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This Repository consists of processed data and code to reproduce the analyses (model fitting, prediction and sampling from the posterior of the best model) for the associated article: Accounting for spatio-temporal distribution changes in size-structured abundance estimates for a data-limited stock of Raja clavata DOI : https://doi.org/10.1093/icesjms/fsae106 Research-vessel catch data for the North Sea and Eastern English Channel was obtained from ICES database on trawl surveys (DATRAS) for Raja clavata (WoRMS AphiaID: 105883) and processed to create a final dataset for spatio-temporal analysis with integrated-nested laplace approximation (INLA). The final processed dataset consists of hauls and catches from the International Bottom Trawl Survey (NS-IBTS) for Quarter 1 and 3, the Beam Trawl Survey (NS-BTS) for Quarter 3, and the Channel Groundfish Survey (FR-CGFS) for Quarter 4. It further contains depth, substrate and habitat types associated with haul locations obtained from emodnet for the study area. The data and analyzes covers the period 1988-2023.

Small pelagic fish (SPF) are crucial in marine food webs, transferring energy from plankton to higher trophic levels. This study focuses on herring (Clupea harengus) and sprat (Sprattus sprattus), addressing knowledge gaps in their feeding ecology in a nursery area, theDutch Wadden Sea. We conducted a year-long, monthly survey, and used DNA metabarcoding to analyse zooplankton samples and stomach contents of two size classes of herring and sprat. Intra-, interspecific, and seasonal variations in fish condition, stomach fullness,and diet composition, along with selective feeding, were studied. Our study showed that condition and diet composition of herring and sprat, along with zooplankton density, exhibited a clear seasonal pattern. Juvenile herring and sprat displayed opportunistic feedingbehaviour, rather than showing distinct prey selection. Besides copepods, we regularly observed (larvae of) benthic invertebrates in their diet. This emphasizes the crucial role of SPF as energy transfer agents, not solely between trophic levels, but also from benthic topelagic habitats. Furthermore, fish post-larvae were part of the diet of larger herring (10–15 cm). Because of its unprecedented temporal and taxonomical detail, this study advances the understanding of seasonal dynamics of dominant components at the base of theWadden Sea food web.

Het onderzoekssamenwerkingsproject Data Arme Visbestanden (OSW-DAV) was gericht op verschillende innovaties die de rol van de visserijsector bij het verzamelen van gegevens voor bestandsbeoordelingen versterken. De gegevensverzameling betreft een bedrijfssurvey voor tarbot en griet (BSAS) en DNA-bemonstering voor verwantschapsanalyse voor roggen (RAYS). Beide vormen van gegevensverzameling zijn in de voorgaande OSW 2.0- en OSW 2.1-projecten geïnitieerd en in het huidige project voortgezet om tijdreeksen van minimaal vijf jaar te verkrijgen, hetgeen een voorwaarde is voor het gebruik van de gegevens voor bestandsschattingen. De innovaties betreffen de ontwikkeling van materialen en protocollen die eenvoudig toe te passen zijn door vissers en resulteren in betrouwbare gegevens, zodat de wetenschappelijke kwaliteit gewaarborgd is. De bedrijfssurvey tarbot en griet heeft tot doel gegevens te verzamelen in aanvulling op de gegevensverzameling die al plaatsvindt door wetenschappelijke surveys, met als doel de algehele kwaliteit van de toestandsbeoordelingen voor deze soorten te verbeteren. De bedrijfssurvey werd oorspronkelijk ontworpen en uitgevoerd in het voorgaande project OSW2.0 en de jaarlijkse uitvoering in september-oktober werd voortgezet in het huidige project. Het survey-gebied is gebaseerd op de tarbot- en grietvangsten (LPUE) en de ruimtelijke verdeling van de boomkorvloot (VMS-gegevens), in omvang teruggebracht tot een haalbare omvang voor drie vissersschepen, rekening houdend met hun normale visgronden. De huidige en toekomstige gebieden die gesloten zijn voor de visserij werden verwijderd en er werd een raster van 5x5 km op het survey-gebied aangebracht. Voor elke jaarlijkse survey worden willekeurig 60 rastercellen geselecteerd als survey-station en bevist door drie vissersschepen (elk 20 stations) tijdens reguliere visweken. Schippers moeten de survey-trekken ergens binnen de aangewezen rastercellen starten, maar zijn daarna vrij om de route van de surve

Undersized European plaice dominate the discarded fraction of the catch of the beam trawl fisheries for sole in the Southern North Sea. Effects of environmental conditions at sea and of the use of a water-filled hopper on the survival of undersized European plaice discarded by pulse trawl fisheries were explored. During trips with commercial pulse-trawlers catches were discharged in either water-filled hoppers or conventional dry hoppers. For both hoppers, undersized plaice were sampled from the sorting belt. After assessment of vitality status, sampled fish were housed in dedicated survival monitoring tanks on board. Upon return in the harbour fish were transferred to the laboratory to monitor their survival for up to 18 days post-catch. Conditions at sea, such as wave height and water temperature, as prevailing during these trips were recorded or obtained from public data sources. The overall estimate for the survival probability for plaice discarded by pulse trawl fisheries is 12% (95% CI: 8% - 18%). Both water temperature and vitality status had strong effects on survival probabilities of discarded plaice. Increasing water temperature increased mortality. The vitality of the fish could be moderately increased by using a water-filled hopper to collect the fish on deck, but we found no significant direct effect of hopper type on plaice discard survival. It seems that to increase discards survival, fish need to be landed on deck in much better condition by a reduction of the impact of capture and hauling processes on fish condition

