Comparative phylogeography and diversity of Australian Monsoonal Tropics lizards Rebecca Jan Laver ORCID ID 0000-0002-6319-7213 Doctor of Philosophy January 2017 The School of BioSciences Faculty of Science The University of Melbourne Submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy Produced on archival quality paper Thesis Abstract Tropical savannah biomes cover ~20% of the world’s landmass, however the biodiversity encompassed within these environments and the underlying processes that have shaped it remain poorly understood. Recent increased research to address this knowledge gap have begun to reveal surprisingly high amounts of deep, geographically- structured diversity, much of which is cryptic or hidden within morphologically similar species complexes. These patterns are especially emphasized in vertebrate taxa which are intrinsically linked to rock escarpments and ranges that dissect the savannah woodlands and grasslands of many of these biomes, hinting at a role of heterogeneous topography in structuring diversity. The remote Australian Monsoonal Tropics (AMT) spanning the north of the Australian continent is a particularly vast, and relatively undisturbed, tropical savannah region. Recent increased surveys are revealing numerous new species and endemism hotspots, indicating we are only just beginning to uncover the true biodiversity levels within this biome. Not only is there a relative paucity of knowledge regarding the present diversity within this region, but there is also limited understanding of how this diversity came to be. Phylogeographic studies can assist us in establishing current patterns of diversity and their evolutionary significance within regions and biomes. Furthermore, by comparing and contrasting the patterns and timing of diversification within and between biomes for multiple ecologically diverse taxa, we can begin to elucidate the history of these biomes and the environmental processes that have shaped the diversity we observe today. ii In this dissertation I aimed to better assess and establish true patterns of biodiversity and endemism within the Kimberley region of the AMT (Western Australia), and to place these patterns within a broader continental context using intra- and inter-biome comparisons in related taxa. Using geckos as a model system I took a comparative phylogeographic approach, integrating advanced next-generation genetics and morphology to establish patterns and timing of diversification across ecologically variable taxa. Within all Kimberley taxa I studied, I uncovered high levels of cryptic diversity. Much of this diversity involves especially short-range endemic lineages concentrated in key regions typically with one or more of the following factors: highly mesic conditions, island or insular environments, and unique or complex geological formations. In recognising these areas I have provided evidence of novel biodiversity hotspots and emphasised the significance of others as representing important “refugia” within the Kimberley that allow persistence and facilitate divergence of lineages through harsh periods of environmental change. These findings indicate diversification patterns are shaped by complex interactions of climatic variation, topography, and species’ ecology, allowing inference of biogeographic history and a greater ability to predict impacts of future environmental change. iii Declaration This is to certify that: This thesis is my own original work towards the PhD except where otherwise indicated in the Preface. Due acknowledgment has been made in the text to all other material used. The thesis is fewer than 100,000 words in length, exclusive of tables, maps, bibliographies and appendices. __________________ Rebecca Jan Laver The School of BioSciences The University of Melbourne Victoria, 3010 Australia September, 2016 iv Preface To facilitate publication, two of the chapters within this dissertation (Chapters 2 and 3) are presented as they were prepared for stand-alone scientific articles. For these manuscripts which are in preparation for publication I am the primary author as follows: Chapter 2: Laver, RJ, Nielsen, SV, Rosauer, DF, & Oliver, PM. Trans-biome diversity in Australian grass-specialist lizards (Diplodactylidae: Strophurus). In review. Chapter 3: Laver, RJ, Doughty, P & Oliver, PM. Endemism, persistence and introgression across an aridity gradient in two specialised lizard lineages from the Australian Monsoonal Tropics (Oedura spp.). In review. For these chapters and the remainder of this dissertation I i) contributed to conceptualising research projects; ii) conducted majority of the data collection – including collection of specimens, sequencing and assembly of molecular data, and collection of morphological