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Thesis Sci 2021 De Vos Lauren.Pdf BIODIVERSITY PATTERNS IN FALSE BAY: AN ASSESSMENT USING UNDERWATER CAMERAS Lauren De Vos Thesis Presented for the Degree of DOCTOR OF PHILOSOPHY Universityin the Department ofof Biological Cape Sciences Town UNIVERSITY OF CAPE TOWN October 2020 Supervised by Associate Professor Colin Attwood, Dr Anthony Bernard and Dr Albrecht Götz The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town ii DECLARATIONS PLAGIARISM DECLARATION I know the meaning of plagiarism and declare that all the work in this thesis, save for that which is properly acknowledged, is my own. This thesis has not been submitted in whole or in part for a degree at any other university. Signature: Date: 31 October 2020 iii RESEARCH DECLARATION Research was conducted inside the Table Mountain National Park (TMNP) marine protected area (MPA) with permission from South African National Parks (SANParks). Permit Number: CRC-2014-012. Portions of the fish baited remote underwater mono-video system (mono-BRUVs) data, those pertaining to chondrichthyans, used in this thesis are published in De Vos, L., Watson, R.G.A., Götz, A. & Attwood, C.G. 2015. Baited remote underwater video system (BRUVs) survey of chondrichthyan diversity in False Bay, South Africa. African Journal of Marine Science. 37(2): 209-218. doi: 10.2989/1814232X.2015.1036119. Nothing in this publication is repeated here, neither the analyses nor the text. My thesis presents an entirely new interpretation of the data. Angle versus Range data were provided by Andrew Murray from Underwater Surveys Ltd. iv Table of Contents DECLARATIONS .............................................................................................................. ii PLAGIARISM DECLARATION .......................................................................................... ii RESEARCH DECLARATION ............................................................................................ iii List of Figures..................................................................................................................... vi List of Tables ....................................................................................................................... x ACKNOWLEDGEMENTS ................................................................................................ 1 ABSTRACT......................................................................................................................... 4 CHAPTER 1: GENERAL INTRODUCTION ................................................................... 6 1.1. Understanding patterns in marine biodiversity ................................................................ 7 1.2. Understanding patterns and processes to inform protection ............................................. 7 1.3. Assessing patterns of marine biodiversity across spatial and temporal scales .................. 8 1.4. The logistics of biodiversity mapping and monitoring in under-resourced regions .......... 9 1.5. Remote underwater photography and video for long-term monitoring .......................... 10 1.6. South African marine biodiversity ................................................................................ 11 1.7. False Bay as a case study .............................................................................................. 12 1.8. False Bay: the need for synthesis, update, and the application of new methods ............. 17 1.9. AIMS OF THESIS ....................................................................................................... 19 1.10. SPECIFIC OBJECTIVES ........................................................................................... 19 1.11. OUTLINE OF THESIS STRUCTURE ....................................................................... 19 CHAPTER 2: A NEW SYNTHESIS OF THE PHYSICAL SEAFLOOR OF FALSE BAY FROM PHOTOGRAPHS, MULTIBEAM BATHYMETRY AND SEDIMENT SAMPLES ......................................................................................................................... 21 2.1. ABSTRACT ................................................................................................................. 22 2.2. INTRODUCTION ........................................................................................................ 23 2.3. MATERIALS AND METHODS .................................................................................. 29 2.4. RESULTS .................................................................................................................... 41 2.5. DISCUSSION .............................................................................................................. 63 CHAPTER 3: A REMOTE PHOTO ASSESSMENT OF THE RELATIVE COVER AND DISTRIBUTION OF EPIBENTHIC MEGAFAUNA IN FALSE BAY ................ 77 3.1. ABSTRACT ................................................................................................................. 78 3.2. INTRODUCTION ........................................................................................................ 79 3.3. METHODS AND MATERIALS .................................................................................. 87 3.4. RESULTS .................................................................................................................... 99 3.5. DISCUSSION ............................................................................................................ 113 CHAPTER 4: THE DISTRIBUTION AND RELATIVE ABUNDANCE OF ICHTHYOFAUNA IN FALSE BAY FROM MONO- AND STEREO-BAITED REMOTE UNDERWATER VIDEO SYSTEM SURVEYS .......................................... 132 4.1. ABSTRACT ............................................................................................................... 133 4.2. INTRODUCTION ...................................................................................................... 134 4.3. METHODS AND MATERIALS ................................................................................ 138 4.4. RESULTS .................................................................................................................. 156 4.5. DISCUSSION ............................................................................................................ 184 v CHAPTER 5: SYNTHESIS OF BIODIVERSITY PATTERNS ACROSS FALSE BAY AND CONCLUSIONS .................................................................................................... 209 5.1. Towards a new description of grounds in False Bay.................................................... 210 5.2. Accounting for similarities in invertebrate and ichthyofauna distributions .................. 217 5.3. Integrating descriptions of the seafloor to provide an ecological view ......................... 218 5.4. Methods to sample pattern and process in False Bay ................................................... 219 5.5. Environmental drivers of community composition across False Bay ........................... 220 5.6. The application of remote imagery techniques to monitor the Table Mountain National Park (TMNP) marine protected area (MPA) ...................................................................... 221 5.7. The application of remote imagery techniques to monitor and manage False Bay ....... 225 5.8. The application of remote imagery techniques in monitoring of South Africa’s MPAs 226 5.9. Conclusion ................................................................................................................. 227 REFERENCES ................................................................................................................ 229 Appendix 1....................................................................................................................... 257 Appendix 2....................................................................................................................... 265 vi List of Figures Figure 1. The location of False Bay in the context of South Africa (inset map) and the Western Cape Province (inset map). Key sites are shown to give geographical context in relation to the terrestrial topography (EKZNW 2015), river network (SANBI 2011), subtidal reef geology (Van Zyl 2011) and ocean depth (m) (Van Zyl 2011) of the region. All the no-take zones (restricted zones) are shown for the Table Mountain National Park (TMNP) marine protected area (MPA) (DEA 2019a). The TMNP no-take MPAs in False Bay are the Paulsberg, Castle Rock and St James Restricted Zones. The Helderberg MPA, managed by the City of Cape Town, is shown separately (DEA 2019a). ............................................................................ 14 Figure 2. The location and name of eight study transects delineated for jump camera photographic sampling, perpendicular to the prevailing depth (m) contours (Van Zyl 2011) in False Bay, South Africa. Multibeam sonar tracks, jump camera photographs and sediment grab samples were collected on separate sampling occasions on these same transects. False Bay is shown in the context of the surrounding terrestrial topography (EKZNW 2015), subtidal reef geology (Van Zyl 2011) and marine protected areas (MPAs) (DEA 2019a). ........................ 30 Figure 3. a) A stainless-steel jump camera rig with GoPro camera
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