Testing the decline of the threatened New Holland Mouse (Pseudomys novaehollandiae) Phoebe Ann Burns https://orcid.org/0000-0003-1015-3775 Submitted in total fulfilment of the requirements for the Degree of Doctor of Philosophy School of BioSciences University of Melbourne Parkville, Victoria 3010 January 2019 I conducted the fieldwork component of this research on the traditional lands of the Gunaikurnai Nation, the Boon wurrung and Wadawurrung people of the Kulin Nation, and the Gadubanud people. I wrote this thesis on the lands of the Wurundjeri and Boon wurrung people of the Kulin Nation, the Gunaikurnai Nation, the Jardwadjali and Djab wurrung people of Gariwerd, and the Tongva and Tlingit Nations of Turtle Island. I pay my respects to their rich cultural histories and futures, to their Elders, past, present, and emerging, their relationship with the Land as custodians, and to the Land itself. I pay my respects to the Traditional Custodians of these lands who lost their lives at the hands of invaders in many locations that I visited and the land on which I live. I acknowledge these atrocities and recognise that the Land and People still bear these scars. i Abstract Delineating the distribution of a threatened species is critical for identifying threats and guiding conservation management. The process is challenging, however, especially when a species is rapidly declining, and so changing its distribution. In this context, species distribution modelling (SDM) often lacks the precision needed to inform fine-scale management decisions, but on-ground surveys to test species’ distributions are time and resource intensive. The dilemma can be mitigated to some extent by careful examination of historical data, and optimal monitoring. The New Holland Mouse (NHM; Pseudomys novaehollandiae) is one of many Australian rodent species to have undergone drastic distributional declines since European invasion. Initially recorded in Victoria in 1970, by 2015 NHMs were thought to occur in only 3 of 12 historically occupied regions. I tested this decline with statistical rigour, using extensive Elliott and camera trapping surveys at >500 sites across Victoria. Combining my survey data with 48 years of others’ efforts, I evaluated the utility of standard Elliott trapping surveys and the efficacy of camera trapping for NHMs. I tested whether NHMs were where we would expect based on state-government threatened fauna SDMs, and whether the species’ purported early- successional fire association explained occurrence or abundance. I confirmed the species’ persistence in 5 of 12 historical regions – including regions where NHMs had not been detected in 5-21 years – and expanded the species’ known distribution in two regions. However, these finds can be attributed to a paucity of i prior survey effort and were partnered with greater declines elsewhere. Elliott trapping surveys were often inadequate to provide statistical confidence in the species’ absence; camera trap surveys provide a viable alternative for distribution assessments. Standard state-government SDMs provided limited guidance as to the true distribution of NHMs and SDMs for declining species should be interpreted with caution. Time-since-fire did not explain the species’ occurrence and poorly explains abundance, though in certain locations inappropriate fire regimes are a threatening process. Predator control, habitat management, and careful reintroductions are key priorities for conservation of NHMs in Victoria. ii Declaration This is to certify that: i. the thesis comprises only my original work toward the degree of PhD except where indicated in the preface; ii. due acknowledgement has been made in the text to all other material used; and iii. the thesis is fewer than 100,000 words in length, exclusive of tables, maps, bibliographies and appendices. Phoebe A. Burns January 2019 iii Preface This thesis comprises a series of independent publications. Chapters 2-6 comprise co-authored or sole-authored publications that have been or will be submitted for publication in scientific journals. Consequently, there may be some repetition and stylistic differences among chapters. Although chapters 2-5 are co-authored, I performed all fieldwork and analyses (with the exception of developing the species distribution model referenced in chapter 4), wrote all chapters, and incorporated feedback from co-authors where applicable. Specific contributions of each co-author are outlined below. My supervisors, Dr Ben Phillips (University of Melbourne), Dr Marissa Parrott (Zoos Victoria), and Dr Kevin Rowe (Museums Victoria) assisted with the development of research questions and provided feedback on all chapters. Dr Phillips also provided guidance and support for statistical analyses in chapters 2, 3, and 5. Dr Matt White (Arthur Rylah Institute) created species distribution models for chapter 4, and he and Nick Clemann (Arthur Rylah Institute) assisted with development of the research questions, and provided feedback on the chapter. Claire