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  Newport Research Facility, Annual Report No. 66, 2021

  Marine Institute (Marine Institute, 2022)

  This report represents a continuation of the scientific aspects of the Annual Reports published by the Salmon Research Agency of Ireland, now integrated into the Fisheries Ecosystem Advisory Services Group (FEAS) of the Marine Institute. The data presented creates a unique record of fish rearing and wild fish census data for the past 50 years. This data is an essential component in the local, regional and national management of salmon, sea trout and eel and is becoming ever more valuable in the light of increasing pressures on natural stocks, such as exploitation, habitat degradation and global climate change scenarios. The fish monitoring facilities in Newport, along with the reared and ranched salmon stocks held in Burrishoole, are also essential for supporting projects such as development of novel enhancement techniques, alternative stocks and ranching and evaluation of interactions between farmed, ranched and wild strains. An expanding programme in the Burrishoole system is including ecological and genetics research into eel, sticklebacks and stock dynamics of juvenile salmonids and eels.
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  Explorers Turtle Talk with Sea Turtles: Teacher Planning Guide, Lesson Plans, and Activities

  Dromgool-Regan, Cushla; Crowley, Danielle (Marine Institute, 2023)

  The Explorers Turtle Talk with Sea Turtles: Teacher Planning Guide introduces teachers to the module and provides them with space to plan lessons for their class to accompany it
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  Explorers Turtle Talk with Sea Turtles: My Sea Turtle Illustrations for design and creative activities

  Dromgool-Regan, Cushla (Marine Institute, 2023)

  The Explorers Turtle Talk with Sea Turtles: My Sea Turtle Illustrations for design and creative activities is designed to accompany the activities in the My Turtle Talk Workbook, and the designs can be used as templates for activities like making a turtle tote bag or drawing a life-size turtle. The book can also be used as a colouring book for younger classes.
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  Environmental Survey of Coastal Waters (Galway - Dublin – Galway): – Winter nutrients, benthic macro-invertebrate and contaminants monitoring 2022 (CV22-0013)

  O'Beirn, Francis; O'Donnell, Garvan (Marine Institute, 2022)

  The 2022 survey continues the Marine Institute’s Winter Nutrients monitoring that commenced in 1990/91. The survey has evolved and expanded during this time period with respect to target areas, parameters and sampling strategy. In 2011 this survey was re-established as a winter environmental survey with a broader remit to provide supporting information for OSPAR and Water Framework Directive (WFD- Directive 2000/60/EC) assessments and also to maintain the winter time series on key biogeochemical parameters in Irish waters in response to pressures such as land based inputs of nutrients and climate change. Since 2011 the survey circumnavigates the Island of Ireland every two years, alternating south-about and north-about, starting in the Irish Sea and ending in Galway. This provides a complete coverage of Ireland’s coastal waters over 2-year periods. However, given the timing of the surveys, winter by necessity to ensure minimal biological activity and therefore highest concentrations of dissolved nutrients, the weather is a significant factor in determining the actual as opposed to planned coverage of the target stations. The 2022 survey was designed to collect multidisciplinary information on physical conditions, water chemistry (dissolved nutrients, total alkalinity (TA), dissolved inorganic carbon (DIC) and salinity), sediment chemistry (persistent organic pollutants POPs and trace metals), sediment particle size distribution and benthic macroinvertebrates (at targeted waterbodies around the coast). This contributes to data collection needs of various statutory drivers (WFD and the Marine Strategy Framework Directive (MSFD) Directive 2008/56/EC) as well as providing a research dataset on status and changing conditions (trends and variations) for key environmental variables. As a result of the COVID pandemic, in 2021 operational adjustments were implemented such that scientific complement on-board was limited to 2-3 persons at any one time. In light of this, the survey plan was adjusted to allow the survey to be completed in two legs (both south-about): 1. Leg 1 – Galway – Dublin: benthic macro-invertebrate sampling 2. Leg 2 – Dublin – Galway: winter nutrient, carbon and contaminants sampling. This survey structure was continued in 2022. Furthermore, and in order to fully achieve this plan, the number of survey days was increased to 17.
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  Epimers of Azaspiracids: Isolation, Structural Elucidation, Relative LC-MS Response, and in Vitro Toxicity of 37-epi-Azaspiracid-1

