` Diversity of beetles across a land-use gradient in Sabah, Malaysia Adam Christian Sharp Department of Life Sciences Imperial College London A thesis submitted for the degree of Doctor of Philosophy June 2018 1 2 Declaration of originality All work in this thesis is my own, and I have acknowledged instances where I have collaborated with other researchers. Where others are included as authors on individual chapters, those individuals have provided comments on that chapter. Two anonymous reviewers provided a great deal of insight into the analyses in Chapter 3 when that chapter was submitted for publication in the Journal of Applied Ecology. Supervisors Dr Robert Ewers Maxwell Barclay Copyright declaration The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work. 3 Abstract Borneo is one of the most biodiverse regions on the planet but half of Borneo’s forest has been logged and millions of hectares replaced by oil palm plantation. Decomposing biodiversity into its underlying component parts may reveal mechanisms by which diversity loss might be mitigated. I sampled beetles (order: Coleoptera) at the Stability of Altered Forest Ecosystems Project in Sabah to quantify shifts in biodiversity associated with logging and clearing of tropical lowland forest for oil palm plantation. While logged forest maintained high species richness, the beetle species which persisted there were of lower conservation value. Beta-diversity mitigated losses in alpha-diversity in heavily- logged forest to some extent, and in multiple beetle taxa beta-diversity was greatest in that habitat. In both logged and unlogged forest, high beta-diversity was maintained through balanced variation in community composition. Oil palm plantations supported very few beetle species and although beta- diversity remained high, that beta-diversity was attributed to fluxes in the abundances of common species. At small spatial scales, forest quality and topographic roughness were significant determinants of beta-diversity. In unlogged forest, analysis of beta-diversity revealed sites of distinct ecological communities relevant to some that appeared to be defined by microclimate. At larger scales, spatial turnover in community composition was the strongest contributor to diversity followed by habitat structure, microclimate and then topography. Oil palm plantations are of low value and large areas of unlogged forest are evidently of highest value for the conservation of biodiversity. Degraded forest retains remarkable diversity through shifts in the spatial arrangement of ecological communities, and thus I recommend that small areas of even heavily-logged forest should be preserved where they are created in agricultural matrices. Future studies on land-use change in Borneo should incorporate beta-diversity into their designs as the component reveals mechanisms by which diversity loss might be mitigated. 4 Acknowledgements This work was funded by the Stability of Altered Forest Ecosystems (SAFE) Project, who are in turn funded by the Sime Darby Foundation. I would like to thank the SAFE Project and Royal Society’s South East Asia Rainforest Research Partnership for logistical support, and the Sabah Foundation, Maliau Basin Management Committee, the State Secretary, Sabah Chief Minister’s Departments, the Malaysian Economic Planning Unit and the Sabah Biodiversity Council for permission to conduct research. I would also like to thank the Natural History Museum in London for allowing me access to facilities to carry out taxonomic work. The ASTER Global Digital Elevation Model (GDEM) v2 data was retrieved from the online NASA Earthdata Search portal at https://search.earthdata.nasa.gov/search. ASTER GDEM is a product of NASA and METI. Data in the field was collected largely by the SAFE Project team of research assistants – most notably the highly-proficient SAFE Project Invertebrate Team which includes Madani bin Samat (Opong), Mainus bin Tausong, Melvin bin Teronggoh, Muhamed bin Juhanis (Mamat), Risman bin Ajang and Sisoon bin Maunut (Siun). Dr Edgar Turner started the long-term insect sampling work at SAFE Project in 2010 which formed the basis for the majority of this research. Ryan Gray and Min Sheng Khoo were fundamental to keeping SAFE Project running on a day-to-day basis and making sure the team were able to complete their field work. Dr Arthur Chung of the Forest Research Centre in Sepilok, Sabah, offered ongoing valuable advice and assisted in securing research permits to work in the state. There are also countless researchers, students and volunteers who I have crossed paths with who made my time at SAFE so enjoyable. At the Natural History Museum, I would like to thank Max Barclay for his limitless knowledge and support when I was inundated with tens of thousands of beetles. Dr Richard Thomson was also incredibly helpful in aiding with the taxonomic identification of weevils. Alice Haughan, Kara Taylor, Laura Healy and Noel Juvigny-Khenafou all used the SAFE Project insect samples as part of their respective MSc/MRes research projects and contributed to processing or identifying insects in some way. Surveys were facilitated by the Natural History Museum Learning Managers and Investigate 5 Team. At the Oxford Museum of Natural History, Darren Mann and Guillaume de Rougemont provided taxonomy of dung beetles and rove beetles respectively. The Forest Ecology and Conservation group at Imperial College London provided insights into everything from statistical to ecological theory. Prof Rob Ewers contributed excellent supervision for the entirety of the PhD. Dr Lan Qie provided invaluable advice on scientific writing style. Dr Marion Pfeifer and Dr Stephen Hardwick kindly allowed use of the habitat data they collected in the field. Clare Wilkinson, Liv Daniel, Mike Boyle, Nichar Gregory, Phil Chapman, Ross Gray, Sarab Sethi and Dr Terhi Riutta have all been constant help and inspiration. Finally, thank you to all my friends and family who put up with me for the last four years. 6 Table of Contents Declaration of originality .......................................................................................................................... 3 Supervisors ............................................................................................................................................. 3 Copyright declaration .............................................................................................................................. 3 Abstract ................................................................................................................................................... 4 Acknowledgements ................................................................................................................................. 5 Chapter 1 - Introduction ........................................................................................................................ 11 1.1 Biodiversity and its importance ................................................................................................... 11 1.2 Biodiversity in the tropics ............................................................................................................ 12 1.3 Borneo as a biodiversity hotspot ................................................................................................. 13 1.4 Threats to the biodiversity of Borneo .......................................................................................... 14 1.5 Past-documented impacts of land-use modification on biodiversity ........................................... 16 1.6 Spatial scale and conservation ................................................................................................... 18 1.7 Habitat quality and conservation ................................................................................................. 19 1.8 Selecting a suitable study taxon for researching biodiversity patterns ....................................... 20 1.9 The aims of this thesis ................................................................................................................ 21 1.10 Thesis structure ......................................................................................................................... 22 Chapter 2 – High conservation value scarabs are hit hardest by tropical deforestation ...................... 24 2.1 Abstract ....................................................................................................................................... 24 2.2 Introduction.................................................................................................................................. 24 2.3 Methods ....................................................................................................................................... 26 2.4 Results ........................................................................................................................................ 28 2.5 Discussion ..................................................................................................................................