GMIT I GALWAY-MAYO INSTITUTE OF TECHNOLOGY I INSTITIÜID TEICNEOLAIOCHTA NA GAILLIMHE-MAIGH EO Investigation into the early life history of the European flounder (Platichthys flesus L.) with special emphasis in Galway Bay, Irish west coast By Bernadette O’Neill Ph.D. in Fisheries Biology and Ecology Supervisors of research Dr. Deirdre Brophy Dr. David McGrath Submitted to the Higher Education and Training Awards Council February 2012 This project was funded by a grant to DB and DMcG from the Department of Education, Technological sector Research Programme, Strand 1. F.D. was funded through the STRIVE Programme by the Environmental Protection Agency, Ireland. NDP European Regional National Development Plan 2007 - 2013 Development Fund Investing in your Future Additional support was acquired by the networking initiative under the Sea Change strategy with the support of the Marine Institute and the Marine Research Sub- programme of the National Development Plan 2007-2013. Tflarine Institute Foras na Mara NDP National Development Plan 2007 - 2013 Declaration I hereby certify that this material, which I now submit for the award of PhD is entirely my own work and has not been taken from the work of others save and to the extent that such work has been cited and acknowledged within the text of my work. Table of contents Abstract. Acknowledgements. Chapter 1: Genera] Introduction. Chapter 2: Scales of variability in fin ray counts of flounder, Platichthys flesus on the Irish and Welsh coasts........................................................................................................................................... 25 Chapter 3: Investigation of early life events of European flounder {Platichthys flesus L.) within Galway Bay, west Ireland, as described by otolith microstructure.......................................................................................... 39 Chapter 4: Habitat utilisation in 0-group European flounder, Platichthys flesus (L.), in Galway Bay, Ireland.......................................................................................................................................... 64 Chapter 5: An experimental investigation of salinity effects on growth, development and condition in the European flounder (.Platichthys flesus................................................................................ 86 Chapter 6: Spatio-temporal variability in juvenile flounder (Platichthys flesus L.) condition, age and size composition within Galway Bay, west of Ireland.......................................................... 106 Chapter 7: General Discussion 127 Abstract European flounder (Platichthys flesus L.) economic value is estimated to be worth over 68 million to the Irish economy (mainly from recreational angling activities). Despite such large species value, there is a considerable lack of data for this region, particularly concerning stock structure, timing of life history events and juvenile habitat use patterns. This dissertation addresses these knowledge gaps and describes a number of studies which focus on the understanding of flounder nursery ground ecology. Understanding stock structure and the connectivity between geographically distinct groups of fish is critical for the sustainable management of a species. Meristic analysis revealed a modest separation of juvenile flounder from different regions (west coast of Ireland, east coast of Ireland and the Welsh coast). The variation between regions was subtle and there was a large degree of overlap. The technique is therefore not a powerful method of stock identification on its own but may improve the likelihood of detecting flounder stock structure if combined with other markers in a multidisciplinary approach to stock identification. Little is known of the early life traits of flounder and the affect early benthic life has on habitat use patterns and survival. Otolith microstructure analysis established critical baseline data on the timing and duration of early life history events of juvenile flounder. Peak hatching and settlement occurred in February/March and March/April respectively while the average pelagic larval phase was on average 43 days. Spatial and temporal variability in early life history traits and size were identified which may be related to inter/intra estuarine movement of flounder and/or selective mortality of different settlement cohorts. Flounder sampled from beaches and estuaries within Galway Bay showed different habitat use patterns. Individuals on the beaches used the habitat over a short period of time and were either moving away from the beach habitat or undergoing mortality subsequent to arrival; whereas flounder were continuously found in the estuaries until late summer. There is evidence that biochemical (RNA:DNA) and morphometric condition represent different time scales in fishes’ life which can be useful for studying short and long term condition of fish. Under experimental laboratory conditions, post larval flounder held at salinity of 30 had higher RNA:DNA compared to individuals held at salinity of 0 while no difference in morphometric condition was detected. In contrast, in the estuarine environment flounder condition (morphometric and RNArDNA) increased as salinity decreased. The findings of this thesis provided important information on the dynamics of 0-group flounder which can aid conservation of essential juvenile habitats which in turn can positively affect recruitment of 0-group individuals to the adult spawning population. Acknowledgements First and foremost I offer my sincere gratitude to my supervisors Deirdre Brophy and David McGrath for their guidance, support and patience throughout this long and sometimes testing process. Deirdre, your practical advice and logical thinking were integral to this thesis and your unwavering encouragement kept me on the straight and narrow road to finally submit it. David, your immense knowledge on the aquatic environment has been invaluable and your lateral thinking capabilities helped me to reflect on my research and step outside the box. I am immensely grateful to both of you for giving me the opportunity to further my life and academic education in GMIT. My experience in GMIT would not have been the same without all of the post graduate students. Thanks to Edward Helps, Dave Tully, Rebecca O’Connor, Jason Clarke and John Corcoran, for making me feel welcome in GMIT when I first started and to James Keating and Melanie Zoelck for the advice, help and random chats over the last couple of years. Noreen Burke your constant optimism and enthusiasm during the early days were a breath of fresh air and made my life in GMIT all the more enjoyable. A special thanks to Ciara Ni Chualain for encouraging me throughout my post graduate studies, you have a die hard work ethic which has been an inspiration. Wiebka Smith, Clementine Harma and Conor Ryan, you brought diversity into the office. Thank you for sharing many coffee and lunch breaks and for the office banter which sometimes yielded some interesting research question and answers. I would also like to thank Paula Haynes for her advice and insight into the workings of flatfishes. I enjoyed our road trips to the most beautiful beaches in Kerry, Clare and Galway in search of the elusive turbot. My time in GMIT would not have been the same without Fien De Raedemaecker and Stephen Comerford, you guys kept a smile on my face and for that I am very grateful. Your constant slagging reminded me not to take myself too seriously, thank you, I needed reminding. I feel very lucky to have shared my time in GMIT with you both. Fien, thank you for motivating me when times were tough and for always believing in me. Stephen, your practical help and advice on how best to build and operate aquaria and sampling gear were invaluable. I would also like to thank Eugene McCarthy and Brian Quinn for their advice, help and use of equipment in the nucleic acid based research; it was very much appreciated. Thanks must go to the biology, chemistry and physics technicians for providing me with bits and bobs at different stages in my research; they saved me time and more importantly stress. In particular I would like to thank Steve Barratt for always being willing to lend me equipment. I am also grateful to Coilin Minto for making the time to advise me on statistical analysis. Thanks also to Laura McDonagh, Maura Gilligan and all the staff in the research office for their support and to the library staff for their fast and efficient inter- library loan service. To all the staff and students (Richard, Ken, Kieran, Paul, Bob, Anthony, Dolly, Bernadette, Joe, Mike, Damien, Maeve, Salla, Majbritt and Jack) in the Cama research station, thank you for supplying me with artemia eggs and for the many cups of tea and chats during my write up, it kept me sane during this challenging period. Thanks also to Ian O’Connor and Maurice Clarke for participating in my transfer report and for the constructive feedback. To my friends outside of GMIT, Imelda, Barbra, Rosaleen, Laura, Lianne, Fiona, Hazel, Odile, Sadhbh and Jorge thank you for the breaks away from research, I needed them. I am grateful to Lisa and Shane for always offering a bed and a meal and for sharing many very enjoyable surf sessions; I look forward to many more in the near future. Luca my love, your unwavering love and support has given me the strength and courage to be where I am today. Your enthusiasm for life and excitement for even the little things kept me smiling. Moving with you