  Kilcoyne, Jane; McCarron, Pearse; Twiner, Michael J.; Nulty, Ciara; Crain, Sheila; Quilliam, Michael A.; Rise, Frode; Wilkins, Alistair L.; Miles, Christopher O. (American Chemical Society, 2014)

  Since azaspiracid-1 (AZA1) was identified in 1998, the number of AZA analogues has increased to over 30. The development of an LC-MS method using a neutral mobile phase led to the discovery of isomers of AZA1, AZA2, and AZA3, present at ∼2–16% of the parent analogues in phytoplankton and shellfish samples. Under acidic mobile phase conditions, isomers and their parents are not separated. Stability studies showed that these isomers were spontaneous epimerization products whose formation is accelerated with the application of heat. The AZA1 isomer was isolated from contaminated shellfish and identified as 37-epi-AZA1 by nuclear magnetic resonance (NMR) spectroscopy and chemical analyses. Similar analysis indicated that the isomers of AZA2 and AZA3 corresponded to 37-epi-AZA2 and 37-epi-AZA3, respectively. The 37-epimers were found to exist in equilibrium with the parent compounds in solution. 37-epi-AZA1 was quantitated by NMR, and relative molar response studies were performed to determine the potential differences in LC-MS response of AZA1 and 37-epi-AZA1. Toxicological effects were determined using Jurkat T lymphocyte cells as an in vitro cell model. Cytotoxicity experiments employing a metabolically based dye (i.e., MTS) indicated that 37-epi-AZA1 elicited a lethal response that was both concentration- and time-dependent, with EC50 values in the subnanomolar range. On the basis of EC50 comparisons, 37-epi-AZA1 was 5.1-fold more potent than AZA1. This data suggests that the presence of these epimers in seafood products should be considered in the analysis of AZAs for regulatory purposes.
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  Structure Elucidation, Relative LC–MS Response and In Vitro Toxicity of Azaspiracids Isolated from Mussels (Mytilus edulis)

  Kilcoyne, Jane; Twiner, Michael J.; McCarron, Pearse; Crain, Sheila; Giddings, Sabrina D.; Foley, Barry; Rise, Frode; Hess, Philipp; Wilkins, Alistair L.; Miles, Christopher O. (American Chemical Society (ACS), 2015)

  Azaspiracids (AZAs) are marine biotoxins produced by dinoflagellates that can accumulate in shellfish, which if consumed can lead to poisoning events. AZA7–10, 7–10, were isolated from shellfish and their structures, previously proposed on the basis of only LC–MS/MS data, were confirmed by NMR spectroscopy. Purified AZA4–6, 4–6, and 7–10 were accurately quantitated by qNMR and used to assay cytotoxicity with Jurkat T lymphocyte cells for the first time. LC–MS(MS) molar response studies performed using isocratic and gradient elution in both selected ion monitoring and selected reaction monitoring modes showed that responses for the analogues ranged from 0.3 to 1.2 relative to AZA1, 1. All AZA analogues tested were cytotoxic to Jurkat T lymphocyte cells in a time- and concentration-dependent manner; however, there were distinct differences in their EC50 values, with the potencies for each analogue being: AZA6 > AZA8 > AZA1 > AZA4 ≈ AZA9 > AZA5 ≈ AZA10. This data contributes to the understanding of the structure–activity relationships of AZAs.
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  Identification of 21,22-Dehydroazaspiracids in Mussels (Mytilus edulis) and in Vitro Toxicity of Azaspiracid-26

  Kilcoyne, Jane; McCarron, Pearse; Twiner, Michael J.; Rise, Frode; Hess, Philipp; Wilkins, Alistair L.; Miles, Christopher O. (American Chemical Society, 2018)

