Evaluating genetic diversity in the critically endangered orange-bellied parrot: informing species management Caitlin Eleanor Morrison A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy February School of Life and Environmental Sciences, Faculty of Science The University of Sydney Australia 1 DECLARATION I declare that this thesis is the result of my own work and has not been submitted for another degree or qualification. All information derived from published or unpublished work of others has been acknowledged in the text, and a list of references is given at the end of this thesis. Caitlin Morrison November i ACKNOWLEDGEMENTS Firstly, I would like to thank my supervisors, Catherine Grueber, Carolyn Hogg and Rebecca Johnson, for their guidance, support and compassion throughout my PhD. I have been so lucky to have three such attentive, supportive, passionate and intelligent role models. Thank you for demonstrating to me such a variety of different ways to be a scientist, and to be strong. I’m deeply grateful. Thank you also to my family. Thanks to my Mum, for showing me the power of stopping to really look, and the value and importance of scientific thinking. Thanks to my Dad, for his unending curiosity, in everything - and thank you to both of you for teaching me the value of education, and how to find, in nature, a constant source of wonder. This sustains me. Thank you to Amy, my sister, my best friend, for bravely forging the path ahead, even when you weren’t sure about it. I am happy to be walking in your footsteps, and I’m proud of you every day. Thank you to Robin and Imogen, for so often being on the other end of a phone, for being on my team, and for having my back. Even when you’re not near, knowing you’re there makes a world of difference. Thanks also to Michael, for our friendship, for making Sydney more like home, and for listening to all the stories. Life would have been different here without you. A very big thanks must also go to my colleagues and office-mates at the Australian Museum – Greta, Mark, Sally, and all the other members of the Australian Centre for Wildlife Genomics and AMRI. I’ve been so lucky to end up in a workplace so full of beautiful, decent, genuine people, who have so much knowledge, and are so generous with it. Thank you for caring so deeply. A special thanks to Greta, for always looking out for me. You all inspire me. Thanks also to the other PhD students, at the Museum and at the University of Sydney. To Alex, Kyle, Amber, Belinda, Emma, Bec, Kate, Rowena, Elle, Parice, and all other members of the Australasian Wildlife Genomics Group during my time there, thank you for helping me feel less alone. I’m excited to see where all of your science ii journeys lead, and I’m pleased that the world has you to work on some of its challenges. I know you will all go on to do amazing things. Thank you to members of the Orange-bellied Parrot Recovery Team, in particular to Rosemary Gales for hosting me in Tasmania, as well as Shannon Troy and Annika Everaardt for generously sharing information and samples with me. Thanks also for all your work on the OBP over many years. Thank you to Judith Clarke, Annie Philips and David Phalen for sharing veterinary information and additional samples. Thank you to Museum Victoria, the Australian National Wildlife Collection, the Australian Museum and associated staff for frozen tissue loans. Thank you also to the funding bodies which made my research possible: BirdLife Australia, Linnean Society NSW, Nature Foundation SA, the Wettenhall Environmental Trust, Zoos Victoria, the University of Sydney and the Australian Museum. Finally, for the OBPs, and for our wildlife, everywhere. For all that I write about inbreeding depression in an abstract way, I know the real face of it is individual suffering. So to all those individuals who are suffering: from the impacts of inbreeding depression, for the sake of furthering human knowledge, or because we’ve destroyed your habitat, taken away your food or introduced compatriots which you can’t escape or outcompete, I’m sorry. I hope we can keep working out how to make it better. And I hope we can do better, from here. “The best of us are cursed with caring, with a bungling and undying determination to protect whatever looks like beauty, even if our vision is blurry.” - Jon Mooallem, Wild Ones To all those who care, whether they want to or not: thank you, and keep going. This planet, and the myriad of astonishing beings with which we share it, are everything. They’re worth understanding - and they’re worth protecting. iii TABLE OF CONTENTS Declaration ....................................................................................................................... i Acknowledgements ......................................................................................................... ii Table of contents ............................................................................................................ iv A note on the style and layout of this thesis ................................................................ vii Author contributions ................................................................................................... viii Abbreviations ................................................................................................................... x List of tables .................................................................................................................... xi List of figures ................................................................................................................. xii Abstract ............................................................................................................................ Chapter : Introduction .................................................................................................. . Phylogenetic context ............................................................................................ . Distribution and migration .................................................................................. . OBP population history ........................................................................................ .. Population size ............................................................................................... .. Threats and reasons for decline .................................................................... .. Management: establishment of captive population ................................... . Inbreeding and loss of genetic diversity ............................................................ . Recent population management ......................................................................... .. Species management circa ................................................................. .. OBP population genetic studies .................................................................. .. Founder intake / ........................................................................... . Infectious disease affecting the OBP ................................................................. .. Psittacine beak and feather disease............................................................. .. Other infectious agents detected in the OBP ............................................. . Recent OBP status ............................................................................................. . Thesis overview ................................................................................................... .. Genome-wide genetic diversity ................................................................... .. Functional diversity ..................................................................................... .. Genetics and inbreeding depression ........................................................... .. Phylogenetic analyses .................................................................................. . Closing remarks .................................................................................................. iv Chapter : Genetic impacts of conservation management actions in a critically endangered parrot species ................................................................................................ . Background .............................................................................................................. . Main article .............................................................................................................. Chapter : Impact of low innate immune-gene diversity in the critically endangered orange-bellied parrot (Neophema chrysogaster) ............................................................. . Background .............................................................................................................. . Main article .............................................................................................................. Chapter : Heterozygosity, reproductive fitness and disease response in a critically endangered Australian parrot .......................................................................................... . Background .............................................................................................................. . Main article .............................................................................................................. Chapter : Phylogenetic position of the critically-endangered