Agent-based modelling of short-term juvenile bull shark movement in a semi-enclosed Gold Coast estuary Jonas Brandi Mortensen B.Sc. (University of Copenhagen) School of Environment Science, Environment, Engineering and Technology Griffith University Submitted in fulfilment of the requirements of the degree of Master of Philosophy December 2011 I STATEMENT OF ORIGINALITY This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the thesis contains no material previously published by another person except where due reference is made in the thesis itself. .................................................................... Jonas Brandi Mortensen 14th December 2011 II ACKNOWLEDGEMENTS First and foremost I would like to extend my warmest thanks to my Principal Supervisor, Professor Joe Lee, for believing in me and allowing me to undertake this research project under his supervision. Thank you for your guidance and support over the past two years, especially here in the last few dramatic months. Also thanks to Dr Guy Castle for acting as my associate supervisor, and guiding me through the tricky waters of my Confirmation paper back in the early days. Special thanks goes out to Jonathan Werry for helping me establish this project with the Australian Rivers Institute, while also helping me with the shark catching effort and supplying me with the necessary equipment needed for the acoustic tracking campaign. My most sincere thanks goes out to the DHI for supplying me with a free MIKE software license over the course of my study, but most importantly I would like to thank Flemming T. Hansen for all the ABM support he has provided me over the past two years, and for allowing me to stay in his office for three months while teaching me how to use the MIKE ABM module. I would also like to extend a special thanks to Michael Pothoff for his technical ABM troubleshooting, and most importantly; for fixing that bug in the software that prevented me from completing ABM simulations! Furthermore I would like to thank Anders Erichsen and Thomas Uhrenholdt, as well as the many other DHI employees who helped me with technical advice, while also making my stay in Hørsholm a pleasant one. My warmest thanks and gratitude goes out to the Queensland Urban Fish Habitat Management Research Program and the Gold Coast City Council for funding part of my research, as well as the Danish State Government for sponsoring my tuition fees and living costs for the duration of this project. Also I would like to direct a special thanks to the Bureau of Meteorology (BOM), the Queensland Department of Resource Management (DERM) as well as the Environmental Ecosystem Health Program (EHMP) of Southeast Queensland for providing me with essential input data free of charge. Furthermore, I would like to direct my warmest thanks to the following people for aiding me with the many various aspects of this research project: Associate Professor Charles Lemckert - For allowing me to use two very expensive Acoustic Doppler Current Profilers free of charge. It goes without saying that without III your help the available validation data of the hydrodynamic model would have been quite lacking. Paul Maxwell - For helping me with the historical EHMP data, and assisting me in the shark tracking campaign during the latest of hours, while being eaten alive by mosquitoes. Also thanks for the many good laughs in lab. Johan Gustafson - For his help with constructing a mounting frame for the two ADCP‟s, as well as the actual deployment and retraction of the instrument, plus his ongoing moral support throughout the thesis. Geoffrey Turner, Ian Underhill and Malcolm Duncan - For allowing me into the Engineering bay, as well as provide excellent guidance and assistance in the construction of a mountable hydrophone rig for the Portunus. Joshua Reinke - For continuing the water quality campaign during my time away from the Gold Coast, while aiding me on several occasions with the actual shark tracking. Simon Kerville and Alan Richards - For tirelessly helping me out with essential lab equipment for chlorophyll analysis, as well as saving me from trouble in the field. All the many volunteers who have been helping me with the shark tracking campaign and other assorted field work; Ciaran Morris, Alf Okkels Jakobsen, Sophie Olsson- Pons, Thomas Baatz Andersen, Sarah Richmond, Carl Brown-Kenyon, Barbro Haug- land, Sameer Shah and Louise Pointon. Last but not least, I would like to thank my brother, Simon Brandi Mortensen, for providing me with a place to call home these past three years that I have spent in Australia, while also guiding me through the many pitfalls of hydrodynamic modelling and Matlab scripting. I can honestly say that your constant moral support has been the glue that held me together through the hardest of times, and I will be forever grateful to you. Finally, my warmest of thanks goes out to my family and friends back home in Denmark for believing and supporting me throughout this entire venture. Your continuous motivational support has been invaluable and keeps pushing me forever forward. IV ABSTRACT This project investigated the value and future potential of a coupled Eulerian-Lagrangian agent-based modelling approach as an alternative method of investigating the movement and habitat use of juvenile bull shark Carcharhinus leucas in small peri-urban estuaries. Through the use of the MIKE21 modelling suite (DHI), a depth-averaged two-dimensional hydro- dynamic model was developed and implemented as a means to capture the spatio-temporal variation in hydrodynamics of the semi-enclosed Tallebudgera Creek estuary. This system provides a suite of habitats comprising artificial residential canals, polyhaline and brackish creek sections in a peri-urban setting. The hydrodynamic model served as the dynamic foundation of a spatially heterogeneous agent-based model (ABM) developed for juvenile C. leucas. The movement formulation of juvenile C. leucas was represented as a kinesis search for optimal conditions, while a random walk model served as a control. The hydrodynamic model performed satisfactorily in terms of capturing the variations of key physical conditions of Tallebudgera Creek. Modelled values of surface elevation and flow dynamics were in good agreement with measured data sets. Simulated mean levels of salinity and temperature were likewise in good agreement with measured means; however, model analysis revealed a high sensitivity to increased freshwater influxes, and a delay in model response time. Three neonate and juvenile individuals of C. leucas were captured and attached with acoustic tags for tracking of movement in Tallebudgera Creek. Short-term continuous tracks of a juvenile C. leucas were successfully collected as a means to relate observed movement to out- puts of the hydrodynamic model and measurements of water quality, while consecutive data- points of animal position served as validation data for the agent-based model. Analysis of C. leucas track data revealed a high site preference for the middle reach of the system over the course of the tracking campaign, even during periods when salinity levels were < 1 PSU. However, an avoidance of high salinities > 27 PSU was evident. Significant movement of the animal in a downriver direction only occurred after a period of increased flow velocities and turbidity, suggesting that these parameters may play an important role in directing shark movement in conjunction with salinity. V The agent-based models in their current developmental stage performed unsatisfactorily in capturing observed movement, and their predictive ability was generally poor. The current ABM formulation of C. leucas movement is therefore insufficient to capture the observed pattern of behaviour. However, unforseen technical difficulties originating from the narrow and shallow nature of the Tallebudgera Creek system prevented a full assessment of the ABM results. Despite current technical issues that were impracticable to be resolved under the available timeframe, this study represents a first attempt to construct and implement agent-based modelling to investigate bull shark movement and habitat use in a spatially and temporally dynamic hydrologic environment. It is predicted that once these technical difficulties are overcome, agent-based modelling as a research tool holds great promise for future investigation of the habitat ecology of C. leucas to benefit its conservation and management. VI TABLE OF CONTENTS Statement of originality ............................................................................................................. II Acknowledgements .................................................................................................................. III Abstract ..................................................................................................................................... V List of figures ........................................................................................................................... XI List of tables .......................................................................................................................... XVI Ethics approval ................................................................................................................... XVIII Chapter I: General introduction and research aims ............................................................. 1 1.1. General introduction .......................................................................................................