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ICES CM Documents
This collection contains ICES Conference and Meeting (CM) Documents authored/co-authored by Marine Institute staff.
Recent Submissions
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Data-Driven Modelling for Assessing Trophic Status in Marine Ecosystems Using Machine Learning ApproachesAssessing eutrophication in coastal and transitional waters is of utmost importance, yet existing Trophic Status Index (TSI) models face challenges like multicollinearity, data redundancy, inappropriate aggregation methods, and complex classification schemes. To tackle these issues, we developed a novel tool that harnesses machine learning (ML) and artificial intelligence (AI), enhancing the reliability and accuracy of trophic status assessments. Our research introduces an improved data-driven methodology specifically tailored for transitional and coastal (TrC) waters, with a focus on Cork Harbour, Ireland, as a case study. Our innovative approach, named the Assessment Trophic Status Index (ATSI) model, comprises three main components: the selection of pertinent water quality indicators, the computation of ATSI scores, and the implementation of a new classification scheme. To optimize input data and minimize redundancy, we employed ML techniques, including advanced deep learning methods. Specifically, we developed a CHL prediction model utilizing ten algorithms, among which XGBoost demonstrated exceptional performance, showcasing minimal errors during both training (RMSE = 0.0, MSE = 0.0, MAE = 0.01) and testing (RMSE = 0.0, MSE = 0.0, MAE = 0.01) phases. Utilizing a novel linear rescaling interpolation function, we calculated ATSI scores and evaluated the model's sensitivity and efficiency across diverse application domains, employing metrics such as R2, the Nash-Sutcliffe efficiency (NSE), and the model efficiency factor (MEF). The results consistently revealed heightened sensitivity and efficiency across all application domains. Additionally, we introduced a brand new classification scheme for ranking the trophic status of transitional and coastal waters. To assess spatial sensitivity, we applied the ATSI model to four distinct waterbodies in Ireland, comparing trophic assessment outcomes with the Assessment of Trophic Status of Estuaries and Bays in Ireland (ATSEBI) System. Remarkably, significant disparities between the ATSI and ATSEBI System were evident in all domains, except for Mulroy Bay. Overall, our research significantly enhances the accuracy of trophic status assessments in marine ecosystems. The ATSI model, combined with cutting-edge ML techniques and our new classification scheme, represents a promising avenue for evaluating and monitoring trophic conditions in TrC waters. The study also demonstrated the effectiveness of ATSI in assessing trophic status across various waterbodies, including lakes, rivers, and more. These findings make substantial contributions to the field of marine ecosystem management and conservation.
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Standardising long-term eel (Anguilla anguilla) fyke net survey data reveals covariate effects and improves estimates of declining relative abundanceEel recruitment and stock have been in decline since at least the mid 1980s. So far, much research has focussed on conservation objectives and estimating silver eel production in response to the EU Regulation (EC 1100/2007) and most surveys have been on waters subject to exploitation and/or stocking. The aim of this study is to examine a 35-year yellow eel survey dataset to determine relative abundance trends while accounting for survey design, and important physical and operational covariates. Chains of ten, or sometimes five, fyke nets were fished at fixed sites in four lakes on a catchment in the west of Ireland not impacted on by exploitation or stocking. Captured eels (10,474) were counted for each trap, and eel weight was recorded for each chain of nets (5515 net nights fished). Data were analysed using a generalised additive model (GAM) that included smoothed trends over time and covariates day-of-year, depth, gradient, site and net chain. Yearly trends and between-chain variability were significant for all locations with trap depth and gradient being important for some lakes. Standardised trends by number and mass declined markedly in both tidal areas − 84.7% and − 89.5% by count and − 93.5% and − 89.5% by weight; significant declines (− 39.2% by count and − 54.1% by weight) were found in one of the freshwater lakes with the other, the one farthest upstream, having had changes over time but no significant difference between the start and end. This study provides a framework for analysing long-term fyke net catch data for eel, which may be useful for the international analysis of eel survey data.