data; iii) conducted majority of the data analyses; iv) conducted the literature review; v) wrote all manuscripts, and prepared figures and tables. My primary supervisor, Paul Oliver, served as co-author for Chapters 2 and 3, and is credited for his contribution to conceptualising and funding the projects covered in this dissertation, as well as assistance with interpretation of results and editorial comments. v Additional co-authors for the above mentioned manuscripts contributed the following: Stuart Nielsen (University of Mississippi) – contributed to molecular data collection, data analysis, and provided feedback on draft revisions (Chapter 2). Dan Rosauer (Australian National University) – contributed to data analysis, and provided feedback on the manuscript (Chapter 2). Paul Doughty (Western Australia Museum) – contributed to field work, tissue collection, and data collection of morphometric measures, and assisted with revisions of the manuscript (Chapter 3). Though presented in the form of a thesis chapter for this dissertation Chapter 4 was also research conducted as part of a broader collaboration. Contributions of collaborators for this work are detailed as follows: Renae Pratt (Australian National University) – contributed to molecular laboratory work and data collection (next-generation sequencing – exon capture; Chapter 4). Craig Moritz (Australian National University) – contributed to funding, fieldwork, tissue collection, and draft revisions (Chapters 2, 3 & 4). All other assistances to data collection, fieldwork, and analytics are detailed in the Acknowledgements. vi The research detailed in this dissertation was conducted as part of a broader study on lizard diversity in the northern Australian Monsoonal Tropics, and was supported and funded by a linkage grant from the Australian Research Council (ARC) awarded to Paul Oliver, Michael Lee and Paul Doughty, a McKenzie Postdoctoral fellowship to Paul Oliver from the University of Melbourne, and a Discovery Early Career Researcher Award (DECRA) to Paul Oliver. In addition, funding from an Australian Laureate Fellowship from the ARC awarded to Craig Moritz assisted with fieldwork, tissue sampling, and next-generation sequencing. Sampling for this project was covered under a Western Australian license to take fauna, permit number SF009863, issued to Craig Moritz by the Department of Parks and Wildlife, WA. vii Acknowledgements Firstly, I would like to thank my supervisors: Tim Jessop, Jane Melville and Paul Oliver, for providing the opportunity to work on this amazing project and supporting me throughout to ensure I managed to finish it. I greatly appreciated Tim always being available to provide support, advice, guidance, and an ear to listen whenever it was needed. Jane ensured a fantastic start to my PhD by ensuring I was welcomed into the science community at Museum Victoria, and provided access to an office and laboratory facilities. This experience helped me make many important connections and afforded several great educational opportunities which greatly enhanced my student experience and gave me a real appreciation for working in a museum environment. Paul I thank for funding and conceiving the project, providing the chance to conduct fieldwork in some spectacular landscapes and with awesome critters, and enabling me to attend an international conference and visit universities and colleagues overseas. Thank you to the members of my advisory committee, Devi Stuart-Fox and Michael Keough, for keeping track of my progress and being accommodating of delayed reviews and paperwork. In addition I am so grateful to the many people who perused drafts and provided valuable feedback to enhance my written work; in particular Craig Moritz, Richard Harrison, Dominique Potvin, Paul Doughty, and Renee Catullo. Special mention to the late Richard Harrison whose encouragement and guidance re-ignited the passion for my work during the final trying stretch of writing up. Thank you to the many colleagues and collaborators who provided guidance or assisted with various analyses or data collection, greatly enhancing the quality of the work within this thesis. To my co-authors Stuart Nielsen, Paul Doughty, and Dan viii Rosauer, thank you so much for additional analyses and data collection that greatly enhanced the studies covered in Chapters 2 and 3. To my amazing and endlessly patient teachers, Katie Smith and Renae Pratt, thank you for ensuring my competence in the genetics laboratory from traditional Sanger sequencing through to next-generation methods, and for spending many, many hours contributing to collection of molecular data. Thanks to Sumitha Hunjan, Maggie Haines and Bee Gunn, for conducting additional sequencing to assist in completing genetic