ResearchOnline@JCU This file is part of the following reference: Todd, Erica V. (2013) Evolutionary biogeography of Australian riverine turtles: Elseya spp. and Emydura macquarii krefftii. PhD thesis, James Cook University. Access to this file is available from: http://researchonline.jcu.edu.au/39211/ The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owner of any third party copyright material included in this document. If you believe that this is not the case, please contact [email protected] and quote http://researchonline.jcu.edu.au/39211/ EVOLUTIONARY BIOGEOGRAPHY OF AUSTRALIAN RIVERINE TURTLES: ELSEYA SPP. AND EMYDURA MACQUARII KREFFTII Thesis submitted by Erica V. Todd BSc Biology Honours (1st Class), Central Queensland University in June 2013 for the degree of Doctor of Philosophy in the School of Marine & Tropical Biology James Cook University STATEMENT OF ACCESS I, the undersigned, author of this work, understand that James Cook University will make this thesis available for use within the University Library and, via the Australian Digital Thesis network, for use elsewhere. I understand that, as an unpublished work a thesis has significant protection under the Copyright Act and; I do not wish to place any further restriction on access to this work. Erica V. Todd June 2013 i STATEMENT OF ORIGINALITY I declare that this thesis is my own original work and has not been submitted in any form for another degree or diploma at any university or other institution of tertiary education. Information derived from the published or unpublished work of others has been acknowledged in the text and a list of references is given. Erica V. Todd June 2013 ii STATEMENT OF CONTRIBUTION BY OTHERS Supervision Principal supervisors Professor David Blair and Professor Dean Jerry, and co-supervisors Dr Mark Hamann and Dr Kyall Zenger, provided editorial comments on all sections of this thesis and contributed to the original project conception and design. Co-authorship Chapter 2 – David Blair, Dean Jerry and Mark Hamann contributed editorially and to the original experimental design. Chapter 3 – Sharon Farley, under supervision of Arthur Georges, Nancy FitzSimmons, Lachlan Farrington and Col Limpus, generated data for an additional five microsatellite loci that were incorporated into the published version of this chapter. LF also contributed haplotype data used to diagnose the translocated origin of a peripheral population. David Blair and Dean Jerry contributed to the original project design. DB, DJ, AG and NF contributed editorially. Chapter 4 – Arthur Georges provided sequence data for New Guinean species and the R35 locus. Vimoksalehi Lukoschek assisted with molecular dating analyses. David Blair and Dean Jerry contributed to the original project design. All contributed editorially. Chapter 5 – David Blair and Dean Jerry contributed editorially and to the project design. Further assistance Kyall Zenger performed the clean-up and de novo assembly of sequence data used in Chapter 2. Robert Puschendorf provided editorial comments on Chapter 3. Robert Puschendorf and Adella Edwards assisted with GIS applications and figure preparation. Arthur Georges, Ivan Lawler, Jason Schaffer, Alastair Freeman, the Northern Territory Museum, and Eridani Mulder all provided tissue samples for analysis. Financial and in-kind support Project funding was contributed by: Wildlife Preservation Society of Australia, Wildlife Preservation Society of Queensland, Peter Rankin Trust Fund for Herpetology within the Australian Museum, and the Skyrail Rainforest Foundation. The Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER) and the School of Marine and Tropical Biology at James Cook University, provided project funding and in-kind support. I was a recipient of an Australian Postgraduate Award (APA) and a Queensland Government Smart Futures PhD Scholarship (Top Up). iii DECLARATION OF ETHICS The research presented and reported in this thesis was conducted in compliance with the National Health and Medical Research Council (NHMRC) Australian Code of Practice for the Care and Use of Animals for Scientific Purposes, 7th Edition, 2004 and the Qld Animal Care and Protection Act, 2001. The proposed research received animal ethics approval from the JCU Animal Ethics Committee. Approval Number: A1444. iv ACKNOWLEDGEMENTS The generation of this thesis was immensely challenging, but also very enjoyable and fulfilling. Many people contributed to its development in different ways, and are deserving of my thanks. Firstly, my deep gratitude goes to my Oma and Opa, who through many hours of wildlife documentaries, distilled in me a love of the natural world from an early age. This passion was continued by my parents, through