The bare-nosed wombat and its pathogen, Sarcoptes scabiei Alynn M. Martin BSc, MSc, GradCertRes Submitted in fulfilment of the requirements for the Degree of Doctor of Philosophy School of Natural Sciences University of Tasmania, November 2018 Declarations by the author Declaration of originality This thesis contains no material which has been accepted for a degree or diploma by the University of Tasmania or any other institution, and to the best of my knowledge and belief, this thesis contains no material previously published or written by another person, except where due acknowledgement is made in the text of this thesis, nor does the thesis contain any material that infringes copyright. Authority of access This thesis may be made available for loan or limited copying and communication in accordance with the Copyright Act 1968. Statement regarding published work contained in this thesis The publishers of the papers comprising Chapters 2, 3, 5, and Appendix I hold the copyright for that content, and access to the material should be sought from the respective journals. The remaining non-published content of this thesis (Chapters 1, 4, and 6) may be made available for loan and limited copying and communication in accordance with the Copyright Act 1968. Statement of ethical conduct The research associated with this thesis abides by the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes, 7th edition, 2004 and the University of Tasmanian Animal Ethics Guidelines. The research presented in this thesis was carried out under University of Tasmania Animal Ethics Approval A14670 (2015-18) and the Tasmanian Department of Primary Industries, Parks, Water, and the Environment Permits FA1503 (2014- 15), FA15121 (2015-16), FA15122 (2015-16), FA16194 (2016-17), and FA17050 (2017). I acknowledge and agree to the above stated declarations: 01 November 2018 Alynn M. Martin Date PhD Candidate i Statement of co-authorship The following people and institutions contributed to the publication of research undertaken as part of this thesis: Alynn M. Martin: School of Natural Sciences, University of Tasmania (Candidate) Scott Carver: School of Natural Sciences, University of Tasmania (Supervisor) Christopher Burridge: School of Natural Sciences, University of Tasmania (Co-supervisor) • • • • • Sam Banks: College of Engineering, IT and Environment, Charles Darwin University Tamieka Fraser: School of Natural Sciences, University of Tasmania & Animal Research Centre, University of the Sunshine Coast Jillian Garvey: School of Humanities and Social Sciences, La Trobe University Janeane Ingram: School of Natural Sciences, University of Tasmania John Lesku: School of Life Sciences, La Trobe University Kellie Lovell: Tasmanian Department of Primary Industries, Parks, Water, and the Environment Adam Polkinghorne: School of Science and Engineering, University of the Sunshine Coast Kirstin Proft: School of Geography and Spatial Science, University of Tasmania Hayley Ricardo: Manaaki Whenua – Landcare Research Shane Richards: School of Natural Sciences, University of Tasmania Georgia Roberts: School of Science and Engineering, Federation University & School of Humanities and Social Sciences, La Trobe University Adrianna Tompros: Colorado State University ii Publications produced as part of this thesis with contributions by co-authors: Chapter 2 has been published in Royal Society of Open Science: Martin AM, Fraser TA, Lesku JA, Simpson K, Roberts GL, Garvey J, Polkinghorne A, Burridge CP, and S Carver. 2018. The cascading pathogenic consequences of Sarcoptes scabiei infection that manifest in host disease. Royal Society Open Science (5)4: doi.10.1098/rsos.180018. Contributions: SC, AMM, JAL, and CPB conceived and designed the research; AMM, SC, KS, GLR, JG, AP, TAF and CPB collected the data; AMM, JAL, SC analysed the data; AMM, JAL, SC, CPB interpreted results; AMM, SC drafted the manuscript, and all authors participated in manuscript modifications. Chapter 3 has been published in Journal of Applied Ecology: Martin AM, Burridge CP, Ingram J, Fraser TA, and Carver S. 2018. Invasive pathogen drives host population collapse: effects of a travelling wave of sarcoptic mange on bare-nosed wombats. Journal of Applied Ecology 50(1):331-341. Contributions: SC, JI, and CPB conceived and designed the research; AMM, SC, JI, and CPB collected all data; AMM analysed the data; AMM, SC, CPB, and TAF interpreted results; AMM, SC, and CPB drafted the manuscript, and all authors participated in manuscript modifications. Chapter 4 is in review with the Journal of Applied Ecology: Martin AM, Richards SA, Fraser TA, Polkinghorne A, Burridge CP, and S Carver. Population-scale treatment informs solutions for control of environmentally transmitted wildlife disease. Contributions: SC, AMM, SAR, and CPB conceived and designed the research; AMM, SC, AP, TAF and CPB collected the data; AMM, SC, and SAR analysed the data; SAR developed the statistical models, AMM, SC, SAR, CPB, and AP interpreted results; AMM, SC, and SAR drafted the manuscript, and all authors participated in manuscript modifications. iii