PROTECTING AQUATIC DIVERSITY IN DEFORESTED TROPICAL LANDSCAPES Clare Lucy Wilkinson Division of Ecology and Evolution Department of Life Sciences Imperial College London & Department of Biological Sciences National University of Singapore A thesis submitted for the degree of Doctor of Philosophy 2018 ii 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 distribution, researchers must make clear to others the license terms of this work. iii ABSTRACT _________________________________________________________________________________________________________________ Global biodiversity is being lost due to extensive, anthropogenic land-use change. In Southeast Asia, biodiversity-rich forests are being logged and converted to oil-palm monocultures. The impacts of land-use change on freshwater ecosystems and biodiversity, remains largely understudied and poorly understood. I investigated the impacts of logging and conversion of tropical forest in 35 streams across a land-use gradient on freshwater fishes, a useful biotic indicator group, and a vital provisioning ecosystem service. This research was extended to quantify the benefits of riparian reserves in disturbed landscapes, and examine the interaction of land-use change with extreme climatic events. There are four key findings from this research. (1) Any modification of primary rainforest is associated with a loss of fish species and functional richness. (2) Streams in oil-palm plantations with riparian reserves of high forest quality, and a width of > 64m on either side, retain higher species richness and higher abundances of individual fish species. (3) Although relatively low in species richness, streams in oil-palm plantations retain high biomass of freshwater fish that is readily captured using cast nets (the primary method used by local people), providing an important protein source and supplementary income to local communities. (4) An extreme El Niño drought interacted antagonistically with land-use change, reducing the capture rate of N. everetti, one of the most common species in my study area. These results illustrate the critical impacts of land-use change on tropical freshwater ecosystems, and highlight the need to ensure riparian reserves are retained and primary forested areas are protected. Such actions will be needed to maintain freshwater diversity in modified tropical landscapes. Despite the impacts on fish communities due to land-use change, abundant, tolerant species appear to be resilient to climate-based stressors, while fish in headwater streams represent a sustainable food-resource for communities in human-modified landscapes. iv ACKNOWLEDGEMENTS _________________________________________________________________________________________________________________ This research was funded by a Joint studentship scholarship between Imperial College London and the National University of Singapore. Additional funding for research activities was provided by: the Stability of Altered Forest Ecosystems (SAFE) Project, through their funder Sime Darby for logistical support in Borneo, Royal Geographic Society, Landmark Trust and Imperial College London’s Department of Life Sciences Travel grants. Permission, for which I am very grateful, was given to conduct this research and export samples from Sabah Biodiversity Council (SaBC), Maliau Basin Management Committee (including Waidi Sinun and Rose John Kidi), Danum Valley Management Committee, Royal Society Southeast Asia Rainforest Research Programme (RS-SEARRP), Yayasan Sabah, Sabah Forestry Department, Benta Wawasan, and the Stability of Altered Forest Ecosystems (SAFE) Project. I would also like to thank Henry Bernard and Arman Hadi Fikir for being my local collaborators in Sabah, Malaysia, and for their help and advice with permission applications and my research. I am eternally grateful to all of the SAFE project staff and researchers who have helped me with my research. In particular: Ryan Gray who provided huge amounts of logistical support, delicious food, drinks and always a friendly face; Research Assistants: Kiel Jahuri, James Loh and Wash for their tireless work in the field, putting up with me for 18 months of field work and the blood (leeches), sweat and tears that tried to get in the way; and all the researchers at the SAFE project that make life at the field camp an enjoyable place to be, with extra mentions to Adam Sharp, Philip Chapman, Michael Boyle, Nichar Gregory, Elizabeth Telford, Victoria Kemp for all the laughs, drinks, running, yoga and badminton fun times. In addition, Sarah Luke, who provided invaluable help and advice about work on freshwater streams, and aided in the design of this project and who’s work is cited in everything I have written. I would like to acknowledge the enormous amount of help and support provided by my supervisors Rob Ewers, Darren Yeo and Tan Heok Hui. Thank you for all the ideas, discussions, and general life advice that you have provided over the last four years. Thanks to Heok Hui for a great week in the field that led to the development of the Brantian catchment checklist, and to Darren for supporting my time in Singapore. I am also grateful for the insightful feedback and advice from Guy Woodward, Cris Banks-Leite and David Orme during my PhD. For everyone, past and present, in the Forest Ecology and Conservation lab group in London and the Freshwater and Invasive Biology lab group in Singapore, thank you for making my time in these two v places a wonderful experience, where I have made friends for life. It has been a pleasure to work with you all, and thank you so much for the advice with R code (Adam Sharp and Phil Chapman), discussions, debates, as well as the many group lunches and drinks that we have shared. In addition, thank you to Marion Pfeifer for providing all remotely sensed satellite imagery and processed files of above ground biomass. Lastly, a huge thank you for my friends and family who are always there for me, through the highs and lows of PhD life, and tolerating the many months of absence while I am away doing fieldwork. I hope that the many exotic holiday locations make up for this in some way. vi DECLARTION OF ORIGINALITY _________________________________________________________________________________________________________________ I certify that all material within this thesis is solely the result of my own work, except for the following exceptions. I therefore refer to ‘we’ instead of ‘I’ throughout. Chapter 1: R. M. Ewers and D. C. J. Yeo commented on an earlier draft of this chapter. Chapter 2: R. M. Ewers, D. C. J. Yeo and Tan H. H. provided detailed comments on this chapter. C. Ng, an anonymous reviewer and P. Boon also greatly helped to improve the manuscript during submission to Aquatic conservation: Marine and Freshwater. Chapter 3: R. M. Ewers, D. C. J. Yeo and Tan H. H. provided comprehensive comments on this chapter. X. Giam and an anonymous reviewer also provided significant helpful comments to improve the manuscript during submission to Conservation Biology. Chapter 4: R. M. Ewers, D. C. J. Yeo, Tan H. H. and C. D. J. Orme provided extensive comments on an earlier version of this chapter. Chapter 5: R. M. Ewers, D. C. J. Yeo, and Tan H. H. provided helpful comments on an earlier version of this chapter. P. Chapman provided helpful insights into the analysis using spatially explicit mark recapture models. Chapter 6: R. M. Ewers and D. C. J. Yeo provided comments on this chapter. Appendix 1: Tan H. H. has commented on and put considerable amount of work into this manuscript. vii TABLE OF CONTENTS _________________________________________________________________________________________________________________ COPYRIGHT DECLARATION..................................................................................................................... iii ABSTRACT ............................................................................................................................................... iv ACKNOWLEDGEMENTS ........................................................................................................................... v DECLARTION OF ORIGINIALITY .............................................................................................................. vii TABLE OF CONTENTS ............................................................................................................................ viii LIST OF TABLES ....................................................................................................................................... xi LIST OF FIGURES .................................................................................................................................... xii CHAPTER 1: INTRODUCTION: IMPACTS OF LAND-USE CHANGE ON AQUATIC BIODIVERSITY ............... 1 1.1. FRESHWATER ECOSYSTEMS ........................................................................................................ 1 1.1.1. THE IMPORTANCE OF FRESHWATER ECOSYSTEMS ............................................................. 1 1.1.2. THREATS