their love of natural places. My primary supervisors, David and Dean, I thank for their continued intellectual support and encouragement, from beginning to end, and for their habitual lightning-speed turnaround of drafts. David, your passion for patterns in geography and biodiversity was always inspiring. Dean, your practical approach helped me finish in good time, and you always made your students a high priority. My thanks also go to my co-supervisors, Mark and Kyall. Although I didn’t call on you often, your doors were always open when I needed to chat. I am grateful to many other people who read and commented on drafts, including Arthur Georges, Nancy FitzSimmons, Col Limpus, Rob Puschendorf, Dave Jones, Vimoksalehi Lukoschek, and several anonymous manuscript reviewers. Megan Higgie, the Evolution at JCU group, and the Molecular Ecology and Evolution Lab (MEEL) at JCU also made kind and insightful comments that improved several preliminary conference presentations. I am grateful to Vimoksalehi Lukoschek and Lynne van Herwerden who freely provided technical advice on molecular dating and phylogenetic analyses, respectively. Carolyn Smith- Keune provided extensive technical advice regarding laboratory protocols and scoring of raw microsatellite data. Rob Puschendorf and Adella Edwards were instrumental in helping me produce beautiful maps. This project would not have been possible without the generosity of many people who provided tissue samples. I especially thank Arthur Georges, for making his extensive Australian freshwater turtle tissue library at the University of Canberra available to me. Kate Hodges and others at the UC Wildlife Lab were very welcoming during my week-long tissue raids on Arthur’s library. Ivan Lawler, Jason Schaffer, Alastair Freeman, the Northern Territory Museum, and Eridani Mulder also generously provided samples for analysis. Many people also assisted me in the field while collecting my own samples. Col Limpus and the Queensland Turtle Research team have continued to be welcoming of me on their field trips. I shared many a fun turtling trip with Jason Schaffer, and will never forget snorkeling the clear waters of the Bowen River for Elseya irwini, amidst masses of rainbowfish. I also sincerely thank those who volunteered their time lugging turtle traps, including Blanche D’Anastasi, for v her endless enthusiasm, passion for wildlife and bravery while snorkeling in the middle of winter, Heather Veilleux for being an exceptional field assistant during a record haul of Krefft’s turtles, and Dave Jones and Robert Puschendorf for a most enjoyable trip to Lakefield and Laura. Damien Burrows within TropWATER at JCU provided invaluable in-kind and financial support for field trips. I am indebted to Megan Higgie, Conrad Hoskin and Rob Puschendorf, who were important mentors throughout the PhD experience. You provided me with an important early-career researcher perspective, but also friendship and many laughs. I also thank the staff and students of MEEL and the Aquaculture Genetics Group at JCU, especially Jose, Giana, Georgia, Ashton, Heather, Roger, Hoc, Blanche and Dave, for sharing their friendship, lab tips, exciting results, and the PhD experience over the past four years. My thanks also go to Tatjana Good for energising yoga classes and for encouragement in hanging in there, and Melanie Blanchette for many great chats and an easy level of understanding. You all made what can be a very lonely undertaking, a very enjoyable experience. Special thanks go to my family and friends at home, especially my Mum and Dad, Oma, sister Fini, brother Anthony, and friends Stacey, Tiffany, Jemima, and Liina. Your unwavering belief in me and ongoing encouragement and support in this undertaking gave me much strength. Finally, I thank my partner, best friend, and PhD buddy, Dave Jones. You helped in many aspects of my work, from field trips to IT support. However, it is difficult to find the words to express my gratitude for your day-to-day patience, emotional support, and love throughout what was at times a difficult journey, but also an extremely enjoyable one. I am immensely grateful to have shared the ups and downs of this experience with you, and look forward to our travels and our next challenge together. Thank you. - Erica. vi ABSTRACT Australia supports a highly endemic freshwater fauna. The continent’s long isolation, Gondwanan heritage, and present aridity make it of particular interest to freshwater biogeographers. Recent molecular genetic studies of freshwater fishes and macroinvertebrates implicate diverse processes of landform evolution, climatic change and sea level fluctuation in shaping current patterns of biodiversity. These studies indicate a