Evaluation of Baited Remote Underwater Video Systems (BRUVS) for monitoring fish communities in Lake Malawi/Niassa This thesis is submitted in fulfilment of the requirements for the degree of MASTER OF SCIENCE at RHODES UNIVERSITY by ANGUS VAN WYK December 2019 i ABSTRACT Baited Remote Underwater Video systems (BRUVS) have become a well-established in-situ monitoring technique in clearwater aquatic ecosystems. The relatively low cost, non- destructive and non-extractive nature of this technique permits BRUVS to be employed in a wide range of habitats. To date, the vast majority of studies using BRUVS technology have been conducted in marine habitats. Subsequently, BRUVS applications in freshwater habitats are scant, and techniques are not well developed. The primary objective of this thesis was to address this knowledge gap and develop standard operating procedures for BRUVS employment in Lake Malawi/Niassa and explore the potential of BRUVS as a monitoring tool for fish communities in the African Great Lakes. Eight easily identifiable species groups, representative of Lake Malawi/Niassa inshore fish communities, were used to develop the technique. The optimal BRUVS deployment time to obtain 95 % species accumulation was achieved in a 15-minute recording period. Power analysis, using a pre-determined 80 % power, a confidence interval of 95 % and a significance level of < 0.05 was used to determine annual sampling effort requirements for each species group. The power analysis was performed to detect a 10 % change in abundance over a hypothetical 10-year monitoring scenario. In areas where fish abundance was lower, the sampling effort required to monitor key fisheries species was significantly higher. For example, Chambo, the local Oreochromis (Nyasalapia) species flock, required an annual sampling effort of 120 deployments in Malawi compared to 56 in Mozambique ( < 0.05). Chambo had a higher detection probability in areas of lesser fishing pressure and were found in higher abundances in deeper, less accessible habitats. Deep-water (> 20 m) and rocky habitats were most important in explaining Chambo abundance and detection probability. The size-structure of Chambo in Lake Malawi/Niassa reflects size-specific depth and habitat migrations. Larger Chambo were observed aggregating in waters deeper than 20 m and a broader size range of individuals were observed utilising structured habitat. The effects of fishing are apparent in the size-structure of Chambo in the areas sampled. In study areas exposed to greater levels of fishing pressure – such as Malawi, the BRUVS detected significantly fewer individuals within sexually mature size classes, and the average size was smaller than in areas with less exploitation. Keywords: Freshwater, Africa, Lake Malawi/Niassa, baited remote underwater video, BRUVS ii TABLE OF CONTENTS GENERAL INTRODUCTION ............................................................................................... 1 MONITORING FRESHWATER FISH COMMUNITIES USING REMOTE UNDERWATER VIDEO TECHNOLOGY: A SYSTEMATIC REVIEW OF AFRICAN RESEARCH ............................................................................................................................. 8 INTRODUCTION ................................................................................................................. 9 METHODS & MATERIALS ............................................................................................... 12 RESULTS AND DISCUSSION .......................................................................................... 12 CONCLUSIONS AND RECOMMENDATIONS ............................................................... 25 OPTIMAL BAITED REMOTE UNDERWATER VIDEO SAMPLING DESIGN FOR LONG-TERM MONITORING OF KEY SPECIES IN LAKE MALAWI/NIASSA ...... 27 INTRODUCTION ............................................................................................................... 28 MATERIALS & METHODS ............................................................................................... 31 RESULTS ............................................................................................................................ 48 DISCUSSION ...................................................................................................................... 57 REMOTE UNDERWATER VIDEO MONITORING OF CHAMBO (OREOCHROMIS SPP.) IN LAKE MALAWI/NIASSA .................................................. 63 INTRODUCTION ............................................................................................................... 64 MATERIALS & METHODS ............................................................................................... 69 RESULTS ............................................................................................................................ 