Molecular ecology of hawksbill turtles Eretmochelys imbricata in the Seychelles Karl Peter Phillips Thesis submitted for the degree of Doctor of Philosophy University of East Anglia UK School of Biological Sciences September 2013 © This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derived there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. Thesis abstract Molecular genetics are an invaluable tool in whole-organism biology, allowing the indirect investigation of life history traits and evolutionary processes that are otherwise unobservable. In this thesis, I apply molecular genetic techniques to the study of the hawksbill sea turtle Eretmochelys imbricata, using a population in the Republic of Seychelles. My aim in this study was two-fold. Firstly, to better characterise certain key aspects of the hawksbill’s life history and demography, with a view to better informing hawksbill conservation. Secondly, to test several hypotheses relating to broader evolutionary questions, e.g. regarding the forces shaping mating systems and the link between individual genetic variability and fitness. I found that the majority of females were fertilised by a single male each, and that they used stored sperm to fertilise all of their multiple clutches across a nesting season. There was no evidence of females biasing paternity towards males with particular genetic properties (variability, dissimilarity), suggesting that females are not using sperm storage to promote sexual selection. Males were rarely seen to fertilise more than one female in the study, suggesting low reproductive skew and a large male population that is mobile and/or dispersed. Females at nesting beaches spanning 450 km comprised a single genetic stock, but males were more dispersive than females. I found that the effective size of the population was relatively large, and did not show signs of inbreeding or loss of genetic variation following the substantial reduction in hawksbill numbers caused by historic overhunting. Finally, I found that both male genetic variability and parental genetic dissimilarity can predict nest success, but in a way that might select for a stabilised level of genetic variability. I discuss the implications of these results for both evolutionary biology and the ongoing conservation management of a species internationally listed as critically endangered. i Acknowledgements Acknowledgements Expressing one’s gratitude for a decent supervisor is a difficult task, but extremely decent David Richardson has been over these last four years, and extremely difficult it is to think how to thank him for all that. For his mentoring, for his patience (lots of this!), and for his ability to strip away [my] waffle (lots of this!) and expose the scientific bones underneath, I will be ever grateful. My thanks also to my second supervisor Tove Jorgensen for all her help in getting me this far. I apologise again for once using casual bad language in front of their children! I thank all the members of the Richardson research group over my time at UEA. They are some of the best people I will ever meet, both as friends and as scientists: Lewis Spurgin, Emma Barrett, Dave Wright, Martijn Hammers, Sjouke Anne-Kingma, Cata Gonzalez-Quevedo, David Padilla, Ellie Fairfield, Danni Gilroy, Kat Bebbington, Ada Natoli, Michelle Simeoni and Helena Batalha. I also thank Tracey Chapman’s research group for helping me better ‘get’ mating systems in the early stages of my project – especially Amanda Bretman and Claudia Fricke. I thank all of the other great characters and great friends (many both!) with whom I have spent considerable time at UEA. At the head of the list are Jacob Holland and Becky Laidlaw. We started together, finished together, and have shared each others’ ups and downs of Ph.D. life. They are two top-notch friends. In the office I also thank Janet Mason, Lucy Friend, Mohammad Albeshr, Henry Ferguson-Gow, Christiana Faria, and the immortal Conrad Gillett, for distractions, directions, diversions, and general companionship. In the wider corridors, and this is not an exhaustive list, I thank Alice, Alicia, Aly, Amy, Anna, Cat M, Damian, Danni P, Dave C, Freydis, Iain, Kitson (James), Lotty, Martin, Mike, Phil L, Phil S, Sarah M, Sarah Y, Siân, Tom, Will, and the faculty members, all forever burned into my consciousness in nothing but a positive way. A special extra ‘thank you’ to Kitson for the crash-course in word processing that helped me ‘beautify’ my thesis! ii Acknowledgements My thanks to an exceptional friend in Tim Huggins. One day somebody will write a book about him. Thank you also to Neil and Steve for being decent housemates, on the occasions I left UEA and went home! Thanks to those variously mentioned above who have helped me through my more difficult times. I won’t name you again here – I just want to