SPATIAL MANAGEMENT STRATEGIES FOR DEEP-SEA SHARKS by Ross Kelvin Daley BSc This thesis is submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the CSIRO-UTAS PhD Program in Quantitative Marine Science. Institute of Marine and Antarctic Studies University of Tasmania, Australia 4 th July 2017 Those who go down to the sea in ships, who do business on great waters; they have seen the works of the LORD, and his wonders in the deep. Psalm 107. STAEMENTS AND DECLARATIONS Declaration of Originality This thesis contains no material that has been accepted for a degree or diploma by the University or any other institution, except by way of background information and duly acknowledged in this thesis and to the best of my knowledge and belief, no material previously published or written by another person except where due acknowledgement is made in the text of the thesis, nor does this thesis contain material that infringes copyright. Authority of Access This thesis may be made available for loan and limited copying and communication in accordance with the copyright Act 1968. Statement regarding published work contained in thesis The publishers of the papers comprising Chapters 2 and 3 hold the copyright for that content and access to that material should be sought from those journals. The remaining non- published content of the thesis may be made available for loan and limited communication in accordance with the copyright Act 1968. Statement of Ethical Conduct The research associated with this research abides by Australian Code for the care and use of animals for scientific purposes. The research conducted for this thesis was approved by the Animal Ethics Committee of the Tasmanian Department of Primary Industries, Parks, Water and Environment (Project AEC 1/2009-10). Ross Kelvin Daley Hobart, 15th of March, 2017 i Statement of co-authorship The following people and institutions contributed to the publication of work undertaken as part of this thesis. Dr. Sharon Appleyard, CSIRO National Collections Dr. Matthew Koopman, Fishwell Consulting Dr. Alan Williams, CSIRO Oceans and Atmosphere Mark Green, CSIRO Oceans and Atmosphere Bruce Barker, CSIRO Oceans and Atmosphere Pamela Brodie, CSIRO Oceans and Atmosphere Author details and there roles: Paper 1, Genetic catch verification to support recovery plans for deep-sea gulper sharks. Located in chapter 2 The candidate was the primary author. Sharon Appleyard collected the data analysed in this paper. Mathew Koopman collected some genetic samples, coordinating with the fishing industry. Paper 2, Can marine reserves conserve vulnerable sharks in the deep sea? A case study of Centrophorus zeehaani, (Centrophoridae) examined with acoustic telemetry. Located in chapter 3 The candidate was the primary author. Alan Williams contributed to the acoustic array design, collected sea floor mapping data and contributed to analysis. Bruce Barker and Mark Green provided field support at Sea. Pamela Brodie contributed to coding of the survivorship analysis. We the undersigned agree with the above stated “proportion of work undertaken” for each of We the undersigned agree with the above stated “proportion of work undertaken” for each of the above published peer-reviewed manuscripts contributing to this thesis: Associate Professor Jayson Semmens Professor Chris Carter Primary Supervisor Director Fisheries and Aquaculture Centre Fisheries and Aquaculture Centre Institute for Marine and Antarctic Studies Institute for Marine and Antarctic Studies University of Tasmania University of Tasmania ii ACKNOWLEDGEMENTS I would like to start by expressing my heart-felt gratitude to my supervisors Jayson Semmens and Alistair Hobday for their guidance, support and patience over many years. To the other research voyage leaders Mark Green, Bruce Barker and Alan Williams as well as the scientific and fishing crews of the RV ‘Southern Surveyor, RV ‘Ngerin, RV ‘Bluefin’, RV ’Naturalist’, FV ‘Diana, FV ‘Sarda, FV ‘Lucky S’ and FV ‘Riba’, thank you for your commitment to more than 20 voyages up to 100 miles offshore away from your families. I also thank Justin Bell and Grant Johnson for their contributions to the 2005 surveys that located the population and of C. zeehaani in the Great Australian Bight and developing the handling methods for live Centrophorus that made the tracking studies possible. I would like to acknowledge the contribution of Australian Commonwealth Government Departments to this work. The Australian Fisheries Management Authority developed the recovery plan for C. zeehaani and C. harrissoni with input from the Department of Environment. The Fisheries Research and Development Authority provided financial support and encouragement. I would like to thank my work supervisors Peter Last, John Stevens and Tony Smith for their leadership and encouragement during my 21 years at CSIRO. Scott Cooper (CSIRO) provided database support for the electronic tagging data. John Morongiello (CSIRO) assisted with R coding. I also thank Ken Graham for sharing his interest and 40 years of commitment to deep-sea shark research in Australia. I thank my co-authors of the four papers included as chapters in this thesis. I thank Professor Chris Lowe and Doctor Gregory Skomal for reviewing the thesis. Most importantly I give my heart felt thanks to my family and friends for their continuing support and encouragement. iii TABLE OF CONTENTS LIST OF FIGURES ................................................................................................................... v LIST OF TABLES .................................................................................................................... vi LIST OF ABBREVIATIONS .................................................................................................. vii ABSTRACT ............................................................................................................................... 1 CHAPTER 1. GENERAL INTRODUCTION ........................................................................... 4 1.1 Diversity ........................................................................................................................... 4 1.2 Life history ....................................................................................................................... 8 1.3 Australian continental slope ecology ............................................................................... 9 1.4 Fishery management and conservation .......................................................................... 11 1.5 Home range and movements .......................................................................................... 14 1.6 Research objectives and thesis structure ........................................................................ 15 CHAPTER 2. GENETIC CATCH VERIFICATION TO SUPPORT RECOVERY PLANS FOR DEEPSEA GULPER SHARKS (Genus Centrophorus, family Centrophoridae) – an Australian example using the 16S gene ................................................................................... 18 2.0 Abstract .......................................................................................................................... 18 2.1 Introduction .................................................................................................................... 19 2.2 Materials and methods ................................................................................................... 20 2.3 Results and discussion ................................................................................................... 23 CHAPTER 3. CAN MARINE RESERVES CONSERVE VULNERABLE SHARKS IN THE DEEP SEA? A case study of Centrophorus zeehaani, (Centrophoridae) examined with acoustic telemetry .................................................................................................................... 30 3.0 Abstract .......................................................................................................................... 30 3.1 Introduction .................................................................................................................... 31 3.2 Materials and methods ................................................................................................... 33 3.3 Results ............................................................................................................................ 37 3.4 Discussion ...................................................................................................................... 45 CHAPTER 4. MARINE SPATIAL MANAGEMENT OPTIONS FOR DATA-POOR VULNERABLE MARINE SPECIES ...................................................................................... 50 4.0 Abstract .......................................................................................................................... 50 4.1 Introduction .................................................................................................................... 51 4.2 Methods .......................................................................................................................... 54 4.3 Results ............................................................................................................................ 58 4.4 Discussion ...................................................................................................................... 68 CHAPTER 5. SIMULATION-BASED EVALUATION OF RESERVE NETWORK PERFORMANCE FOR A VULNERABLE MARINE