  Azaspiracids (AZAs) are marine biotoxins produced by the genera Azadinium and Amphidoma, pelagic marine dinoflagellates that may accumulate in shellfish resulting in human illness following consumption. The complexity of these toxins has been well documented, with more than 40 structural variants reported that are produced by dinoflagellates, result from metabolism in shellfish, or are extraction artifacts. Approximately 34 μg of a new AZA with MW 823 Da (AZA26 (3)) was isolated from blue mussels (Mytilus edulis), and its structure determined by MS and NMR spectroscopy. AZA26, possibly a bioconversion product of AZA5, lacked the C-20–C-21 diol present in all AZAs reported thus far and had a 21,22-olefin and a keto group at C-23. Toxicological assessment of 3 using an in vitro model system based on Jurkat T lymphocyte cells showed the potency to be ∼30-fold lower than that of AZA1. The corresponding 21,22-dehydro-23-oxo-analogue of AZA10 (AZA28) and 21,22-dehydro analogues of AZA3, -4, -5, -6, -9, and -10 (AZA25, -48 (4), -60, -27, -49, and -61, respectively) were also identified by HRMS/MS, periodate cleavage reactivity, conversion from known analogues, and NMR (for 4 that was present in a partially purified sample of AZA7).
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  Ocean Superhero Comic Book Template

  Dromgool-Regan, Cushla (Marine Institute, 2022)

  Template to create a comic about an ocean superhero that tackles climate change. This can be used to complement the other lessons on an ocean climate superhero.
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  Population structure and connectivity in the genus Molva in the Northeast Atlantic

  McGill, L; McDevitt, A D; Hellemans, B; Neat, F; Knutsen, H; Mariani, S; Christiansen, H; Johansen, T; Volckaert, F A M; Coscia, I (Oxford University Press (OUP), 2023)

  In fisheries, operational management units and biological data often do not coincide. In many cases, this is not even known due to the lack of information about a species’ population structure or behaviour. This study focuses on two such species, the common ling Molva molva and the blue ling M. dypterygia, two Northeast Atlantic gadoids with overlapping geographical distribution, but different depth habitats. Heavily exploited throughout their ranges, with declining catches, little is known about their population structure. Genotyping-by-sequencing at thousands of genetic markers indicated that both species are separated into two major groups, one represented by samples from the coasts of western Scotland, Greenland, and the Bay of Biscay and the other off the coast of Norway. This signal is stronger for the deeper dwelling blue ling, even though adult dispersal was also identified for this species. Despite small sample sizes, fine-scale patterns of genetic structure were identified along Norway for common ling. Signatures of adaptation in blue ling consisted in signs of selections in genes involved in vision, growth, and adaptation to cold temperatures.
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  CV21_04 INFOMAR Survey Report

  Sheehan, Kevin; INFOMAR Survey Team (Marine Institute, 2022)

  Geological Survey Ireland (GSI) and Marine Institute (MI) conducted seabed mapping between 2003 and 2005 under the auspices of the Irish National Seabed Survey (INSS) and this continued from 2006 to present day under the INtegrated mapping FOr the sustainable development of Irelands MArine Resource (INFOMAR) programme. INSS was one of the largest marine mapping programmes ever undertaken globally, with a focus on deep water mapping. INFOMAR is a joint venture between the GSI and the MI and is funded by the Irish Government through the Department of the Environment, Climate and Communications (DECC). INFOMAR Phase 1, 2006 to 2015 focused on mapping 26 priority bays and 3 priority areas around Ireland and creating a range of integrated mapping products of the physical, chemical and biological features of the seabed in those areas. INFOMAR Phase 2, 2016 to 2026 intends to map the remainder of Ireland’s entire seabed. As of 2018 the remaining survey area has been split at the 30 nautical mile limit (Nm). The inshore survey fleet, managed by GSI is responsible for mapping inshore of the 30Nm limit and the MI vessels are responsible for mapping the offshore.
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  Towards vibrant fish populations and sustainable fisheries that benefit all: learning from the last 30 years to inform the next 30 years

  Cooke, Steven J.; Fulton, Elizabeth A.; Sauer, Warwick H. H.; Lynch, Abigail J.; Link, Jason S.; Koning, Aaron A.; Jena, Joykrushna; Silva, Luiz G. M.; King, Alison J.; Kelly, Rachel; et al. (Springer Science and Business Media LLC, 2023)