86 DISCUSSION .................................................................................................................... 100 GENERAL DISCUSSION AND CONCLUDING REMARKS ...................................... 107 REFERENCE ....................................................................................................................... 115 APPENDIX ............................................................................................................................... I iii ACKNOWLEDGEMENTS My MSc degree has been a great adventure. It would not have been possible, however, without my two supervisors. Professor Olaf Weyl and Doctor Anthony Bernard. Olaf, I will always be thankful for the opportunities that you have given me and for taking time out of your busy life to help me become a better researcher and scholar. And Ant, I cannot thank you enough for all your help and great advice that you have given me over the past few years – it has been a pleasure to be your student. I acknowledge use of infrastructure and equipment provided by the South African Institute for Aquatic Biodiversity (SAIAB) and funding channelled through the NRF-SAIAB Institutional Support system I want to express my sincere gratitude to my master’s degree funder, the National Research Foundation (NRF) of South Africa, DSI-NRF – South African Research Chairs Initiative of the Department of Science and Innovation (Grant No. 110507), to the funder of the Lake Malawi remote imagery research, the World Wide Fund for Nature (WWF) and the Department of Ichthyology and Fisheries Science (Rhodes University). The research that went into this thesis would not have been possible, of course, without a great team of international collaborators. This includes Antonio Pegado and Carlos Jonasse from the Instituto de Investigação de Pesquera, Eugido Gobo from WWF-Mozambique, Maxon Ngochera from the Malawi Fisheries Research Institute and the incredible research team at the SAIAB. Jeff, Sanet, Ferdi, Josie, Taku and the rest of the SAIAB family, thank you all so much for your help along the way. Two anonymous external examiners are also thanked and acknowledged for providing helpful and constructive comments which improved the thesis My final massive thank you is to my partner, family and friends. Megan, thank you for always being in my corner and for your endless positivity. To my dad and Mavic, thank you again for tirelessly supporting me and my decisions. I could not have two better parents and role models. iv DECLARATION I have read and understood the University’s Policy on Plagiarism. All of the work in this essay is my own. I have not included ideas, phrases, passages or illustrations from another person’s work without acknowledging their authorship. Name: Angus van Wyk Date: December 2019 This thesis has been formatted for journal submission. NRF FILE PLAN: ANIMAL ETHICS - 25/4/1/7/5 v CHAPTER 1 GENERAL INTRODUCTION GENERAL INTRODUCTION Deployment of stereo-BRUVS into Lake Malawi (Top), image of the bright yellow Metriaclima estherae upon a reef in the Lake Niassa Reserve (Bottom). P.C. Angus van Wyk (SAIAB) CHAPTER 1 GENERAL INTRODUCTION On a global scale, destructive human practices and climate change are driving biodiversity loss at an unprecedented rate (Pimm et al. 2014). Determining trends and definite effects of these losses remains, however, a significant challenge – the consequences of which, are devastating for those human populations dependent upon the affected systems (Cardinale et al. 2012, Hoffmann et al. 2014, Schmeller et al. 2017). No more is this occurrence as apparent as it is in freshwater lakes, rivers, streams and wetlands. Freshwater habitats, although only comprising 1 % to the total surface area of Earth, contribute a disproportionate number of vertebrate species and approximately 40 % of all described fish species (Dudgeon et al. 2006, Darwall et al. 2018). Nevertheless, there is a significant paucity in understanding both the rate and effects of biodiversity loss in the freshwater realm which has, in the past lead to fisheries management being reliant upon adaptive measures – lacking baseline information or a thorough understanding of the system and its supported species (Strayer and Dudgeon 2010, Weyl et al. 2010). Lake Malawi, also referred to as Lake Niassa (11.670°S, 34.686°E), is one such freshwater system that supports high levels of biodiversity whilst simultaneously being exposed to multiple stressors (Weyl et al. 2010). Lake Malawi is the 9th largest lake in the world and the 3rd largest lake in Africa. Although not being the Earth’s largest or deepest lake, Lake Malawi supports over half a million people through its various fisheries and boasts