University of Bath PHD Population genetic consequences of mating systems and dispersal D'Urban Jackson, Josephine Award date: 2019 Awarding institution: University of Bath Link to publication Alternative formats If you require this document in an alternative format, please contact: [email protected] General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 08. Oct. 2021 Population genetic consequences of mating systems and dispersal Josephine D’Urban Jackson A thesis submitted for the degree of Doctor of Philosophy University of Bath Milner Centre for Evolution Department of Biology and Biochemistry September 2018 Copyright notice Attention is drawn to the fact that copyright of this thesis rests with its author. A copy of this thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and they must not copy it or use material from it except as permitted by law or with the consent of the author. Declaration of any previous submission of the work The material presented here for examination for the award of a higher degree by research has not been incorporated into a submission for another degree. Candidate’s signature ………………………………………………. Declaration of authorship I am the author of this thesis, and the work described therein was carried out by myself personally, with the exception of Chapters 2-5 (data chapters) where my contribution was between 75-90%. In these chapters 25-10% of the work was carried out by co- authors, see the Statement of Authorship before each chapter for details. Candidate’s signature………………………………………………. 2 Contents Acknowledgements 4 Thesis Summary 6 Chapter 1 Introduction 7 Overview and objectives 19 Chapter 2 Polygamy slows down population divergence in shorebirds 34 Abstract 37 Article 38 References 51 Supplementary Material 63 Chapter 3 Population differentiation and demography of the threatened 80 snowy plover Charadrius nivosus Abstract 83 Article 84 References 104 Supplementary Material 113 Chapter 4 Genomic signatures of classical polyandry in Actophilornis 122 jacanas Abstract 125 Article 126 References 147 Supplementary Material 157 Chapter 5 Ecology, evolution and threat status of the Madagascar jacana. 169 Abstract 172 Article 173 References 188 Supplementary Material 194 Chapter 6 Discussion 199 Appendix I Dynamics and genetics of a disease- driven species decline to 216 near extinction: lessons for conservation. Hudson et al. 2016 Appendix II An integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding 217 turnover in an endangered avian population. Hou et al. 2018 A thesis commentary is presented before and after Chapters 2-5. 3 Acknowledgements This PhD has taken me all over the world and introduced me to so many incredible people who have all played vital roles in this thesis. There are too many people to name them all but I am so grateful for the help they have given me, this thesis is for you all. To Mike, Tamás and Clemens, Thank you for handing me this golden ticket. I am extremely grateful that you provided me the opportunity, encouragement and space in which to develop as a scientist. I have learnt so much from you all and hope we can continue as collaborators in the future. I am so grateful to you for supporting me to pursue my avenues of interest…even when they are not the safest of bets! Tamás, you may be right that plovers are a model field organism to work with, but nothing beats the adrenaline of dodging crocs, hippos and bilharzia for those jacanas! To Sama, Thank you for making the Madagascar field work possible. You are a brilliant, devoted, and highly talented scientist, thank you for sharing some of your knowledge with me. The field work we conducted is definitely a highlight of the past four years. As you said to me before I left for Madagascar, “this will be a great adventure” and I think you spoke for my whole PhD experience. To my Cardiff lab ladies, men, and fish and dog- past and present, As I sit here in the office all alone during OnE away day, I have been thinking of what amazing people you all are and how lucky I am to have friends who are also my colleagues. There have been such fun times, I honestly don’t want them to end. I could not have done this without you (and it’s not even over yet!) and I for that I am eternally grateful. Although I have not experienced many other labs, I am sure that the unquestioned guidance and support everybody gives to one another here is one of the most uniquely fantastic traits of C5.15, and I will be singing your praises wherever I end up. Thank you so much for putting up with my obsession with celebrity gossip, eating of all your food (most of you probs don’t even realise I did that; not yours Gilson), lack of physical contact, and lab meeting niggles. Please promise me you will continue to jump out of boxes, hide Gilson from Mark Lewis, pour water over dry ice to look like real scientists, get Nia so pi**ed she can’t remember where she locked her bike, write blanket emails, reply-all, and generally be the marvellous humans you are. I know I will be back at some point so I am not going to say goodbye, just keep my seat warm (and Gilson alive). I can’t name you all but here are some special thank yous. Isa thank you for your eternal wisdom, amazing teaching skills, angelic singing voice, and generally making the whole lab function. To Mafalda for feeding me endless Portuguese tarts, welcoming me into the Frozen Ark team, showing me that despite being a scientist, you can still believe in star signs, electrifying traffic lights and “close” family relations ;P. To Pablo for kindly being proud that I was your first student and always being there for my mild breakdowns. To Frank for, as Nia said recently, your mysterious ability to know more about our mental states than we know ourselves, always looking out for us, and your patience and willingness to offer advice and support at all times – sorry that it was usually more than “just a quick question”. To my little Rose for genuinely keeping me afloat when things were tough, your optimistic outlook on life and for you – also - being a wonderful human. To Nia showing me the way of the bikes, all the adventures, times you have fed me, introducing me to loads of awesome people and your perpetual positivity – please do not change one bit. To Sophie for your friendship, hilarious worrying abilities, wonderful tea making skills and introducing me to climbing with Lorna. To Kath, you are just so wise, colourful and such a strong person, the world needs more people like you! To Isa P, it’s such a shame we didn’t have more time in the lab together, but for the little time we did, you really made it better! To Hannah, Niall, Dave, Mario and Pier, although you aren’t in the lab anymore, you taught me the fundamentals of this place and my first couple of years here with you were so much fun! Long live #BrufordKingdom. To my GW4 buddies, I think the best thing to come out of this DTP program is the support of you all in this last year and I am so grateful for it. Even though we are a big mix of ecologists, geologists, chemists and more, I feel like we have been a team through this process, all the way from those hotdogs in Newquay to dressing up like real adults 4 at the ball. I am so glad to have shared this experience with you. A particular thankyou to Katy for being a great friend and colleague, always answering my panicked text message, that video, and for tag teaming Bath! To Mumma, Tim and Matthew, Thank you for being there for me all this time, for nodding when I speak to you about genetics and for not asking me, “so what are you going to do afterwards?”. Thank you mumma for the making the decision to build that frog pond all those years ago and for always supporting us in whatever we choose to do, “do what you love” is the best advice you could have given us, and I am so grateful for that. You are such a strong, generous and kind person and I hope I can make you proud. And especially to Tim and Mathilde for housing, feeding and generally looking after me in this last month! To my non-sciencey friends, I am almost 95% sure you still think my PhD is on frogs. Sorry I have been really rubbish recently, I promise I will be better soon! I know for the last few years I flutter on the periphery of your lives but I am so grateful that we have such amazing friendships that when I come home it is like not a moment has passed! A particular thank you to Cat, Dom, and Felicity, those packages made me overwhelmingly happy! You are such kind people, always there even when I have gone a bit off the radar.