  A common goal among fisheries science professionals, stakeholders, and rights holders is to ensure the persistence and resilience of vibrant fish populations and sustainable, equitable fisheries in diverse aquatic ecosystems, from small headwater streams to offshore pelagic waters. Achieving this goal requires a complex intersection of science and management, and a recognition of the interconnections among people, place, and fish that govern these tightly coupled socioecological and sociotechnical systems. The World Fisheries Congress (WFC) convenes every four years and provides a unique global forum to debate and discuss threats, issues, and opportunities facing fish populations and fisheries. The 2021 WFC meeting, hosted remotely in Adelaide, Australia, marked the 30th year since the first meeting was held in Athens, Greece, and provided an opportunity to reflect on progress made in the past 30 years and provide guidance for the future. We assembled a diverse team of individuals involved with the Adelaide WFC and reflected on the major challenges that faced fish and fisheries over the past 30 years, discussed progress toward overcoming those challenges, and then used themes that emerged during the Congress to identify issues and opportunities to improve sustainability in the world's fisheries for the next 30 years. Key future needs and opportunities identified include: rethinking fisheries management systems and modelling approaches, modernizing and integrating assessment and information systems, being responsive and flexible in addressing persistent and emerging threats to fish and fisheries, mainstreaming the human dimension of fisheries, rethinking governance, policy and compliance, and achieving equity and inclusion in fisheries. We also identified a number of cross-cutting themes including better understanding the role of fish as nutrition in a hungry world, adapting to climate change, embracing transdisciplinarity, respecting Indigenous knowledge systems, thinking ahead with foresight science, and working together across scales. By reflecting on the past and thinking about the future, we aim to provide guidance for achieving our mutual goal of sustaining vibrant fish populations and sustainable fisheries that benefit all. We hope that this prospective thinking can serve as a guide to (i) assess progress towards achieving this lofty goal and (ii) refine our path with input from new and emerging voices and approaches in fisheries science, management, and stewardship.
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  Explorers Turtle Talk With Sea Turtles: My Turtle Talk Workbook

  Dromgool-Regan, Cushla (Marine Institute, 2023)

  The Explorers Turtle Talk With Sea Turtles: My Turtle Talk Workbook is an accompanying workbook to the Turtle Talk With Sea Turtles: An Introduction to Sea Turtles book which introduces children aged 10 - 12 to the five fascinating sea turtles that have been recorded in Irish waters, their adaptations to survive, and the threats facing them.
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  Explorers Turtle Talk With Sea Turtles: An Introduction to Sea Turtles

  Dromgool-Regan, Cushla; Crowley, Danielle (Marine Institute, 2023)

  The Explorers Turtle Talk With Sea Turtles: An Introduction to Sea Turtles introduces children aged 10 - 12 to the five fascinating sea turtles that have been recorded in Irish waters, their adaptations to survive, and the threats facing them.
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  Celtic Sea Herring Acoustic Survey Cruise Report 2022, 09 - 29 October 2022

  O’Donnell, Ciaran; Mullins, Eugene; Daly, E.; Keogh, Niall; Shine, Andrew (Marine Institute, 2022)