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Climate-Driven Oceanic Range Shift of Saint John River Atlantic Salmon Revealed by Multidecadal Stable Isotope TrendsMarine migration patterns of unique or regional stocks of Salmo salar (Atlantic Salmon) are poorly known. Atlantic Salmon (AS) utilizing the North Atlantic Subpolar Gyre (NASpG) for foraging and growth consist of stocks from the United States (41°N) to Greenland (64°N) in the western Atlantic and from Spain (41°N) to Norway (70°N) in the eastern Atlantic. Wide latitudinal range and unique riverine characteristics probably result in stocks selecting differing suites of marine sea-surface temperatures (SST) within the species' known selection range (i.e., their Grinnellian niche). We analyzed trends in stable carbon isotope (δ13C) composition from archived scale tissues in relation to long-term variation of SST for the North Atlantic Ocean to identify marine feeding regions used by adult AS successfully returning to the Saint John River, Canada, during the period 1982–2011. Marine foraging regions were determined for individuals that spent 1 winter (1SW) or multiple winters (MSW) at sea. During 1982–1991 and 1992–2001, AS which successfully returned, exploited more southern regions of the NASpG, while returning adults from 2002–2011 exploited more northern regions. Historically presumed marine feeding regions, which were identified by the isotopic model as probable during 1982–2001, have experienced a warming trend, and data suggests that AS returning to the Saint John River have been migrating further north in the NASpG in response to recent global climate change. The northward range shift as the North Atlantic warmed is consistent with recent biogeographical changes found among other marine species also following their Grinnellian niche.
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Global warming will change the thermal structure of Lough Feeagh, a sentinel lake in the Irish landscape, by the end of the twenty-first centuryRecent developments in impact modelling of global warming on lakes have resulted in a greater understanding of how these vital ecosystems are likely to respond. However, there has been little quantitative analysis of this in an Irish context, despite the importance of lakes in the island's landscape. Here, we explore the impact of global warming on the hydrodynamics and thermal structure of a sentinel Irish lake under future climate scenarios. A 1D lake model, Simstrat, was calibrated and validated using water temperature data collected from Lough Feeagh, a site of long-term ecological research in the west of Ireland. Once validated, the model was then driven by daily climate model projections to generate informative thermal metrics for the time period of 2006–2099. Despite the moderating influence of the Atlantic, projections indicate that global warming will have a marked effect on the thermal structure of Feeagh, with surface water temperatures set to warm by 0.75°C under a more stringent mitigation pathway (RCP 2.6) and 2.42°C under a non-mitigation pathway (RCP 8.5). While warming was projected to be greatest in summer in the epilimnion, winter warming was greater than in other seasons in the hypolimnion. Stratification is projected to become more stable and earlier, and the growing season to be longer by 11 to 47 days, depending on mitigation pathways. Future studies could use a similar modelling workflow to investigate the possible implications of global warming on other Irish lakes, particularly those of specific societal importance or those of conservation interest.
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Structure Elucidation, Relative LC–MS Response and In Vitro Toxicity of Azaspiracids Isolated from Mussels (Mytilus edulis)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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Population structure and connectivity in the genus Molva in the Northeast AtlanticIn 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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Towards vibrant fish populations and sustainable fisheries that benefit all: learning from the last 30 years to inform the next 30 yearsA 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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Science Communication: Stakeholder perceptions of Real-time Incentive Fisheries ManagementIn these changing times, with political and environmental uncertainty surrounding us, fisheries management needs to become more adaptive in order to respond to the changes in our natural environment and changing management frameworks. Based on close to real-time information updates, and harnessing modern technology, Real-Time Incentive (RTI) fisheries management is designed to evolve with the fish stocks, enabling managers to respond more quickly and efficiently to management issues as they arise. Through the use of a credit system that makes use of regularly updated fine-scale information, incentives can be incorporated as rewards to encourage desirable actions such as data collection or ‘fishing-for-litter’ activities. However, in order for a new system such as this to be useful and become accepted, stakeholders must be involved in the development and design process. This paper details the consultative process carried out with Irish demersal fishery stakeholders in an effort to identify their likes and dislikes of the system, and work towards tailoring the RTI system into a practical solution that works for them. In this process, we achieved a detailed understanding of the fishery, the complexity of the system, and the challenges faced by the stakeholders, all of which must be considered when attempting to implement a new management system such as RTI. A range of proposals were made by stakeholders, including new ideas for the future development of the RTI system. Most striking were the numerous ideas and approaches to tackling key issues currently facing the industry, many of which also have relevance to existing fisheries management. Given the freedom and support to do so, fishing industry stakeholders are eager to contribute to solving many of their own problems.
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Lessons from a Marine Spatial Planning data management process for IrelandThis paper presents a framework containing ten components to deliver a data management process for the storage and management of data used for Marine Spatial Planning (MSP) in Ireland. The work includes a data process flow and a recommended solution architecture. The architecture includes a central data catalogue and a spatial storage system. The components of the process are presented to maximise the reuse potential of any dataset within an MSP context. The terms ‘Suitability’ and ‘Readiness’ in the MSP context are offered as both formal and considered assessments of data, as is the applicability of a data stewardship maturity matrix. How data contained in such a storage system can be published externally to potential consumers of these data is also explored. The process presents a means of managing data and metadata to ensure data lineage is optimised by carrying information about the origin of and the processing applied to the data; to evaluate the quality and relevance of geospatial datasets for use in MSP decisions in Ireland. The process was piloted in the National Marine Planning Framework for Ireland in the development of draft map products; feedback from the public consultation is ongoing and not presented.
