Hamilton, Nora Handrek, Daniella Hanf, Emily Hanley, Lisa-Marie Harrison, Lauren Hawkins, Joe Heard, Nikki Hume, Lonneke IJsseldijk, Kim Jaloustre, Camille Jan, Vanessa Jaith, Ben Jenhinson, Maria Carmen Jimenez, Martyn Kelly, Anna Kopps, David Kranitz, Krista Krijger, Alexis Levengood,
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