1 Intra-river scale (Moy) Introduction Genetic Stock - PDF document

Outline Application of genetics in Atlantic salmon fisheries management (in the pelagic ecosystem)  Role of genetic methods in fisheries management;  Philip McGinnity Genetic stock identification (GSI) for Atlantic salmon – how it works; Principal Investigator  EU SALSEA-Merge Project (2008-2011); Beaufort Marine Research Award  Examples of the application of GSI in salmon in Fish Population Genetics management;  Salmon and the pelagic ecosystem; Presentation to the Pelagic AC General Assembly, The Hague  Summary 2 October, 2014 Questions/Issues Maker Development 2. Food security Population genetic Sustainability of wild fisheries; structuring 1. Common 3. Food safety Project Design Aquaculture; ranching; selective Fisheries Policy Genetic Stock Consumer confidence (horse breeding; GMOs; micro-biomes; Identification (GSI) Illegal; Unreported; meat scandal); mislabelling; disease management . Infrastructure Unregulated; location linked contaminants Parentage Sample Acquisition (laboratory and Discards. e.g. sushi from Fukushima. assignment field facilities, archived samples, Pedigree genetic baselines reconstruction Genotyping and databases, IT) Marine ecosystem and Skilled personnel fisheries management advice 6. Evolutionary 4. Food origin Bioinformatics (role of genetics) Cost impacts of man Data analyses Wild v farmed; protected Technological Climate change; designation of origin advances fisheries; (branding); eco-certification Biological Interpretation domestication; (MSC). (Genetics + Ecology + Biology) escapes; hybridisation; disease; habitat Population genetics Control (IUU) change; alien spp.; (ID of management units, ESUs) Data for policy impacts on resilience; Conservation formulation abundance; 5. Environment (GES) Within species diversity = Environment adaptability. Environmental quality – MSFD populations (spatial & temporal e.g. Advisory process Ecosystem Irish Sea cod; Norwegian Spring (2008/56/EC); environmental Policy formulation functioning impact assessments; spatial herring); conservation. planning; ecosystem dynamics; Food safety food web disturbance. Regulation Food security e.g. Sea Bass as example….implement conservation measures Fisheries Statutory obligations in protection of fisheries Risk assessment Genetic applications Policy development and marine environment (IUU) (traceability) • Redrawing of statistical - Common Fisheries • • Over-exploitation Species & population areas linked to populations; Policy (CFP); Marine identification; • • Strategy Framework Illegal; Spatially explicit population • Genetic stock specific quotas; Directive(MSFD) • Unreported; identification – • Marine Protected Areas • Unregulated; assigning any linked to populations; individual to its • Mixed stocks; • population of origin Certification • Discards; In MSFD, 10 of 11 descriptors have a genetic based element 1

Intra-river scale (Moy) Introduction Genetic Stock Identification (establishing a baseline for Atlantic salmon) Intra-river scale Inter-regional scale (26,813 samples; 467 sites; 284 rivers; 85% of the production) Dillane et al. (2008) Molecular Ecology 17, 4786-4800 Markers (Analogous to physical markers) Statistically derived assignments rather than absolute – so quality of assignment will be a function of the quality of the baseline, which depends on coverage and molecular differentiation of the elements SALSEA-Merge 2

Population specific Population biology specific growth rates Determining the composition of the Irish drift net fishery 100.0 80.0 60.0 40.0 20.0 0.0 Dundalk Drogheda Dublin Waterford/Lismore Wexford Cork Kerry Limerick Galway Connemara Ballinakill Bangor Ballina Ballyshannon Sligo Letterkenny Northern Ire Farmed UK/Fr/Sp Atlantic salmon fisheries 100.00 80.00 60.00 40.00 20.00 0.00 Dublin Wexford Waterford Lismore Cork Kerry Limerick Galway Ballinakill Bangor Sligo Letterkenny Farmed UK/Fr/Sp Dundalk Drogheda Connemara Ballyshannon 100.0 80.0 60.0 40.0 20.0 0.0 k a n e k y y a r n y e d a l d l i r d r r r c k a r i l l o n a g o o n r e S p d e b o o C o e r r i w m a a k n g i l i l n n n I m / n g h D u x f m K e a l n a l a S n e r r F r u o W e i s m G n e l i B B h a r k h e F a / D r L L i n a l s e t U K D d / o B y e t t o r o r C a l l L N r f B e a t W 3

West Greenland catch 2002-2012 West Greenland 2002-2012 assigned to country Denise Deschamps ICES non-maturing 1SW fish PFA predictions (2002-2012) Denise Deschamps Development of very powerful new markers allows GSI for marine spp. Salmon in the pelagic ecosystem & potential interactions (ecological & by- catch) 4

Trenkel et al. 2014 How many smolts ICES advice to NASCO 2014 (estimates range from 60 to 1 million post-smolts in pelagic by-catch annually – best estimate 154,482 or 5% of the PFA 2005) – since then expansion of the pelagic fisheries Iceland/Faroes) 5

Screening Future Meta-genomics eDNA (technology, bio-sensors – don’t Water is a “ soup ” of genetic have to see the material (metabolic waste, bodies) skin, cells, damaged tissue) Ecosystem relationships (elucidating food webs) Take home messages Take home messages  Atlantic salmon are a constituent element of the pelagic ecosystem in the North  For new knowledge co-operation with pelagic fisheries sector is essential; possible Atlantic; similar and overlapping ocean phase biology to mackerel and herring; salmon indicator of ecosystem health; reproductive juvenile biology very different; numbers game is different by several  orders of magnitude; Occurrence of salmon in the marine pelagic ecosystem (migration routes; competitive interactions; ecosystem processes) and potential interaction with  Salmon experiencing period of substantial decline (linked to factors in the marine pelagic fisheries (which overlap in space and time) warrants major research actions environment) contemporaneously with increased biomass in some pelagics to accurately measure impacts as per recent ICES recommendation to NASCO; (ecological) and increased catches (fisheries by-catch);  Impacts may or may not be significant; need good numbers to provide evidence  Post-smolts occur with variable frequency (temporal and spatial aspects) within based management advice. commercial pelagic fish catches; this could represent significant mortality to individual salmon populations;  Genetic methods represent extraordinarily powerful tool for identifying river/region origin of individual fish (marker assisted GSI); presence or absence (possibly numbers) among discards; equipment; vessels (environmental DNA); potential to elucidate of various aspects of Atlantic pelagic ecosystem; 6

Beaufort Marine Research Award in Fish Population Genetics Acknowledgement: This Beaufort Marine Research Award is carried out under the Sea Change Strategy and the Strategy for Science Technology and Innovation (2006-2013), with the support of the Marine Institute, funded under the Marine Research Sub-Programme of the National Development Plan 2007 – 2013. 7