Little is known about the migratory behaviour of sharks and rays in the Greater North Sea ecoregion. While several ray stocks were widespread in the early 20th century, the population declines resulted in a reduced distribution area of most rays, with the east coast of the UK and the Eastern English Channel being the hotspots for abundance for most larger species. The recovery in abundance also results in a larger distribution area, including parts of the Dutch EEZ. The question is how these different areas are connected in terms of migration and population genetics. To study migration of rays, we tagged 224 specimens of three ray species; spotted ray (Raja montagui), blonde ray (Raja brachyura), and thornback ray (Raja clavata). This tagging was done using CEFAS G5 Data Storage Tags (DSTs). Each tag was attached to an individual ray at the basis of the tail. To ensure minimum effect of the tag on the ray, a protocol was developed to attach the tag to a ray, with the goal of having a procedure for attachment that was as short as possible, and with minimum effect on the ray. DSTs measure and store temperature and depth of the individual that they are attached to, The G5 DSTs used in this study can be programmed to detach from the animal (‘pop-off’) after a set time. Because the DSTs are slightly buoyant, they will float to the surface and be taken to land by currents and winds. When the tags were found by fishers on live rays, or by beach combers, the temperature and depth records can be downloaded from the tag and analyzed. These temperature and depth profiles can subsequently be used to reconstruct the migration pattern of the individual rays. Because the pop-off time for the deployed tags has not been reached, we now have a limited set of returned tags: 30 tags were returned, with the majority being found on beaches. Most returned tags were retuned within 6 months after release. Of the 30 tags which were returned, 7 were reported by fishers and therefore both capt

Fisheries are supposed to be for the benefit of society, producing food, providing livelihoods and enabling cultural continuity. Biological productivity goals for fish stocks operationalised through Harvest Control Rules (HCRs) are central to contemporary fisheries management. While fisheries policies often state socio-economic objectives, such as enhancing the livelihoods of coastal communities, those are rarely, if ever, incorporated into operationalised management procedures. The lack of articulation of social objectives and lack of monitoring of social outcomes around HCRs amounts to poor public policy. In this article, we explore the potential for social HCRs (sHCRs) with reference points and agreed predefined actions to make the social dimensions of fisheries explicit. sHCRs cannot cover all social dimensions, so should be considered as one tool within a broader framework of fisheries governance. Moreover, successful sHCRs would require sound deliberative and participatory processes to generate legitimate social objectives, and monitoring and evaluation of fisheries management performance against those objectives. We introduce two potential types of sHCRs, one based on allocation of catch within biological limit reference points, and one for when fishing exceeds biological limit reference points. The application of sHCRs, we argue, can foster accountability and help avoid non-transparent negotiations on size and distribution of the catch. Our proposal is a call to action for policy makers and fisheries managers to properly integrate social criteria into fisheries governance, and for both biophysical fisheries scientists and social scientists to do better in practical collaboration for methods and knowledge development to support this integration.

The objective of WKFISHDISH2 was to develop a standardized and open-source way of routinely using trawl survey data to produce distribution maps which can be easily updated. To do so, workshop participants (i) reviewed models that can produce distribution maps from survey data in DATRAS and MEDITS formats, (ii) considered best practice guidance for data, and models, (iii) implemented best practice to produce distribution maps in a transparent manner, and (iv) populated an ICES repository with distribution maps and associated scripts. Nine models were reviewed, seven of which were considered appropriate to produce distribution maps using survey data. The two models excluded failed to estimate gear standardization factors. Best practice for data should consider the following: correct/remove erroneous observations, account for changes in haul duration/timing affecting catchability, use species-specific modelled areas, remove gears/surveys with no observations to reduce model converging time, and include appropriate explanatory variables. A step-by-step list to preprocess survey data was provided. Best practice for models should consider the following: account for skewed distribution of survey data by exploring different statistical error distributions, use open-source models able to reproduce distributions from simulated data, consider the complexity of the model required vs. the run-time (e.g. number of knots), avoid extrapolating the model to areas/depths where the species is not observed, and perform relevant model diagnostics/model selection. To compare distribution estimated by different models, the SPAtial EFficiency metric (SPAEF) was used together with centres of gravity, biomass hot spots (90 th percentile), and effective occupied areas. All seven models were able to produce satisfactory distribution maps for at least one species within the workshop time constraints, both with DATRAS data in the Atlantic and the MEDITS data in the Mediterranean. Comparisons be

