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Applications and Limitations of Spatially-Explicit Mechanistic Models for Animal Conservation’

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Applications and Limitations of Spatially-Explicit Mechanistic Models for Animal Conservation’ UNIVERSITY OF SOUTHAMPTON Applications and limitations of spatially-explicit mechanistic models for animal conservation by Alice Elizabeth Ball PhD Thesis in Biological Sciences, Faculty of Natural and Environmental Sciences, and Institute for Complex Systems Simulation June 2018 1 UNIVERSITY OF SOUTHAMPTON ABSTRACT BIOLOGICAL SCIENCES, FACULTY OF NATURAL AND ENVIRONMENTAL SCIENCES, and INSTITUTE FOR COMPLEX SYSTEMS SIMULATION Doctor of Philosophy APPLICATIONS AND LIMITATIONS OF SPATIALLY-EXPLICIT MECHANISTIC MODELS by Alice Elizabeth Ball We live in a world of human-induced rapid environmental change, where the frequency of extinctions and resulting loss in biodiversity has reached levels associated with a mass extinction event. At the same time, technological developments in computing have facilitated the growth of highly complex, mechanistic models across all scientific fields. The challenge for conservation biologists is then to develop models that can predict how organisms respond to conservation measures and increasing anthropogenic pressures. Here I explore the potential and limitations for conservation applications of spatially-explicit mechanistic models of habitat selection, by developing a simulation applicable to large felids. I demonstrate that initial choice of resolution may bias the parameterisation process of spatially-explicit models, when applied to spatially-explicit empirical data. I use mechanistic models to address two current problems in conservation biology: (a) efficient calculation of movement metrics from telemetry data, tested with a virtual ecology approach; and (b) accounting for interacting influences on populations, quantified with a model that controls for confounding variables. I identify the major caveats to accurately predicting the complex behaviour of large-bodied animals. The spatially-explicit mechanistic models developed here, and applied to real-world problems, demonstrate the potential of these types of simulation for confronting otherwise impossible questions in diverse areas of conservation biology. 2 Table of contents Abstract ................................................................................................................................................ 2 Table of contents ................................................................................................................................. 3 List of figures ...................................................................................................................................... 5 List of tables ........................................................................................................................................ 6 Acknowledgements ............................................................................................................................. 9 Abbreviations and Definitions ........................................................................................................... 10 Chapter 1. Introduction ..................................................................................................................... 11 1.1 Agent-based modelling in ecology .............................................................................................. 12 1.2 Optimisation and parameterisation of agent-based models ......................................................... 17 1.3 Virtual ecology for developing empirical methodology ............................................................. 20 1.4 Mechanistic models in conservation ........................................................................................... 24 1.5 Thesis aims .................................................................................................................................. 33 Chapter 2. Effects of model resolution on fit to empirical data ...................................................... 35 2.1 Introduction ................................................................................................................................. 37 2.2 Methods ....................................................................................................................................... 40 2.3 Results ......................................................................................................................................... 49 2.4 Discussion .................................................................................................................................... 61 2.5 Appendix I. Overview, Design concepts and Details .................................................................. 65 Chapter 3. A method for correcting estimates of metrics derived from radiotelemetry movement data ....................................................................................................................................................... 71 3.1 Introduction ................................................................................................................................. 73 3.2 Methods ....................................................................................................................................... 76 3.3 Results ......................................................................................................................................... 79 3.4 Discussion .................................................................................................................................... 87 Chapter 4. Using a high-resolution mechanistic model to evaluate anthropogenic impacts on jaguar populations .............................................................................................................................. 93 4.1 Introduction ................................................................................................................................. 95 4.2 Methods ....................................................................................................................................... 97 4.3 Results ....................................................................................................................................... 105 4.4 Discussion .................................................................................................................................. 114 4.5 Appendix I. Overview, Design concepts and Details ................................................................ 118 3 Chapter 5. Discussion ....................................................................................................................... 125 5.1. Introduction .............................................................................................................................. 126 5.2 Parameterisation of spatial models ............................................................................................ 126 5.3 Models for use in virtual ecology .............................................................................................. 128 5.4 Simulation of responses to HIREC ............................................................................................ 130 5.5 Limitations ................................................................................................................................. 130 5.6 Future work ............................................................................................................................... 132 5.7 Concluding statements ............................................................................................................... 133 Bibliography ...................................................................................................................................... 135 4 List of figures Chapter 2. Effects of model resolution on fit to empirical data Figure 1. The location of the study site, Cockscomb Basin Wildlife Sanctuary (CBWS), within Belize. ....................................................................................................................... 41 Figure 2. Process for each replicate. .................................................................................... 44 Figure 3. Flowchart for each time step. ............................................................................... 45 Figure 4. The process for the move.. ................................................................................... 47 Figure 5. Summary statistics as from empirical and modelled data. ................................... 53 Figure 6. Summary statistics as a function of cell size. ....................................................... 55 Figure 7. MCP size as a function of grid cell size. .............................................................. 57 Figure 8. Normalised parameter values selected by the parameterisation process for three different resolutions. ............................................................................................................ 58 Chapter 3. A method for correcting estimates of metrics derived from radiotelemetry movement data Figure 1. The relationship between time-lag and error (in metres) in step length for six movement algorithms. .......................................................................................................... 82 Figure 2. The relationship between time-lag and error (in metres) in MCP for six movement algorithms.. ......................................................................................................... 86 Chapter 4. Using a high-resolution mechanistic model
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