Chapter 5 is accepted to be published in Evolutionary Applications: Martin AM, Carver S, Proft K, Fraser TA, Polkinghorne A, Banks S, and CP Burridge. Isolation, marine transgression, and translocation of the bare-nosed wombat (Vombatus ursinus). Contributions: AMM, SC, and CPB conceived and designed the research; AMM, SC, AP, TAF, SB and CPB collected the data; AMM, KP, and CPB analysed the data; AMM, SC, SB, CPB, and KP interpreted results; AMM, SC, and CPB drafted the manuscript, and all authors participated in manuscript modifications. Appendix I is published (online) in Australian Mammalogy: Martin AM, Ricardo H, Tompros A, Fraser TA, Polkinghorne A, S Carver. Burrows with resources have greater visitation and may enhance mange transmission among wombats. Australian Mammalogy, DOI: 10.1071/AM18013 Contributions: AMM and SC conceived and designed the research; AMM, SC, AP, and TAF collected the data; AMM, AT, and HR analysed the data; AMM, SC, HR, and AT interpreted results; AMM and SC drafted the manuscript, and all authors participated in manuscript modifications. • • • • • We, the undersigned, agree with the above stated proportion of work undertaken for each of the above published (or submitted) peer-reviewed manuscripts contributing to this thesis: Scott Carver Christopher Burridge Greg Jordan Candidate’s supervisor Candidate’s co-supervisor Head of Discipline School of Natural Sciences School of Natural Sciences School of Natural Sciences University of Tasmania University of Tasmania University of Tasmania Date: 08/11/2018 Date: 08/11/2018 Date: 08/11/2018 iv Acknowledgements It goes without saying that to be at this point after four years of postgraduate research, I have received an overwhelming amount of support, encouragement, and help from many people, and a deep and heartfelt ‘thank you’ is in order. First and foremost, thank you to my supervisors, Drs. Scott Carver and Christopher Burridge. Without your guidance and support, none of this would have been possible. Thank you for challenging me to be a better researcher, for understanding my limits and encouraging me to work beyond them, for always making time and having an open door throughout this process, and for believing in me when I doubted myself. I dare say you are the best pair of advisors any postgraduate student could hope for, and I have been extremely lucky. You have made all the difference in my PhD journey. To all of those who volunteered with me over the past four years: to Katja Gutwein and Nick Bean for helping me set up more than 100 burrow flaps in Narawntapu National Park; to Tierney O’Sullivan, Marion Fourquez, Jo Horton, Chris Kozakiewicz, and Belle Monk for helping me trap and process wombats in the cold of winter; to Danielle Madden, Alyce Hennessey, Samantha James, Sybil Sim, Dana Maxwell, Alex Doyle, Weibke Knoblauch, Lisa Mckay, Renee Dodd, Emma Nichols, and Jeremy O’Wheel for putting in long and hard hours surveying wombats and wombat burrows; and to Adri Tompros, Hayley Ricardo, and Sandon James, for your help in data collection and organization. To the staff in the School of Natural Sciences: to Adam Smolenski for spending countless hours with me in the lab providing me with invaluable knowledge and expertise; to Jodi Noble, Morgan Green, Amanda Noble, Clancy Carver and Anna McEldowney for always having answers and solutions to my questions; to Ashley Edwards for giving me the opportunity to develop my skills as a demonstrator and a teacher; and last but not least, to Helen Stephens for her endless optimism in reading and editing countless drafts of my grant proposals – thanks for having faith in my work. To all of the people and associations who provided my project essential funding and resources to carry out this research: Sally Bryant from the Tasmanian Land Conservancy (TLC), Dr. Bill Holsworth (Holsworth Wildlife Research Endowment), the Wildlife Disease Association Australasian Sector, and Mange Management. To my office mates: Riana Gardiner (my other half), Rowena Hamer, Sebastien Comte, David Hamilton, Vince Scoleri, and Cat Hamilton – thank you all for being my home away from home and my TAS family, for all the laughs, coffee breaks, office dinners, life chats, and adventures. To the Carver Lab and Funky Genomics Group: thanks for hearing out my ideas and brainstorming with me. You’re the finest group of researchers I know, and I look forward to v ongoing collaborations with you in the future. To the gym crew – special mention Luke Granger, Trudy Kennedy, Adam Shephard, Anthony Koutoulous, Aon Poolprem-Johnson, and Ray Mouchet – for all the epic workouts and comradery. To my dear friends who have been there for me through the entire four years – Amy Edwards, Erfan Aghasian, Mesfer Al Qhanti, Terry Hisiridis – thanks for being a huge and irreplaceable part of my life. Last but certainly not least, to my family, who has been my rock throughout this journey. To my parents, William and Theresa Martin, for always encouraging me to pursue my academic and career goals, for lifting me up in my times of failure, and for loving me unconditionally.