Multidisciplinary investigation into stock structure of small pelagic fishes in southern Africa S. L. Hampton Thesis Presented for the Degree of DOCTOR OF PHILOSOPHY in the Department of Biological Sciences UNIVERSITY OF CAPE TOWN August 2014 Univeristy of Cape Town 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 Multidisciplinary investigation into stock structure of small pelagic fishes in southern Africa S. L. Hampton August 2014 Supervisors: Coleen Moloney (Ma-Re, University of Cape Town) Paulette Bloomer (MEEP, University of Pretoria) Carl van der Lingen (DAFF) The financial assistance of the National Research Foundation (NRF) towards this research is hereby acknowledged. Opinions expressed and conclusions arrived at, are those of the author and not necessarily to be attributed to the NRF. Declaration I know the meaning of Plagiarism and declare that all the work presented in this thesis is my own, except where it is properly acknowledged in the text. This thesis has not been submitted in whole or in part for a degree at another university. S.L. Hampton 15 August 2014 Multidisciplinary investigation into stock structure of small pelagic fishes in southern Africa Table of Contents Pages Acknowledgements i-iii Abstract 1 Chapter 1: An introduction to small pelagic fish and stock identification in southern Africa. 3 Chapter 2: Investigating stock structure in small pelagic fish of southern Africa using otolith morphology. 33 Chapter 3: Spatial and temporal variability in elemental signatures of sardine otoliths in South Africa. 61 Chapter 4: Mitochondrial and microsatellite loci indicate high diversity with low geographic structure in southern African sardine (Sardinops sagax) . 89 Chapter 5: A preliminary investigation of genetic differentiation using microsatellite loci hints a break of gene flow between sites for anchovy (Engraulis encrasicolus) off the coast of South Africa. 133 Chapter 6: Synthesis: Variable patterns of stock structure evident in a dynamic environment. 151 References 165 Glossary 191 Appendix 2: R Code used in Chapter 2 196 Appendix 3: Code used in Chapter 3 201 Appendix 4: Supplementary material from Chapter 4 205 Appendix 5: Supplementary material from Chapter 5 213 Acknowledgements I am very grateful for generous financial contributions from SAPFIA - the project could not have gone ahead without their support. Financial support was provided by the SEAChange Project of the South African Network for Coast and Oceanic Research, funded by the Branch: Marine and Coastal Management and the National Research Foundation, and by the Ma-Re BASICS project of the UCT Vice- Chancellors Strategic Initiative. The financial assistance of the National Research Foundation (NRF) towards this research is also gratefully acknowledged, as is financial support from UCT’s Harry Crossley Foundation. I am also grateful to ACEP for their contribution towards running expenses, and to ACEP, SAEON-GSN and MBRC for financial contributions to travel expenses. I am extremely grateful to my three supervisors. They enabled me to dive into a whole new field, and made it possible for a relative novice to work on an important question. Each of them has provided critical support in different ways. I can’t say a big enough thank you to them: Thank you to Coleen Moloney for being willing to take on the most expensive project in her lab’s history, for covering my travel expenses between Cape Town and Pretoria, for my amazing office in Cape Town and your input into every chapter of my thesis. You are truly an inspiration to me. Thank you too for sponsoring my SAMSS Cape Town 2008 and Grahamstown 2011, and my trip to WMBC in Aberdeen in 2011. Thank you to Paulette Bloomer for introducing me to the magical world of DNA, for your patience and understanding during lab work frustrations, and for encouraging me in science and life. Thank you for sponsoring ZSSA Illovo Beach 2009 and SAGS Pretoria 2008. Thank you to Carl van der Lingen for your unfaltering (up to the gills) enthusiasm! You shared and encouraged my excitement about this project. Thank you for the great experience of going to sea on the MCM pelagic spawner biomass cruise in 2007 and i 2008, and for the freezers full of fish. Thanks to all those poor sardine, anchovy and round herring who unwittingly donated their bodies and eggs to science. Thank you to the team (Maylis Laybonne, Eric Morize, and Eric Dabas) at the IRD’s CHRONOS Research Unit (University of Brest) who, through Carl, provided the sardine otolith microchemistry data and let me further develop initial analyses. I enjoyed this new challenge and believe that it complements the rest of the