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Dunlop, Katherine Mary (2013) Baited Underwater Camera Studies of the Biodiversity and Abundance of Animals in the Temperate, Tr

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Dunlop, Katherine Mary (2013) Baited Underwater Camera Studies of the Biodiversity and Abundance of Animals in the Temperate, Tr Dunlop, Katherine Mary (2013) Baited underwater camera studies of the biodiversity and abundance of animals in the temperate, tropical and Antarctic marine environment. PhD thesis. http://theses.gla.ac.uk/4633/ Copyright and moral rights for this thesis are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the Author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the Author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Glasgow Theses Service http://theses.gla.ac.uk/ [email protected] Baited underwater camera studies of the biodiversity and abundance of animals in the temperate, tropical and Antarctic marine environment Katherine Mary Dunlop Bsc Marine and Environmental Biology/ Mres Marine and Freshwater Biology and Environmental Management Submitted in fulfillment of the requirements for the Degree of Doctor of Philosophy Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow September 2013 1 Abstract Baited underwater camera (BUC) systems are becoming popular in the shallow water environment to monitor the relative diversity and abundance of fish and invertebrate assemblages. This thesis describes methods developed to use BUCs in temperate, tropical and Antarctic environments and their application to questions concerning the factors controlling shallow water marine biodiversity and abundance. In Chapter 2 the design and development of a BUC system suitable for attracting, identifying and counting temperate shallow water (< 30 m) fish and crustacean species on the West coast of Scotland is described. The use of BUC systems has been limited in temperate waters and a cost- and – time efficient method could be valuable to monitor the before and after impact of the proposed Scottish Marine Protected Area network. As a test of the BUC, deployments were made in Lamlash Bay no-take zone (NTZ) and in two control open sites to provide baseline data early in the life of the NTZ against which future BUC studies can be compared. The tropical Gulf of Aqaba supports unique coral reef fish assemblages and it is important to perform a study specific in this distinct biogeographical region to understand whether BUC surveys could be useful in this sensitive environment. In Chapter 3 we therefore compared the predatory fish assemblages recorded in BUC deployments to the established method of Underwater Visual Census (UVC) surveys in the northern Gulf of Aqaba. Abundance metrics from the arrival pattern of fish at the BUC did not correlate with population abundance estimates from UVCs and it was concluded that until improved methods of interpreting BUC data are developed the deployment of BUCs could be used to assess predator species richness but is not able to indicate relative variation in population abundance. Chapter 4 demonstrates how BUC systems can be used to gather data on a complicated ecological question in extreme conditions. A BUC system was used to examine the distribution of scavenging fauna in relation to the spatial variation in exposure to iceberg impacts experienced at difference iceberg scouring conditions and depths within Marguerite Bay. The results indicate that different scavenger species are adapted to high and low iceberg scouring environments and that they are distributed in accordance with the recognised pattern of decreasing iceberg scouring frequency with depth. The above studies used relative measures of abundance such as recording the highest number of individuals observed at a single time (MaxN). Such measures are limited in their usefulness but there are no robust means of estimating absolute abundance, especially for complex shallow water systems. In Chapter 5 a modelling approach, using a stochastic 2 simulation, was developed and used to estimate population abundance for species commonly observed in the above studies. Model abundance estimates were generally found to be comparable to those from corresponding UVC transects. This modelling approach has the potential to substantially improve the ability of BUC systems around the world to assess fish and invertebrate diversity and abundance. 3 Table of Contents Chapter 1. Overview ……..………………………………………………………..1 - 28 1.1 What is Marine Biodiversity?………………….