Fisheries management requires the best scientific knowledge on the exploitation and conservation status of stocks. This is challenging for by-catch species, for which necessary data for their assessment is more limited than for target ones. That is the case for the thornback ray, Raja clavata, in the Balearic Islands (western Mediterranean), whose exploitation and conservation status are addressed here for the first time, in an integrative approach, by using innovative assessment methods and genetic diversity analysis. The time series of fishing landings from 1964 and MEDITS trawl survey data from 2004 were used to apply CMSY++ and Bayesian state-space Schaefer production models. We also estimated the genetic diversity of the Cytochrome C Oxidase subunit I mitochondrial gene from 31 individuals collected during MEDITS surveys. The species showed overexploitation with a current fishing mortality (F) below that producing maximum sustainable yield (FMSY), but with a current stock biomass (B) lower than BMSY. Despite the fact that the exploitation status is stable or even has improved in the last decades, the overexploitation period since the late 1970s seems to have reduced levels of genetic diversity, below those of related species and other populations of R. clavata. This low genetic diversity may entail the loss of adaptive potential, making the species more vulnerable to fishing and the current climate change., This study has been cofunded by the EU through the European Maritime and Fisheries Fund (EMFF) within the Data Collection National Program, management and use of data from fisheries sector; also by the Ministry of European Funds, University and Culture of the Baleric Islands through the grants for the training of research personnel 2021 (F. Ferragut-Perelló) and the Post-doctoral contract (S. Ramírez-Amaro) of the Vicenç Mut Estabilitat program co-financed by the Government of the Balearic Islands and the European Social Fund. N. Petit-Marty is supported by MSCA-PF FishAdapt 101066785. This research was partly funded by the European Union’s Horizon 2020 Research and Innovation Program (H2020-BG-10-2020-2), grant number No. 101000302—EcoScope (Ecocentric management for sustainable fisheries and healthy marine ecosystems). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript., Peer reviewed

Within the context of the ecosystem approach to fisheries management, an ecosystem model was developed for the Balearic Islands in the early 2000s, covering from 0 to 800 m of depth. The aim of the study was to describe the structure and functioning of the ecosystem together with the fishing impacts. The results show that the biomass of the primary producers (PP), mainly dominated by Posidonia oceanica meadows and red algae beds, represented a high percentage of the biomass (39.20%) in the ecosystem. Most of the trophic flows occurred between PP (mostly benthic) and trophic level II. The mixed trophic impact analysis also highlighted a positive impact of the functional groups (FGs) at the base of the food web. Besides, there were important trophic flows between several demersal FGs, and many groups of the pelagic compartment, confirming the importance of the benthopelagic coupling previously reported. The mean trophic level of the catch (mTLc=2.76) was lower than those reported in adjacent areas due to the discard of benthic producers. By excluding benthic PP, the Balearic Islands showed the highest mTLc (3.44) among all the Mediterranean areas modelled, probably due to differences in the trophic structure, lower fisheries exploitation levels and lower development of the purse seine fleet targeting small pelagic fishes. The mean transfer efficiency (21.80%) was double than the global average (10%), which highlights the oligotrophy of the system, the importance of demersal production which has lower rates of transfer through the food web, and a more efficient use of nutrients in the ecosystem. Sponges, one of the most important groups of benthic invertebrates in the Balearic Archipelago, are known to recycle dissolved organic matter, which is reintroduced into the food web similar to the microbial loop, but the magnitude of this and other processes remains still unknown in this area. The present study is a first step to develop spatio-temporal simulations under different exploitation scenarios and to calculate ecological indicators to assess the state of the marine environment in this region., BALAR surveys were funded by the Instituto Español de Oceanografı́a (IEO) and later-on integrated in the MEDITS programme. These data, together with the information of landings and data from observers on board was collected within the National Programme of collection, management and use of data in the fisheries sector and support for scientific advice regarding the Common Fisheries Policy, co-funded by the IEO and the EU through the European Maritime and Fisheries Fund (EMFF). This research was partly funded by the European Union’s Horizon 2020 Research and Innovation Program (H2020-BG-10-2020-2), grant number No. 101000302 – EcoScope (Ecocentric management for sustainable fisheries and healthy marine ecosystems). CANAL project was co-funded by Fundación Biodiversidad and the EC (LIFE+ INDEMARES project). DRAGONSAL project was funded by the Balearic Islands Government (EU Fisheries Fund). IDEADOS project was funded by the Spanish Government (CTM2007-65844-C02-01-02-03). The project is a contribution to the project “Mejora del conocimiento cientı́fico-técnico para la sostenibilidad de las pesquerı́as demersales del Mediterráneo occidental”, funded by Next Generation European funds (Plan de Recuperación, Tranformación y Resiliencia), with an agreement between the Spanish Ministry of Agriculture, Fisheries and Food and CSIC by means of the IEO. MC would like to acknowledge the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S) and the European Union’s Horizon 2020 research and innovation programme under grant agreement No 869300 (FutureMares), With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Peer reviewed