thesis. Thank you to Deon Durholz and Cynthia Mtengwane for access to the microscope and camera at DAFF, and to Deon for sharing your knowledge of otoliths. And thanks to the late Marc Hendricks for showing me how to interpret the insides of fish and for collecting my samples onboard the RV Africana and at the sardine run. I hope he knew how grateful I am for everything he did for me so patiently and with a smile on his face. DAFF has lost a kind and generous man and he will missed by me and many others. Thank you to Allan Connell for collecting egg samples in KwaZulu-Natal and to Nadine Morhoff for facilitating the use of Namibian samples through the Namibian Ministry of Fisheries and Marine Resources. And to J-P Roux for collecting samples from lovely Lüderitz. Thank you to Andrew Markham for struggling through Elliptical Fourier Analysis with me, and to Carel Oosthuizen for his assistance with analysis. I couldn’t have gotten through the changes to the genetics chapters without the input I received from Romina Henriques. Thanks to Jaquie Bishop and Sophie von der Heyden for being so willing to discuss my results and providing useful suggestions. Thanks to Dr. Iratxe Zarraonaindia, Dr Alex Hon-Tsen Yu and Dr Axayacatl Rocha-Olivares for suggestions on PCR and extraction techniques in small pelagics, and to James Rohlf and Simon Robertson for their assistance in otolith techniques. A huge thanks to Ilkser Erdem Kiper for voluntarily helping me with my lab work. Thanks to Jon Havenhand and Gerry Quinn for an amazing course on Experimental Design and Data Analysis in R, and to the EDDAMS 2012 team for making it a fantastic trip to Sweden. And thank you to Richard Sherley, Henning Winkler and Louis du Buisson (an awesome office-mate) for keeping me on track in R. In Cape Town, thank you to the MBRC and particularly Gilly Smith, for every day cheerful helpfulness and organising the Namibia trip. Thank you to the amazing ii people in the zoology department - I am so lucky to go to work with people that I am excited to see every day. In Pretoria, the MEEP lab introduced me to pipettes and PCR’s. They shared thoughts and techniques with me as well as smiles, sighs and sobs. It was so helpful to be surrounded by people that were going through the same things as me and could relate to my frustrations and triumphs, and I made some special friends. My family has been wonderfully supportive, generous and patient. I will never take for granted how lucky I was to have them behind me. A very big thank you to my fantastic folks, Philip and Carol Hampton, who have provided unfailing support in so many different ways. Your love and unwavering support has given me the courage to follow my dreams. Thank you to Kerri and Chris McDonald for always welcoming me in Joburg. Thank you Kerri for your help with proof reading and editing. Thank you Ian for all your support and advice, and your helpful comments on drafts. Thanks Tess for always being so willing to read through chapters and meet me for adventures in Paris. Thank you to all of my friends in Cape Town, Joburg, Oxford, the middle-of- nowhere-Tanzania and Pretoria (and Benoni) for keeping me sane and grounded and reminding me that an outside world exists. I know that I’ve been hard work at times, thank you for sticking around and being so generous with your friendship, your support and your food. Thanks for being so supportive of my “whining and wining”. A special thanks to everyone that helped with airport runs, and to those who kept me company on long drives between Cape Town and Joburg. And finally thank you to Jessica, Emily, Charles, Graeme, Carrie, Mom, Dad, Tessa and Kate for reading and commenting on early drafts of my chapters. Thank you to the three anonymous examiners that provided useful comment and suggestions on the first editions of this thesis. iii Multidisciplinary investigations into stock structure of small pelagic fishes in southern Africa Three abundant small pelagic fish species co-occur in the Benguela upwelling ecosystem off southern Africa: sardine (Sardinops sagax), anchovy (Engraulis encrasicolus) and round herring (Etrumeus whiteheadi). It is hypothesised that populations of these species have a complex structure that reflects the complexity of their varying habitats. On the basis of the locality and timing of spawning, and morphological, meristic and parasite studies, it has been proposed that there are separate stocks of sardine in South African waters west and east of Cape Agulhas. Consequently, new operational procedures for managing the fishery are based on the premise of two such stocks, termed the west and south coast stocks respectively.