McCall (Wildlife Unlimited) identified the original hypothesis regarding moon phase in chapter 2 and provided feedback on the chapter. iv The thesis includes the following chapters for publication: Chapter 2 submitted to Diversity and Distributions: Burns, P. A., McCall, C., Rowe, K. C., Parrott, M. L. and Phillips, B. L. (in review). Accounting for detectability and abundance in survey design for a declining species. Chapter 3 published by Australian Mammalogy online on 21 August 2017: Burns, P. A., Parrott, M. L., Rowe, K. C. and Phillips, B. L. (2018). Identification of threatened Pseudomys species using infrared and white-flash camera surveys. Australian Mammalogy 40, 188–197 (DOI 10.1071/AM17016). Chapter 4 submitted to Austral Ecology: Burns, P. A., Clemann, N., and White, M. (in review). Testing the utility of generic approaches to species distribution modelling for species in decline. Chapter 5 submitted to the Journal of Mammalogy: Burns, P. A., and Phillips, B. L. (in review). Time since fire is an over-simplified measure of habitat suitability for the New Holland Mouse (Pseudomys novaehollandiae). Chapter 6 submitted to Australian Mammalogy: Burns, P. A. (in review). Testing the decline of the New Holland Mouse (Pseudomys novaehollandiae) in Victoria. v This work was facilitated by generous financial support from an Australian Government Research Training Program Scholarship, Parks Victoria, Zoos Victoria, the Holsworth Wildlife Research Endowment, the Royal Zoological Society of NSW through a Paddy Pallin Science Grant and the Ethel Mary Read Research Fund, the Linnaean Society of New South Wales via the Joyce W. Vickery Scientific Research Fund, and the Field Naturalists Club of Victoria through their Environment Fund. Parts of this work were also funded by the Department of Environment, Land, Water, and Planning (DELWP) Biodiversity on Ground Actions funding. I conducted all fieldwork under permit numbers 1000 7493, 1000 7606 and 1000 7834 from the Department of Environment, Land, Water, and Planning, and with the approval of the Museums Victoria Animal Ethics Committee. vi Acknowledgments Thank you to my supervisors Ben Phillips, Marissa Parrott, and Kevin Rowe for your support and guidance over the years. Ben, thank you for convincing me that I can do stats – under your mentorship I’ve grown from having a mild distain for ‘R’, to finding a peculiar enjoyment in spending weeks running models that occasionally converge. Thank you for always reaffirming that my research is valuable and meaningful, and thank you for adding to that value and meaning. You have an incredible knack for instilling confidence in people in the most relaxed, down-to- earth manner and I am so grateful for that. Marissa, thank you for being the ultimate one-woman cheer squad! Your relentless enthusiasm, passion, and optimism is delightful and you’ve brought so much energy and encouragement to this project. Kevin, thank you for introducing me to the wonderful world of rats, for supporting and encouraging my initial growth as a scientist, fostering my independent nature and encouraging me to challenge myself. Thank you for teaching me more about island biogeography theory than I ever anticipated. To my weird and wonderful family – thank you for always being there, showing (feigning?) enthusiasm and interest for my work, and for accepting without question that I spent nine years at uni. Mum, thank you for always balancing me out and for putting up with my erratic behaviour and the mountains of fieldwork gear flooding the house and veranda for years. Thank you also for being my keenest fieldwork vollie ever. Dad, thank you for making up stories about possums and platypuses that inspired a love of nature in me as a kid, and for all the philosophical chats that have vii helped shape the way I think. Kate, thank you for your deep-rooted belief in me, endless encouragement, and your willingness to help out in any way possible (Andy, you’re great too). Allan, thank you for reminding me that there is life outside study, keeping me grounded in frivolous joy and feeding me way too many hash browns. Henry & Willow, thank you for telling me how boring I am when I’m working and for constantly checking when I’ll be finished my ‘assignment’. Nick, thank you for always loving everything I write, for being genuinely excited about my research, and for all the adventuring. Thank you to my Museums Victoria crew for being there through a crazy wild ride and for somehow infiltrating the rest of my life. Emily, the Rat Gene Queen, thank you for being an ever-willing sounding board for everything and anything. Thank you for all our epic science plans and for the dozens of papers we may never actually write (just because we’ll be too busy writing others). Kiz and Kate, thank you for all the comic relief and PT chats, thank you especially for your amazing lyric-altering abilities. Pete, thank you for being my lab buddy through the early years, thanks for all the laughs, and for the years of oversharing.