……………………………………..1 1.2. Why is Marine Biodiversity Important? …………………………………………2 - 4 1.3. Measuring Marine Biodiversity………………………………………………….4 - 5 1.4. Spatial Patterns in Marine Biodiversity………………………………………….5 - 6 1.5. Threats to Marine Biodiversity…………………………………………………6 - 10 1.5.1. Fisheries………………………………………………………………………7 - 10 1.6. Survey and Monitoring of Marine Biodiversity ……………………………....10 - 16 1.6.1. Fisheries - Dependent Data………………………………………………….10 - 11 1.6.1.1 Fisheries Indicator Species…………………………………………………11 - 12 1.6.2. Fisheries - Independent Data………………………………………………...12 - 16 1.6.2.1 Research Trawls ………………………………………………………………..12 1.6.2.2 Acoustic Surveys ……………………………………………………………….13 1.6.2.3. Egg Surveys……………………………………………………………………..13 1.6.2.4 Underwater Visual Census (UVC) Surveys………………………………..13 - 15 1.6.2.5 Surveys Using Underwater Camera Systems ……………………………..15 - 16 1.7. Baited Underwater Camera …………………………………………………...16 - 25 1.7.1. Baited Underwater Cameras in the Deep Water Environment ……………..17 - 19 1.7.2. Baited Underwater Camera in the Shallow Water Environment……………19 - 22 1.7.2.1. Baited Underwater Camera in the Tropical Shallow Water Environment...19 - 21 1.7.2.2. Baited Underwater Cameras in Temperate Coastal Waters…………….……...21 1.7.2.3 Baited Underwater Cameras in Shallow Polar Waters…………………….21 - 22 1.7.3. Baited Underwater Camera Data Analysis Methods………………………..22 - 25 1.7.3.1 Abundance and Diversity…………………………………………………..22 - 25 1.8. Conclusion………………………………………….……………………………....25 1.9. Thesis Aims and Objectives …………………………………………………..25 - 27 1.10. Thesis Content Flowchart………………………………………………………....28 2. Development of a low-cost baited underwater camera survey method for UK coastal marine systems and its application to a “no take zone” and two open areas in the Firth of Clyde, Scotland………………………………...………………….29 - 68 2.1. Abstract……………………………………………………………………………..29 2.2. Introduction……………………………………………………………………30 - 34 2.3. Aims and Objectives…………………………………………………………..34 - 36 2.3.1. Objective 1…………………………………………………………………..33 - 35 2.3.2. Objective 2……………………………………………………………………….35 2.4. Material and Methods…………………………………………………………35 - 45 4 2.4.1. Objective 1…………………………………………………………………..35 - 40 2.4.1.1. Baited Underwater Camera Equipment………………………………………..35 2.4.1.2. Deployment Equipment…………………………………………………...35 - 37 2.4.1.3. Methodological Tests…………………………………..………………………38 2.4.1.4. Lighting Effects………...………………………………………………………38 2.4.1.5. Test Deployment Details…………………………………..…………………...38 2.4.1.6. Image and Data Analysis…………………………………………………........39 2.4.2. Objective 2…………………………………………………………………..41 - 45 2.4.2.1. Deployment Equipment and Procedure………………………………..………41 2.4.2.2. Deployment Sites………………………...………………………………..41 - 42 2.4.2.3. Image and Data Analysis………………………………..………………...43 - 45 2.5. Results………………………………………………………………………....45 - 61 2.5.1. Objective 1 ………………………………………………………………….45 - 49 2.5.1.1. Camera Settings………………………………………………………………...45 2.5.1.2. Lighting Effects ……………………...………………………………………...45 2.5.1.3. Species Attracted and Duration of BUC Deployments…………………...46 - 49 2.5.2. Objective 2…………………………………………………………………...50- 55 2.5.2.1. Species Richness………………………………..………………………....50 - 51 2.5.2.2. MaxN……………………………………………………..…………….….51 - 52 2.5.2.3. tarrival ………………………………………………………...…………………..52 2.5.2.4. tmaxN……………………………………………..……………………………...52 2.5.2.5. Assemblage………………………………………………………………..56 - 61 2.6. Discussion …………………………………………………………………….62 - 66 2.6.1. Objective 1…………………………………………………………………..62 - 63 2.6.2. Objective 2…………………………………………………………………..64 - 66 2.7. Conclusion………………………………………………………………………….66 2.8. Acknowledgements………………………………………………………………...67 Chapter 3. Comparisons between baited underwater camera and visual census surveys of shallow coral reef fish communities in the northern Gulf of Aqaba……………………………………………………………………………....68 - 108 3.1. Abstract……………………………………………………………………………..68 3.2. Introduction……………………………………………………………………69 - 72 3.3. Aims and Objectives………………………………………………………………..72 3.3.1. Objective 1…………………………………………………………………..72 – 73 3.3.2. Objective 2………………………………………………………………………..73 3.4. Materials and Methods………………………………………………………...73 - 80 3.4.1. Study Area……………………………………………………………………73 - 74 5 3.4.2 Baited Underwater Camera System………………………………………….74 - 75 3.4.2.1. Deployment Methods……………………………………………………...75 - 76 3.4.3. Underwater Visual Census………………………………………………….76 - 78 3.3.4. Image and Data Analysis……………………………………………………78 - 80 3.5. Results…………………………………………………………………………80 - 94 3.6. Discussion……………………………………………………………………..94 - 99 3.6.1. Differences in Sample Area…………………………………………………96 - 97 3.6.2. UVC Abundance Estimation ………………………………………….…....97 - 98 3.6.3. Previous Comparisons……………………………………………………….98 - 99 3.6. Conclusion………………………………………………………………………….99 3.7. Acknowledgements………………………………………………………………...99 4. Chapter 4. The impact of iceberg scouring on scavenger diversity, abundance and behaviour in the West Antarctic Peninsula………………………………………100
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