  In the southwest of Ireland and the Celtic Sea (ICES Divisions VIIaS, g and j), herring are an important commercial species to the pelagic and polyvalent fleet. The local fleet is composed of dry hold polyvalent vessels and a smaller number of large purpose built refrigerated seawater vessels (RSW). The stock is composed of both autumn and winter spawning components with the latter dominating. The fishery targets pre-spawning and spawning aggregations in Q3-4. The Irish commercial fishery has historically taken place within 1-20nmi (nautical miles) of the coast. However, since the mid-2000s RSW fleet have actively targeted offshore aggregations migrating from summer feeding in the south Celtic Sea. In VIIj, the fishery is traditionally active from mid-November and is concentrated within several miles of the coast. The VIIaS fishery peaks towards the year end in December, but may be active from mid-October depending on location. In VIIg, along the south coast herring are targeted from October (offshore) to January at a number of known spawning sites and surrounding areas. Overall, the protracted spawning period of the two components extends from October through to February, with annual variation of up to 3 weeks. Spawning occurs in successive waves in a number of well known locations including large scale grounds and small discreet spawning beds. Since 2008 ICES division VIIaS (spawning box C) has been closed to fishing for vessels over 15m to protect first time spawners. For those vessels less than 15m a small allocation of the quota is given to this ‘sentinel’ fishery operating within the closed area. The stock structure and discrimination of herring in this area has been investigated recently. Hatfield et al. (2007) has shown the Celtic Sea stock to be fairly discrete. However, it is known that fish in the eastern Celtic Sea recruit from nursery areas in the Irish Sea, returning to the Celtic Sea as young adults (Brophy et al. 2002; Molloy et al., 1993). The stock identity of VIIj herring is less clear, though there is evidence that they have linkages with VIIb and VIaS (ICES, 1994; Grainger, 1978). Molloy (1968) identified possible linkages between young fish in VIIj and those of the Celtic Sea herring. For the purpose of stock assessment and management divisions VIIaS, VIIg and VIIj have been combined since 1982. For a period in the 1970s and 1980s, larval surveys were conducted for herring in this area. However, since 1989, acoustic surveys have been carried out, and currently are the only tuning indices available for this stock. In the Celtic Sea and VIIj, herring acoustic surveys have been carried out since 1989. Since 2004 the survey has been fixed in October and carried out onboard the RV Celtic Explorer. This year, the survey was conducted onboard the RV Tom Crean. Survey design and geographical coverage have been modified over the time series to adapt to changes in stock size and behaviour. Since 2016, the wider core distribution area has been surveyed by means of two independent surveys and supplemented with small high resolution adaptive surveys focusing on areas of high abundance.
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  Shellfish Stocks and Fisheries Review 2022: an assessment of selected stocks

  Marine Institute; Bord Iascaigh Mhara (Marine Institute, 2023)

  This review presents information on the status of selected shellfish stocks in Ireland. In addition, data on the fleet and landings of shellfish species (excluding Nephrops and mussels) are presented. The intention of this annual review is to present stock assessment and management advice for shellfisheries that may be subject to new management proposals or where scientific advice is required in relation to assessing the environmental impact of shellfish fisheries especially in areas designated under European Directives. The review reflects the recent work of the Marine Institute (MI) in the biological assessment of shellfish fisheries and their interaction with the environment. The information and advice presented here for shellfish is complementary to that presented in the MI Stock Book on demersal and pelagic fisheries. Separate treatment of shellfish is warranted as their biology and distribution, the assessment methods that can be applied to them and the system under which they are managed, all differ substantially to demersal and pelagic stocks. Shellfish stocks are not generally assessed by The International Council for the Exploration of the Sea (ICES) and although they come under the competency of the Common Fisheries Policy they are generally not regulated by EU TAC and in the main, other than crab and scallop, are distributed inside the national 12 nm fisheries limit. Management of these fisheries is within the competency of the Department of Agriculture, Food and Marine (DAFM). A co-operative management framework introduced by the Governing Department and BIM in 2005 (Anon 2005), and under which a number of fishery management plans were developed, was, in 2014, replaced by the National and Regional Inshore Fisheries Forums (NIFF, RIFFs). These bodies are consultative forums, the members of which are representative of the inshore fisheries sector and other stakeholder groups. The National forum (NIFF) provides a structure with which each of the regional forums can interact with each other and with the Marine Agencies, DAFM and the Minister. Management of oyster fisheries is the responsibility of The Department of Environment, Climate and Communications, implemented through Inland Fisheries Ireland (IFI). In many cases, however, management responsibility for oysters is devolved through Fishery Orders or Aquaculture licences to local co-operatives. The main customers for this review are DAFM, RIFFs, NIFF and other Departments and Authorities listed above.
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  Explorers Ocean Questions and Answers

  Crowley, Danielle; Burke, Noirin; McAvinney, Rory (Marine Institute, 2023)

  The following questions and answers are about the ocean, tides, currents, and more. This PowerPoint can be used in the class to spark discussions and learn the amazing answers to questions like "how much oxygen comes from the ocean?", "how deep is the ocean?", and "why is the Gulf Stream current important to Ireland?" This PowerPoint may be used for educational purposes and the images must retain all of their image copyright details.
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  Explorers Marine Invertebrates Questions and Answers

  Crowley, Danielle; Burke, Noirin; McAvinney, Rory (Marine Institute, 2023)

