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Conservation Genetics of the Growling Grass Frog, Litoria Raniformis, in Urbanising Landscapes by Claire C

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Conservation Genetics of the Growling Grass Frog, Litoria Raniformis, in Urbanising Landscapes by Claire C CONSERVATION GENETICS OF THE GROWLING GRASS FROG, LITORIA RANIFORMIS, IN URBANISING LANDSCAPES CLAIRE CATHERINE KEELY Bachelor of Science (Hons) Submitted in total fulfillment of the requirements of the degree of DOCTOR OF PHILOSOPHY AUGUST 2016 School of BioSciences The University of Melbourne ORCID ID: 0000-0002-7243-4639 Conservation genetics of the Growling Grass Frog, Litoria raniformis, in urbanising landscapes By Claire C. Keely ! 2016 Supervisors: Kirsten Parris, Geoff Heard, Jane Melville and Andrew Hamer Title Page: Litoria raniformis juvenile, photo by C. C. Keely For Dan and Max Abstract The proportion of the world’s human population living in cities and towns (urban areas) grew rapidly over the 20th century. Indeed, the global urban population grew by an order of magnitude during this period, from 220 million to 2.8 billion. By 2030, the global urban population is expected to swell to almost 5 billion. Urbanisation is a key threatening process for amphibians, with the global amphibian assessment listing greater than one-third of the world’s known amphibian species as currently threatened by urbanisation. As is the case for biodiversity more generally, habitat loss and fragmentation represent pervasive impacts of urbanisation for amphibians. The International Union for Conservation of Nature (IUCN) recognises genetic diversity as one of three forms of biodiversity requiring conservation. However, surprisingly few studies have focused on the genetic consequences of urbanisation for amphibians. With the global rate of urbanisation set to steadily increase, and its recognition as a key threatening process to amphibians, the application of genetic techniques will be an important component of conservation planning for these animals. This thesis investigates the conservation genetics of the Growling Grass Frog, Litoria raniformis, around Melbourne, Australia. This species has declined significantly since the late 1970s, largely due to habitat loss and fragmentation, drought and disease. Remnant populations around Melbourne occur in four main regions, three of which are marked for urban growth, causing further loss, degradation and fragmentation of habitat for L. raniformis. The aim of this thesis was to assess the genetic structure and diversity of remnant populations of L. raniformis across Melbourne. There were four main objectives: 1. Assess four different genetic sampling techniques for amphibians, using a multi- criteria decision framework and L. raniformis as a case study. 2. Document the genetic structure and diversity of L. raniformis across Melbourne’s urban fringe, using mitochondrial DNA (mtDNA) and microsatellites. i 3. Investigate the population genetic structure of L. raniformis in the northern region of urbanising Melbourne and develop a model of the landscape determinants of gene flow for the species. 4. Undertake a Bayesian metapopulation viability analysis for L. raniformis, incorporating estimates of gene flow to define population connectivity. The thesis concludes by outlining directions for further research on the conservation genetics of the Growling Grass Frog and its management. ii Declaration This is to certify that: i. The thesis comprises only my original work towards the PhD except where indicated in the Preface, ii. Due acknowledgement has been made in the text to all other material used, iii. The thesis is fewer than 100,000 words in length, exclusive of tables, maps, bibliographies and appendices. _______________________________________________ Claire C. Keely August 2016 iii iv Preface This thesis was prepared as a collection of publications. Each data chapter (Chapters 2 to 5) constitutes an independent paper. Therefore, there may be some repetition between chapters, however this has been avoided where possible. These publications have been prepared in co-authorship. However, the contents of these chapters are my own work, except where outlined below. Co-authorship reflects a supervisory role in most cases (K. M. Parris, G. W. Heard, J. Melville, and A. J. Hamer), but the result of collaboration in other instances. J. M. Hale provided genotypes and COI mtDNA sequences for 198 Litoria raniformis individuals (used in Chapters 3 and 4). J. Sumner provided advice on genetics laboratory techniques for Chapters 2 and 3 and A. Moran-Ordonez assisted with GIS analysis (Chapter 4). The thesis is made up of the following chapters (Chapters 2 to 5) for publication: Keely, C.C., Heard, G.W., Sumner, J.M., Parris, K.M. and Melville, J. Comparing genetic sampling techniques for amphibians with a multi-criteria decision framework Keely, C.C., Hale, J.M., Heard, G.W., Parris, K.M., Sumner, J.M. Hamer, A.J. and Melville, J. 2015. Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region. Royal Society Open Science 2(8): 1-13. Keely, C.C., Heard, G.W., Hale, J.M., Moran-Ordonez, A., Parris, K.M. and Melville, J. Impacts of urbanisation on the population genetic structure of a threatened amphibian, Litoria raniformis Keely, C.C., Parris, K.M., Melville, J. and Heard, G.W. Integrating genetic connectivity measures with stochastic patch occupancy models for metapopulation management All research procedures reported in the thesis were approved by The University of Melbourne Animal Ethics Committee (approval number 1011804.1) and conducted under a scientific research permit from the Victorian Department of Environment, Land, Water and Planning (permit number 10005649). v This study was generously funded by an Australian Research Council Linkage Grant (LP0990161, with the Australian Research Centre for Urban Ecology, Growling Grass Frog Trust Fund, Melbourne Museum, Melbourne Water, Parks Victoria and Victorian Department of Environment, Land, Water and Planning), The National Environmental Research Program, Environmental Decisions Hub, ARC Centre of Excellence for Environmental Decisions, The University of Melbourne (Melbourne Abroad Travelling Scholarship and School of Botany Postgraduate Student Travel Award), Museum Victoria (Museum Victoria 1854 Student Scholarship) and Australian Society of Herpetologists (ASH Student Travel Grant). vi Acknowledgements I dedicate this thesis to my incredible husband, Dan, and my beautiful PhD baby, Max. Dan, I’m sorry I disappeared to do field work for entire summers. Thank you for your endless encouragement and strength, for helping put things in perspective and for always being a welcome distraction from the challenges of a PhD. I will never be able to thank you enough for choosing me. Max, thank you for being a constant inspiration (and such a good sleeper, so I could address paper revisions when you were only a few weeks old). Your smiles and laughter and watching you grow into the most amazing tiny human have encouraged me to continue working and hopefully make you proud of your mama. My parents, Cate and Kelvin, thank you for a lifetime of support. From finally giving in and allowing me to have my first pet frog at the age of seven, to entertaining Max Steel for countless days while I completed my PhD. I wish to thank my supervisors, Kirsten Parris, Geoff Heard, Jane Melville and Andrew Hamer, who have all played important roles during different stages of my PhD. Geoff, I couldn’t have done this without you, thank you for being such an amazing supervisor and for sharing your passion for Growling Grass Frogs with me. We have very different attitudes towards this species and it’s behaviour towards others, however definitely share a love and respect for the little guys. Kirsten and Jane, I’m so happy that I chose two strong, intelligent women to guide me through this process, thank you for being great role models, as well as supervisors. Kirsten, I really admire your scientific integrity and the ongoing commitment and support you provide your students, especially after they’re no longer students. Jane, I really appreciate your ability to turn a piece of writing into a story. Andrew, thank you for some fun field adventures. Josh Hale, thank you for allowing me to follow on from your PhD work and being so patient as you taught me how to navigate a genetics lab. Your guidance and support, especially at the beginning of my candidature, were so important to me. vii Thank you to all my friends at Melbourne Museum. Katie Date, my amazing friend and PhD mentor, I cannot imagine these years without you. I’m so lucky to have such an intelligent and caring kindred spirit. Claire McLean (the ‘other me’). Thank you for all your help and encouragement. Thank you also to Jo Sumner for all your guidance and lab support, you always felt like an honarary supervisor and to Maggie, Susi, Sumi, Shandiya, Nat, Zoe, Alice, Bec, Adnan and many more. I’ve been really lucky to be part of such a friendly and supportive Uni lab. Lab retreats, writing retreats and attending conferences have definitely been highlights and there are far too many people to mention everyone individually. However, I would particularly like to mention Stefano Canessa, my field work companion for the entire first season. Thank you for all your hard work, expert frog-catching skills and always being so incredibly accommodating (your constant reply of ‘as you wish’ would make me smile every time). Reid Tingley, my official mentor, thank you for the interesting stories and always having a smile on your face. Alejandra, thank you for your incredible help with ArcGIS, and Will and John B for your patient computer support. And to the incredible mamas in the lab, especially Emily and Carly, thank you for your advice on balancing PhD and babies and for general inspiration. Thank you also to James, Kim, Chris, Freya, Luke, Laura, Els, Matt, Pia, Casey, Heini, the list goes on... I had so much fun in the field during my PhD, and would like to thank the amazing people out with me – Stefano, Susi, Nat, Fran, Dani, Geoff and Andrew. Thank you for all the adventures. During my canditure I undertook part-time work with the Live Exhibits Department of Melbourne Museum.
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