Niche partitioning of 5 sympatric Bornean ungulates in response to spatiotemporal variation in fruit availability and resulting implications for predator-prey interactions BY RACHEL SELWYN A thesis submitted to Victoria University of Wellington in fulfilment of the requirements for the degree of Master of Science in Ecology & Biodiversity School of Biological Sciences Faculty of Science Victoria University of Wellington July 2020 0 Author’s watercolour depiction of a Sunda clouded leopard. 1 ABSTRACT Borneo’s rainforests are experiencing some of the fastest deforestation rates worldwide and are home to increasingly vulnerable species, most of which remain poorly understood. Bornean rainforests exhibit dramatic fluctuations in fruit and seed availability during mast-fruiting events which can exert considerable influence on frugivore ecology. Comprehensive spatiotemporal assessments of habitat use, resource partitioning, and responses to fruit availability in mast-fruiting rainforests are lacking for most species, including ungulates. The distribution and habitat use of an apex predator, the Sunda clouded leopard (Neofelis diardi), may be largely shaped by the availability of these ungulates. Yet, factors driving the spatial ecology of this elusive felid remain uncertain. I aimed to quantify spatiotemporal habitat use dynamics of these species and consequently inform effective conservation planning. Specifically, I quantified the effects of human activity, forest type, elevation, and mast-induced fluctuations in resources on the habitat use of lesser mousedeer (Tragulus kanchil), greater mousedeer (T. napu), Bornean yellow muntjacs (Muntiacus atherodes), red muntjacs (M. muntjak), and bearded pigs (Sus barbatus) in Gunung Palung National Park, West Kalimantan, Indonesian Borneo. I applied data from an extensive camera trapping study (n = 42,610 trap nights) to a modified single-season occupancy model to evaluate habitat use over space and time. I then applied estimates of occurrence (훹) of the five ungulate species to quantify if habitat use of the Sunda clouded leopard was influenced by prey occurrence and thus if this apex predator responded to bottom-up effects of resource variability. The results from the ungulate modelling revealed that forest type was an important predictor of habitat use of all ungulate species, each preferring different forest habitats. Habitat use estimates were highest in peat swamp forests for lesser mousedeer (훹̂ = 0.92 ± 0.05), alluvial bench forests for greater mousedeer (훹̂ = 0.52 ± 0.08), lowland granite forests for yellow (훹̂ = 0.95 ± 0.07) and red muntjacs (훹̂ = 0.98 ± 0.09), and freshwater swamp forests for bearded pigs (훹̂ = 0.84 ± 0.07). Bearded pigs exhibited a link between variation in fruit availability and habitat use, indicating an ability to respond to resource variability. Occupancy modelling for Sunda clouded leopards revealed forest type, fruit availability, and bearded pig occurrence as the best predictors of habitat use. The highest estimates were associated with lowland granite forests (훹̂ = 0.87 ± 0.09). My results reveal a novel pattern of niche partitioning through both food and habitat resources among five sympatric ungulate species and demonstrate that Sunda clouded leopards may use fruiting events as a cue for abundant prey. My research sheds light on important factors influencing habitat use of understudied ungulates and an apex predator and can be 2 used to refine estimates of habitat suitability across a greater landscape to inform conservation practice amidst continually shrinking remnant forests in Indonesian Borneo. 3 ACKNOWLEDGEMENTS I am extremely grateful to Dr. Heiko U. Wittmer, my supervisor, for his guidance, insight, and patience. Thank you for putting up with my frequent impromptu meetings and for giving me this opportunity that ignited my interest in research. Thank you, Dr. Andrew Marshall, for all your help; for making yourself available to talk through any challenges that arose and always offering suggestions. I would like to express my gratitude for the financial support from the Eastbourne-Bays Community Trust through the Eastbourne Freemasons scholarship, and Victoria University of Wellington through the Hunter postgraduate scholarship that gave me the privilege to focus on this research without distraction. A huge thank you to the many field assistants involved in collecting the data for this project, who conducted field work in the hot humid forests and regularly trekked up the mountainside to service the cameras. I would like to extend my appreciation to Agus Trianto for the endless hours spent identifying species recorded on videos, maintaining the database, and helping work through the kinks of acquiring the data. Johannes, thank you for not only inspiring me with your beautiful graphs and analytical modelling skills, but for putting up with my endless questions. Grace—thank you for always looking out for me, the endless emotional support, and continually reminding me that it would soon be over. I cannot possibly acknowledge everyone who has helped me over the past couple years, so thank you to the many un-named supportive wonderful people around me—you are much appreciated. Mum and dad, thank you for all your support, seeing me through the frustrations, always lending an ear for advice, and the wonderful home-cooked meals that gave me sustenance. Thank you for the endless supply of walnuts that no doubt contributed some brain power. Lastly, my biggest thanks go to Henry: you stood by me through it all, I cannot put my gratitude into words. You have gotten very good at pep talks, especially through a global pandemic and the often- unpleasant process of writing up a thesis. Truly my anchor in the storm. 4 Contents Abstract ......................................................................................................................................................... 2 Acknowledgements ....................................................................................................................................... 4 List of figures ................................................................................................................................................. 7 List of tables .................................................................................................................................................. 8 Acronyms ...................................................................................................................................................... 9 Chapter 1. General introduction ........................................................................................................... 10 1.1 Introduction ...................................................................................................................................... 10 1.2 Aims................................................................................................................................................... 17 1.3 Study site ........................................................................................................................................... 18 1.4 Data collection .................................................................................................................................. 24 Chapter 2. .................................................................................................................................................... 25 Habitat use and niche partitioning of ungulates in response to spatiotemporal variation in fruit availability at Gunung Palung National Park ............................................................................................... 25 2.1 Abstract ............................................................................................................................................. 25 2.2 Introduction ...................................................................................................................................... 25 2.3 Aims................................................................................................................................................... 28 2.4 Methods ............................................................................................................................................ 30 2.4.1 Study Site ................................................................................................................................... 30 2.4.2 Data Collection ........................................................................................................................... 30 2.4.3 Occupancy modelling ................................................................................................................. 31 2.4.4 Hypothesized predictors of habitat use and detection ............................................................. 34 2.4.5 Modelling the effects of covariates on occupancy and detection probabilities ........................ 36 2.4.6 Candidate models ...................................................................................................................... 36 2.4.7 spatial overlap analysis .............................................................................................................. 37 2.5 Results ............................................................................................................................................... 37 2.5.1 Lesser mousedeer .....................................................................................................................