The implementation of ecosystem-based fisheries management requires knowledge on the ecological impact of fishing activities on species and their habitats – those both targeted and not targeted by fisheries. To identify whichecological impacts are key and what is known about them, SEAwise consulted stakeholders through European Advisory Councils and conducted a systematic review of the scientific literature to map the available knowledge and evidence. Specific reference was given to the bycatch of Protected, Endangered and Threatened (PET) species, benthic habitats, food webs and biodiversity, and impact from fisheries-related litter and ghost nets. At the stakeholder consultations, sharks and/or elasmobranchs, turtles, species interactions, and seals or marine mammals were identified as top ranked in at least three out of the five regions. Other terms identified by at least two Case Study regions were: seabirds, sensitive species, benthic habitats, litter, PET species, invasive species and species interactions.Relevant data were extracted from 549 retained papers. The majority of studies were conducted in the Mediterranean Sea, whereas only few papers reported on fishing impacts in the Baltic Sea (see figure below). Bony fish (teleosts) and benthos were the most studied ecosystem components in all Case Study regions, whereas marine mammals and cartilaginous fish were often studied in relation to bycatch of PET species. Out of the 549 papers, most of them were related to fishing impacts on food webs and biodiversity and benthic habitats, followed bybycatch of PET species and other fishing impact studies (not related to any task). Fewest studies were related to the impact of fisheries-related litter and ghost nets. Demersal trawls were by far the most studied gear in studies on commercial fishing impacts. For recreational fisheries, hooks and lines, in particular angling, was the most studied fishing activity. Among the items identified by the stakeholders, marine ma

With a sixth mass extinction looming and freshwater biodiversity declining at unprecedented rates, evaluating ecological efficacy of river restoration efforts is critical in combatting global biodiversity loss. Here, we present a comprehensive study of the functioning for fishes of 46 river restoration projects in the river Rhine, one of the world's most heavily engineered lowland rivers. Floodplains with permanent, either one- or two-sided lateral connectivity to the main channel, favour total fish abundance, and are essential as nursery areas for riverine fishes. Habitat heterogeneity had a strong positive effect on species richness but was negatively related with fish abundances. However, the effects of environmental variables varied between ecological groups and spatial scales. Surprisingly, richness of critical rheophilic fishes declined with large-scale habitat heterogeneity (~1000 m), while it increased at small scales (~100 m), possibly because of the presence of unfavourable habitats for this ecological group at larger scales. Clearly, there is no one-size-fits-all design for river restoration projects. Whether a river section is free-flowing or impounded dictates the scope and efficacy of restoration projects and, within a river section, multiple complementary restoration projects might be key to mitigate freshwater fish biodiversity loss. An essential element for success is that these projects should retain permanent lateral connection to the main channel.

Data for training and evaluation of a method for detection and counting demersal fish species in complex, cluttered and occluded environments that can be installed on the conveyor belts of fishing vessels. The data mainly exists of images of fish on a conveyer belt with the corresponding annotations. This was used to train a neural network (YOLOv3) to detect and classify fish species. Because each fish is visible in multiple images, the fishes were tracked over consecutive images and the total number of fish per specie was counted. These counts were compared to human review.

This paper presents and evaluates a method for detecting and counting demersal fish species in complex, cluttered, and occluded environments that can be installed on the conveyor belts of fishing vessels. Fishes on the conveyor belt were recorded using a colour camera and were detected using a deep neural network. To improve the detection, synthetic data were generated for rare fish species. The fishes were tracked over the consecutive images using a multi-object tracking algorithm, and based on multiple observations, the fish species was determined. The effect of the synthetic data, the amount of occlusion, and the observed dorsal or ventral fish side were investigated and a comparison with human electronic monitoring (EM) review was made. Using the presented method, a weighted counting error of 20% was achieved, compared to a counting error of 7% for human EM review on the same recordings.

Climate change is anticipated to have long-term and widespread direct consequences for the European marine ecosystems and subsequently for the European fishery sector. Additionally, many socio-economic and political factors linked to climate change scenarios will impact the future development of fishing industries. Robust projection modeling of bioeconomic consequences of climate change on the European fishing sector must identify all these factors and their potential future interaction. In this study, four socio-political scenarios developed in the EU project CERES (Climate change and European aquatic RESources) were operationalized and used in model projections of marine wild capture fisheries. Four CERES scenarios (“World Markets,” “National Enterprise,” “Global Sustainability” and “Local Stewardship”) were based on the IPCC framework of Shared Socio-economic Pathways (SSPs). For each of these scenarios, a set of quantitative outputs was generated to allow projections of bio-economic impacts to mid-century (2050) on wild-capture fisheries operating in different European regions. Specifically, projections accounted for future changes in fisheries management targets, access regulations, international agreements, fish and fuel prices, technological developments and marine spatial planning. This study thoroughly describes the elements of these four fisheries scenarios and demonstrates an example of the “regionalization” of these scenarios by summarizing how they were applied to the North Sea flatfish fishery. Bioeconomic projections highlight the importance of future developments in fuel and fish price development to the viability of that and other fisheries. Adapting these scenarios for use in other models and regions outside the 10 European fisheries examined in CERES would be highly beneficial by allowing direct comparison of the bioeconomic risks and opportunities posed by climate change.