THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: HEAGNEY First name: Elizabeth Other name/s: Clare Abbreviation for degree as given in the University calendar: PhD (Ecology) School: Biological, Earth and Environmental Sciences Faculty: Science Title: Pelagic fish in coastal waters: hydrographie habitats, fine scale population structure and implications for spatial management Abstract Pelagic fish research and management is usually conducted at large spatial scales (100s to 1000s of kilometres) in line with the assumption that pelagic species are highly migratory, have large home ranges and comprise a single homogenous stock across their range. However, the spatial concentration of coastal pelagic fisheries, combined with unexpected increases in the abundance and biomass of selected pelagic species within coastal Marine Protected Areas (MPAs), suggest that the population dynamics and/or behavioural traits of coastal pelagic fish stocks may be structured at much smaller spatial scales. I have adapted two existing research techniques - baited remote underwater video (BRUV) and otolith chemistry - to investigate habitat associations, population structure and movement patterns of selected pelagic species at small spatial scales (100s of metres to kilometres) in two MPAs in south-east Australian waters. I combined a novel midwater BRUV technique with in situ hydrographie measurements to determine the distribution, abundance and habitat associations of selected pelagic species {Carcharhinus galapagensis, Seriola rivoliana, S. lalandi, Tractiurus novaezelandiae and Scomber australasicus) at Lord Howe Island and Jervis Bay Marine Parks, and identified areas of preferred 'habitat' for each species which were characterised with reference to hydrographie characteristics and/or small-scale oceanographic processes. I also identified significantly higher abundances of C. galapagensis in MPA sanctuary zones compared to adjacent fished waters. Multi-season otolith chemistry signatures were used to investigate the small-scale population structure and movement patterns of T. novaezelandiae in Jervis Bay Marine Park, and identified three migratory contingents within the MPA: one sub- population that was resident to the inner region of the bay, an area -60 km^ over the 9-month survey period, and two migratory sub-populations that were present in the bay over a 5 month period, but absent in our final sampling season. I also identified a significant effect of parasitism by the isopod Ceratothoa imbricata on otolith Li:Ca, Mg:Ca and Sr:Ca, which may provide an important insight into the mechanisms driving otolith elemental concentrations and the utility of this technique in discriminating pelagic fish stocks at small spatial scales. My findings contradict previous assumptions about the ecology and behaviour of pelagic species. They also have important implications for the sustainable management of coastal pelagic fish stocks, particularly in terms of the potential for relatively small coastal MPAs to protect pelagic fish populations, and the MPA zoning strategies that could be employed to maximise any potential benefit to these heavily exploited stocks. Declaration relating to disposition of project thesis/dissertation I hereby grant to the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or in part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all property rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstracts International (this is applicable to doctoral theses only). Signal u Witness Date The University recognises that there may be exceptional circumstances requiring restrictions on copying or conditions on use. Requests for restriction for a period of up to 2 years must be made in writing. Requests for a longer period of restriction may be considered in exceptional circumstances and require the approval of the Dean of Graduate Research. FOR OFFICE USE ONLY Date of completion of requirements for Award: THIS SHEET IS TO BE GLUED TO THE INSIDE FRONT COVER OF THE THESIS Pelagic fish in coastal waters: hydrographie habitats, fine scale population structure and implications for spatial management Elizabeth Heagney University of New South Wales PhD Thesis Supervised by Prof. Iain Suthers Submitted April 2009 ORIGINALITY STATEMENT 'I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.' Signed Date ^^.i.-.O'T, COPYRIGHT STATEMENT 'I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968.1 retain all proprietary rights, such as patent rights. I also retain the right to use in future wori<s (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstract International (this is applicable to doctoral theses only). I have either used no substantial portions of copyright material in my thesis or I have obtained permission to use copyright material; where pennission has not been granted I have applied/will apply for a partial restriction of the digital copy of my thesis or dissertation.' Signed ..Ur. Date AUTHENTICITY STATEMENT 1 certify that the Library deposit digital copy is a direct equivalent of the final officially approved version of my thesis. No emendation of content has occun'ed and if there are any minor variations in fomriatting, they are the result of the conversion to digital fonnat.' Signed Date 1- \l-[o Acknowledgements This project was supervised by Iain Suthers (University of New South Wales), with selected chapters co-supervised by Russ Babcock (Commonwealth Scientific and Industrial Organisation - CSIRO), Bronwyn Gillanders (University of Adelaide) and Tim Lynch (Jervis Bay Marine Park). Research funding was provided by Sea World Research and Rescue Foundation Inc., CSIRO and the New South Wales Marine Parks Authority, and a research stipend was provided by the Australian Government (Australian Post-graduate Award Scholarship). Thanks to Mick Lowry, John Stewart, Doug Ferrell and Will Robbins (New South Wales Department of Primary Industries) for advice on baited video and otolith sampling, and for access to otolith samples and reference collections and to Mark McGrouther (Australian Museum) for assistance with species identification. Thanks to Adrian Nute for assistance designing our mid-water video system, and to charter boat operators Ron Simpson (Simo's Afloat) and Peter Bond. Thanks to Eva Kylberg, Rich Allman and Louise McKenzie for assistance in the field. Thanks to Ash Fowler (now at the University of Technology, Sydney), Eva Kylberg, Andrew Monroe (University of Adelaide) and Angus Netting (Adelaide Microscopy) for assistance with otolith preparation and analysis. Table of Contents List of Tables 5 List of Figures 7 Abstract 9 Chapter 1 - General Introduction 11 Background to pelagic fish and fisheries 11 Pelagic fish and Marine Protected Areas 12 Obstacles to pelagic fish research 14 Mid-water baited remote underwater video 15 Otolith chemistry 16 Structure of the thesis 17 Chapter 2 - Pelagic fish assemblages assessed using mid-water baited video: standardising fish counts using bait plume size 18 Introduction 19 Materials and methods 21 Study site 21 Sampling design 21 Mid-water BRUV design 23 Image analysis 25 Estimating fish abundance 26 Identifying pelagic fish habitat 28 Results 29 Pelagic fish assemblages around Lord Howe Island 29 Estimating fish abundance 31 Identifying pelagic fish habitat 31 Effect of bait plume assumptions 36 Discussion 40 Pelagic and mid-water fish assemblages at Lord Howe Island 40 Estimating fish abundance from mid-water BRUV: accounting for current speed 41 Chapter 3 - Small pelagic fish distribution, abundance and habitat in a coastal Marine Protected Area assessed using mid-water baited video 45 Introduction 46 Materials and methods 48 Study site 48 Sampling design 48 Mid-water BRUV design 50 Video analysis 51 Identifying pelagic fish habitat 53 Results 54 Mid-water BRUV for surveying small pelagics 54 Small pelagic fish distribution and abundance 57 Discussion 66 Small pelagic fish distribution and abundance 66 Mid-water BRUV for small pelagic fish surveys 68 Conclusions 70 Chapter 4 - Population structure and movement patterns of Trachurus novaezelandiae in a coastal Marine Protected