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Implementation of a Data Management Quality Management Framework at the Marine Institute, IrelandThe International Oceanographic Data and Information Exchange of UNESCO’s Intergovernmental Oceanographic Commission (IOC-IODE) released a quality management framework for its National Oceanographic Data Centre (NODC) network in 2013. This document is intended, amongst other goals, to provide a means of assistance for NODCs to establish organisational data management quality management systems. The IOC-IODE’s framework also promotes the accreditation of NODCs which have implemented a Data Management Quality Management Framework adhering to the guidelines laid out in the IOC-IODE’s framework. In its submission for IOCE-IODE accreditation, Ireland’s National Marine Data Centre (hosted by the Marine Institute) included a Data Management Quality Management model; a manual detailing this model and how it is implemented across the scientific and environmental data producing areas of the Marine Institute; and, at a more practical level, an implementation pack consisting of a number of templates to assist in the compilation of the documentation required by the model and the manual.
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Herring larval surveys in the Celtic Sea and division VIIj in 1983/1984Surveys for herring larvae in the Celtic Sea were conducted for the sixth ~ successive season between October 1983 and February 1984. The modifications made to the survey grid in the previous season to take account of the amalgamation of the Celtic Sea and Division VIIj for assessment purposes and to ascertain if larvae drift into the Irish Sea were also adopted for the 1983/84 surveys. A drift of larvae towards the Irish Sea was apparent in 1983/84. The larval abundance index for 1983/84 based on a standard survey area was almost three times higher than any previous value. A continuous increase in larval indices since 1978/79 indicates a recovery of the spawning stock.
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The age Distribution of the Herring Stocks around the Irish Coast during 1993The age distribution of stocks is usually considered as an indication of how healthy a stock may be. In general stocks which are lightly exploited will contain a much larger proportion of older fish than a stock which is heavily exploited. A stock which is heavily exploited will probably be dependent on one year class which will recruit to the fishery and which will immediately be subjected to fishing effort. Obviously in such a fishery failure of recruitment or poor recruitment will have drastic effect on the catches. Herrings can be aged accurately until are about 10 years old and generally recruit to the adult stocks during their third year. During this year, the majority of fish will spawn for the first time.
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Towards a flexible Decision Support Tool for MSY-based Marine Protected Area design for skates and raysIt is recommended that demersal elasmobranchs be managed using spatial proxies for Maximum Sustainable Yield. Here we combine escapement biomass—the percentage of the stock which must be retained each year to conserve it—with maps of predicted Catch Per Unit Effort (CPUE) of four ray species [cuckoo (Leucoraja naevus), thornback (Raja clavata), blonde (Raja brachyura), and spotted (Raja montagui)], created using Boosted Regression Tree modelling. We then use a Decision Support Tool to generate location and size options for Marine Protected Areas to protect these stocks, based on the priorities of the various stakeholders, notably the minimisation of fishing effort displacement. Variations of conservation/fishing priorities are simulated, as well as differential priorities for individual species, with a focus on protecting nursery grounds and spawning areas. Prioritizing high CPUE cells results in a smaller closed area that displaces the most fishing effort, whereas prioritizing low fishing effort results in a larger closed area that displaces the least fishing effort. The final result is a complete software package that produces maps of predicted species CPUE from limited survey data, and allows disparate stakeholders and policymakers to discuss management options within a mapping interface.
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Human Health• Toxin producing phytoplankton, pathogenic vibrios (bacteria commonly found in low salinity water) and noroviruses all have the potential to impact human health. • The relationship between climate change and toxin producing phytoplankton is complex. Considerable unknowns remain about how climate change will impact this part of the plankton community and confidence in predicting these impacts in UK waters remains low. • A recent study in Scotland has shown short term weather events as well as wind mediated transport of offshore phytoplankton populations can influence the toxicity of coastal shellfish. This highlights the requirement for long term data sets to identify the impacts of climate change from shorter term seasonal and interannual variability. • Emerging evidence from peer-reviewed scientific studies has suggested that increasing seawater temperatures and extreme weather events such as heatwaves and extreme precipitation, drive the abundance of pathogenic vibrios in the environment. A recent spate of reported infections in Northern Europe underlines these observations. Climate warming in the region may therefore increase human infections.