reaffirm my enduring appreciation for your support. Away from UEA, I thank the staff and management of Cousine Island, Seychelles, for starting the project, for helping navigate Seychelles bureaucracy, for collecting so many of the samples, and for supporting my stay on the island. In particular, I thank the managers Jock and Janine Henwood, the owner Fred Keeley, and, most especially, the conservation wardens Kevin and San- Marie Jolliffe. Quite what they made of my scrawny, gangly, excruciatingly pale form when it first jumped on to Cousine’s beach, with a silly hat and large camera, I don’t know, but they showed it great hospitality nonetheless. It was a privilege to work with them, and to thereby be able to work with my study species ‘in the flesh’. I thank the current management team of Cousine, and the new conservation warden Julie Gane, for their continued support. Also in Seychelles I thank Jeanne Mortimer, for advising on various research proposals, for helping with Seychelles bureaucracy, for sharing unpublished data, and for orchestrating the collection of samples from beyond Cousine. Across those other islands, I thank, P-A Adam, T Jupiter, A Nahaboo, D Jupiter, A Duhek, R Jeanne and Island Conservation Society (Desroches, Alphonse, St François Islands); D’Arros Research Centre for enabling Jeanne to collect samples on D’Arros and St Joseph Islands; G Canning and T Raposo (Frégate Island); L Vanherck (North Island); and J van de Crommenacker, N Bunbury and Seychelles Island Foundation (Aldabra). I thank Sarah Vargas, Mike Jensen and Nancy FitzSimmons for sharing unpublished data with me. iii Acknowledgements I was blessed with spending several months at the NERC Biomolecular Analysis Facility at the University of Sheffield, where I performed the greater part of my lab work. Chiefest of thanks to Andy Krupa (for technical support and for once letting me camp in his garden), as well as to Deborah Dawson, Gavin Horsburgh, Alain Frantz, Lucy Wright (for the use of her primers!), and Terry Burke. I also thank Steph Hodges and Jodie Crane. By putting me up in their spare room they gave me a home-while-away-from-home, and I can’t put a value on what that meant. I thank the folk at the UEA Research Computing Service for supporting my use of the High Performance Computing Cluster, and answering all my inane ‘this doesn’t work’ questions. Similar thanks go to Jinliang Wang of ZSL for answering my many, many questions about the programme COLONY. I thank my thesis examiners Annette Broderick and Martin Taylor for three hours of challenging but enjoyable discussion on my project, and for their suggestions that improved the presentation of the finished product. I also thank Fred Janzen, Jon Slate, and two anonymous reviewers for helpful comments on chapter 2 during its peer review for publication. I thank my funders: the UEA Dean of Science for my scholarship, the Natural Environment Research Council for the molecular work, and Cousine Island for considerable in-kind support. I also thank everybody whose financial support allowed me to attend and speak at several conferences: the John & Pamela Salter Charitable Trust, the Richard Warne Memorial Fund, the International Sea Turtle Symposium, and the International Society for Behavioral Ecology. Finally, last but not least, I thank Old Mother Phillips, Father Bear, and my brother Kurt, for everything they’ve ever done for me that has allowed me to get to this point. I love them all. iv Chapter contributions and publications Chapter contributions and publications All parts of this thesis have been written by Karl Phillips, in consultation with David S. Richardson and Tove Jorgensen. Chapter 3 was also written in consultation with Jeanne Mortimer (Island Conservation Society and University of Florida). The idea of a hawksbill turtle molecular ecology project was initiated by David S. Richardson after a conversation with Jock Henwood of Cousine Island. Below are estimates of percentage contributions to the initial concepts, specific planning, data collection (‘conducting’), and data analysis, as well as the publication status, for each chapter. Chapter 2: published as Phillips KP, Jorgensen TH, Jolliffe KG, Jolliffe S-M, Henwood J, Richardson DS (2013) Reconstructing paternal genotypes to infer patterns of sperm storage and sexual selection in the hawksbill turtle. Molecular Ecology 22: 2301-2312. In the thesis, the ‘Methods’ section from the publication has been replaced with a reference to the thesis ‘General methods’. Concept: D Richardson 50%, K Phillips 50% Planning: D Richardson 30%, J Henwood 20%, T Jorgensen 10%, Cousine Island staff 10%, K Phillips 30% Conducting: Cousine Island staff 30% (field), K Phillips 70% (20% field, 50% laboratory) Analysis: K Phillips 100% Chapter 3: in revision following rejection by Biological Conservation.