  Marine invertebrates are animals without a backbone. The following questions and answers are about marine invertebrates including crabs, lobsters, and jellyfish. This PowerPoint can be used in the class to spark discussions and learn the amazing answers to questions like "what is the most dangerous jellyfish?", "are sea anemones animals or plants?", and "how long do lobsters live?" This PowerPoint may be used for educational purposes and the images must retain all of their image copyright details.
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  Explorers Marine Vertebrates Questions and Answers

  Crowley, Danielle; Burke, Noirin; McAvinney, Rory (Marine Institute, 2023)

  Marine vertebrates are animals that have a backbone. The following questions and answers are about marine vertebrates including fish, birds and mammals. This PowerPoint can be used in the class to spark discussions and learn the amazing answers to questions like "what is the fastest fish in the sea?", "do reptiles live in the ocean?", and "what seabird has the longest migration?" This PowerPoint may be used for educational purposes and the images must retain all of their image copyright details.
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  Catch and bycatch in the tangle net fishery for crayfish (Palinurus elephas) off the south west coast of Ireland

  Tully, Oliver; Palma-Pedraza, S. (Marine Institute, 2022)

  Crayfish or spiny lobster is fished off the south west coast of Ireland. There are also smaller fisheries on the west and north west coasts. Although historically, prior to the 1970s, the main fishing gear used in the fishery was top entrance traps crayfish are now targeted with large mesh tangle nets. The selectivity of these nets is poor and there is known to be a by-catch of finfish, skates and rays and protected species such as grey seal. The fishery usually occurs from mid-March to December. The species composition and size distribution of the catch and by-catch was surveyed over a 4 year period from 2017-2020 from Dingle Bay north to the Shannon Estuary. Additional data south of this area was obtained in 2020. A crayfish tagging programme was undertaken in 2017 and 2018. Between 2 and 6 vessels participated in the programme depending on year Most of the data was reported directly by Skippers and crew who were contracted to supply data. Scientific observers covered a proportion of trips in 2017 and 2019. A total of 1500 nmiles of tangle net hauls were surveyed across 6 vessels. A total of 11792 crayfish and 899 lobsters were measured, 1234 crayfish were tagged and released and 45 recaptures were reported. Spider crab, brown crab and crayfish were the numerically dominant species in the catch. Lobster, pollack, thornback ray, spurdog, monkfish and turbot were caught regularly in low numbers. There was no cetacean by-catch. A total of 200 grey seals were caught over the 4 year period by the vessels participating in the survey. Endangered and critically endangered species, including flapper skate, common skate, angel shark and white skate, were caught in very low numbers. The finfish catch is mainly lost to scavengers or seal depredation before nets are retrieved and because of long soak times which averaged 8 days. This reduces the value of the catch. The average value of the live crustacean (crayfish, lobster, brown crab) catch was approximately €300 per mile of net hauled. Crayfish were tagged and released in 2017 and 2018 and recaptured during the period 2017-2020. Three crayfish tagged by IFREMER off Brittany in 2015 and 2016 were recaptured off the south west and west coast of Ireland in 2019. The northern most recapture was off Erris Head Co. Mayo. The tagging data shows that most crayfish were recaptured locally close to release points even in the years following tagging. It is still unclear if crayfish are resident or if they migrate in and out of the tagging area as the reporting rate of recaptures outside the tagging area is unknown. The by-catch of critically endangered species poses a high risk to the continued presence of these species in Irish waters and indeed in European waters given that the area is known to hold the last European remnant populations of species such as angel shark and white skate. Grey seal by-catch was related to the distance between the fishing event and the nearest seal colony haul out at the Blasket Islands. Sixty % of seals were caught within 10km of the haul out. The probability of capture in a single net haul declined from 30-35% within 10km to 9-14% at distances of 10-30km to 4% at distances of 40-60km and zero at distances greater than 60km (data for 39 hauls >60km). The high by-catch of grey seal is a significant risk to the Blasket Island seal colony. It is unlikelythat the Blasket population can sustain this level of by-catch mortality without inward migration fromother colonies.
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  The Irish Maritime Transport Economist Volume 19

  Irish Maritime Development Office (Marine Institute, 2022)

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