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Population Structure and Mating System of the Australian Sea Lion (Neophoca Cinerea) Heidi Ahonen

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Population Structure and Mating System of the Australian Sea Lion (Neophoca Cinerea) Heidi Ahonen Population structure and mating system of the Australian sea lion (Neophoca cinerea) Heidi Ahonen To cite this version: Heidi Ahonen. Population structure and mating system of the Australian sea lion (Neophoca cinerea). Neurons and Cognition [q-bio.NC]. Université Paris Sud - Paris XI; Macquarie university (Sydney, Australie), 2013. English. NNT : 2013PA11T059. tel-01070276 HAL Id: tel-01070276 https://tel.archives-ouvertes.fr/tel-01070276 Submitted on 1 Oct 2014 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITE PARIS-SUD ÉCOLE DOCTORALE : ED 419 BioSigne Laboratoire Centre de Neurosciences Paris Sud (CNPS) DISCIPLINE Neurosciences THÈSE DE DOCTORAT soutenue le 30/09/2013 par Heidi AHONEN Population Structure and Mating System of the Australian sea lion ( Neophoca cinerea ) Directeur de thèse : Thierry AUBIN DR (CNRS, UMR 8195, Univ. Paris Sud XI) Co-directeur de thèse : Adam STOW PR (Macquarie University, Sydney, Australia) Composition du jury : Président du jury : Sylvie GRANON PR (CNRS, UMR 8195, Univ. Paris Sud XI) Rapporteurs : Fritz TRILLMICH PR (Univ Bielefeld, Bielefeld, Allemagne ) Martin WHITING PR (Macquarie University, Sydney, Australia) Examinateurs : Isabelle CHARRIER CR (CNRS, UMR 8195, Univ. Paris Sud XI) TABLE OF CONTENTS STATEMENT OF CANDIDATE ……………………………………………………………………………………… ..3 STATEMENT OF CONTRIBUTION ……………………………………………………………………………... ....4 ACKNOWLEDGEMENTS ………………………………………………………………………………………………..5 EXTENDED SUMMARY ………………………………………………………………………………………………… 9 RÉSUMÉ ÉTENDU ………………………………………………………………………………………………………. 12 CHAPTER 1: Introduction ……………………………………………………………………………………………16 Genetic structure and dispersal capacity in highly mobile organisms …………………………17 Land-breeding marine animals and possible processes driving genetic structure ………19 Vocalisation and social structure -alternative way to look differentiation …………………. 21 Australian sea lion as study species ……………………………………………………………………………24 Acoustic vocalisation in male Australian sea lion ………………………………………………………. 29 Thesis rationale and aims ………………………………………………………………………………………… ..31 Additional data as Appendices ………………………………………………………………………………… ..32 CHAPTER 2: Materials and Methods …………………………………………………………………………. 34 Study sites …………………………………………………………………………………………………………………35 Animal identification and marking …………………………………………………………………………… .38 Genetic sample collection …………………………………………………………………………………………42 Laboratory procedures and genetic data analyses …………………………………………………… .45 Acoustic sample collection ……………………………………………………………………………………… ..47 Analysis of acoustic parameters ……………………………………………………………………………… ..49 CHAPTER 3: Characterization of 12 novel microsatellite loci and cross-amplification of four loci in the endangered Australian sea lion (Neophoca cinerea) ………………………… .52 Abstract …………………………………………………………………………………………………………………… .53 Introduction ………………………………………………………………………………………………………………53 Materials and Methods ……………………………………………………………………………………………. .54 Results and Discussion ………………………………………………………………………………………………. 55 CHAPTER 4: Local Lads: Spatial genetic structure in male Australian sea lions (Neophoca Cinerea) …………………………………………………………………………………………………………………… .57 Abstract …………………………………………………………………………………………………………………… ..58 Introduction ……………………………………………………………………………………………………………….58 Materials and Methods ………………………………………………………………………………………………62 Results ……………………………………………………………………………………………………………………… .67 Discussion ………………………………………………………………………………………………………………… .77 1 CHAPTER 5: The sound remains the same? Adult male Australian sea lion barking calls reveal clear geographic variations that do not reflect known genetic structure ………… 84 Abstract ……………………………………………………………………………………………………………………..85 Introduction ……………………………………………………………………………………………………………….85 Materials and Methods ………………………………………………………………………………………………89 Results ……………………………………………………………………………………………………………………….95 Discussion ………………………………………………………………………………………………………………..105 CHAPTER 6: Sharing the love: paternity analysis within and between three Australian sea lion colonies …………………………………………………………………………………………………….. .113 Abstract ……………………………………………………………………………………………………………………114 Introduction ……………………………………………………………………………………………………………..115 Materials and Methods …………………………………………………………………………………………...120 Results ……………………………………………………………………………………………………………………..129 Discussion ………………………………………………………………………………………………………………..142 CHAPTER 7: General discussion ………………………………………………………………………………..148 REFERENCES …………………………………………………………………………………………………………….168 APPENDIX 1 …………………………………………………………………………………………………………… ..184 APPENDIX 2 ……………………………………………………………………………………………………………..185 APPENDIX 3 ……………………………………………………………………………………………………………..186 APPENDIX 4……………………………………………………………………………………………………………..187 APPENDIX 5……………………………………………………………………………………………………………..188 APPENDIX 6 ……………………………………………………………………………………………………………..196 2 STATEMENT OF CANDIDATE I certify that the work in this thesis has not previously been submitted for a degree nor has it been submitted as part of requirements for a degree to any other university or institution other than Macquarie University. I also certify that the thesis is an original piece of research and it has been written by me. Any help and assistance that I have received in my research work and the preparation of the thesis itself have been appropriately acknowledged. In addition, I certify that all information sources and literature used are indicated in the thesis. The research presented in this thesis was approved by DEH SA Wildlife Ethics Committee (44/2008) and conducted under permission obtained from Department for Environment and Heritage, South Australia (permit number Z25675) and Department of Environment and Conservation, Western Australia (DEC WA License SF007255 and SF008193). Heidi Ahonen Date: 16.7.2013 3 STATEMENT OF CONTRIBUTION General Introduction, General Materials and Methods and General discussion are written by me with feedback from my principle supervisors. The majority of the lab work was carried out by me. I want to acknowledge the contributions of following people who have been working under my supervision to help complete parts of this study: Jessica Boomer, Heather Baldwin, Siobhan Dennison, Anne- Sophie Lafuite, Lara Paranhos and Simon Giuliano. Chapter 3 : Characterization of 12 novel microsatellite loci and cross-amplification of four loci in the endangered Australian sea lion ( Neophoca cinerea ) Ahonen, H., Lowther, AD., Goldsworthy SD., Harcourt RG., Stow AJ. 2012 Characterization of 12 novel microsatellite loci and cross-amplification of four loci in the endangered Australian sea lion (Neophoca cinerea). Conservation Genetic Resources 5:283-285 Conception: 95%, Data Collection: 100%, Analysis: 90%, Writing: 95% Chapter 4: Local Lads: Spatial genetic structure in male Australian sea lions (Neophoca Cinerea) Conception: 95%, Data Collection: 100%, Analysis: 90%, Writing: 95% Chapter 5 : The sound remains the same? Adult male Australian sea lion barking calls reveal clear geographic variations that do not reflect known genetic structure Conception: 95%, Data Collection: 100%, Analysis: 100%, Writing: 95% Chapter 6: Sharing the love: paternity analysis within and among three Australian sea lion colonies Conception: 95%, Data Collection: 100%, Analysis: 95%, Writing: 95% 4 ACKNOWLEDGMENTS There are many people that helped and supported me during this journey and to all of them I owe much gratitude. Firstly I would like to thank my supervisors Adam Stow and Isabelle Charrier whose expertise, guidance, understanding and patience have been invaluable during this PhD. Adam, eight years ago you welcomed me with open arms into your group, gave me the opportunity to explore the world of research and encouraged me to go forward. Years have passed, but I will never forget how it all started. Isa, you introduced me to the world of acoustic communication and offered friendship and support in every situation. You also showed me the French way of living and made sure my time in Paris was wonderful. I am also grateful for Rob Harcourt and Simon Goldsworthy for their guidance and support in different stages throughout my candidature. You have introduced the world of Australian sea lions to me and given me an adventure of a lifetime. Thank you also Simon for welcoming me to SARDI, giving me a place to work and showing me the joys of Adelaide. I want to especially thank Andy Lowther and Ben Pitcher, my fellow Australia sea lion researchers. You showed me the way and shared many of these adventures with me. I am grateful of the advice and guidance, but also all the fun time we had in the field. During this PhD I have been lucky to be able to be part of three excellent research teams: the Marine Mammal Research Group and the Conservation Genetics Group at Macquarie University and the Bioacoustics Team at l'Université Paris Sud. Thank you for making me 5 feel welcomed and as a part of each of the teams. I have met so many wonderful people and hope our paths will still cross in the future. I would like to express my special gratitude to The Bioacoustics
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