20 pages, 13 figures, 3 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmars.2023.1155480/full#supplementary-material.-- Data availability statement: The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding author, Recent decades have witnessed declines in the amount of fishing catch due to changes in the marine ecosystem of the Eastern Mediterranean Sea. These changes are mainly a consequence of direct human activities as well as global warming and the entry of invasive species. Therefore, there is a need to improve fisheries management so that it accounts for the various stressors and uses of the marine environment beyond fishing, while providing sustainable catches and maintaining a healthy ecosystem. The ability to understand, and sustainably manage, the fishing industry relies on models capable of analyzing and predicting the effects of fishing on the entire ecosystem. In this study, we apply Ecospace, the spatial-temporal component of the Ecopath with Ecosim approach, to study the Israeli continental shelf to evaluate the impact of climate change and alternative management options on the ecosystem. We examine several management alternatives under the severe assumption of the RCP8.5 climate change scenario for the region. Results indicate that under business-as-usual conditions, the biomass of the native species will decrease, the biomass of the invasive species will increase, and there will be a decrease in the fishing catch. In addition, of the management alternatives examined, the alternative of prohibition of fishing in the northern region of Israel along with the establishment of a network of marine nature reserves provides the optimal response for the ecosystem and fisheries. The Achziv Nature Reserve is projected to be successful, improving the biomass of local species and reducing, to some extent, the presence of invasive species. These results are consistent with visual surveys conducted inside and outside the reserve by the Israeli Nature and Parks Authority. Furthermore, simulation results indicate spill-over effects in areas close to nature reserves yielding higher catches in those regions, This work was funded by the H2020 European project Ecoscope under Grant Agreement ID 101000302, with Grant Agreement ID 101000302 and by the Israeli Ministry of Energy in a grant to GG. XC was supported by the Spanish National Program Juan de la Cierva-Formación (MCIN / AEI / 10.13039/501100011033 FJC2020-044367-I) funded by the Government of Spain (Ministry of Science and Innovation (MCIN) and the State Research Agency (AEI)) and the European Union (NextGenerationEU/PRTR). [...] MC acknowledge partial funding from European Union’s Horizon 2020 research and innovation programme under grant agreement No 869300 (FutureMares) and No 101059877 (Ges4Seas), and the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Peer reviewed

25 pages, 10 figures, 3 tables, supporting Information https://doi.org/10.1029/2023EF004295.-- Data Availability Statement: The EcoOcean time series output used in this MS is available on Figshare (Steenbeek, 2023a) and the source code to the MEM multi-run framework prototype is available via Steenbeek (2023b). The ESM driver data for this manuscript was generated under the TRIATLAS project and is available via Bethke et al. (2019) and EC-Earth-Consortium (2022). The EcoOcean model is a work in progress, but can be used under a project collaboration by contacting the lead author, Marine Ecosystem Models (MEMs) are increasingly driven by Earth System Models (ESMs) to better understand marine ecosystem dynamics, and to analyze the effects of alternative management efforts for marine ecosystems under potential scenarios of climate change. However, policy and commercial activities typically occur on seasonal-to-decadal time scales, a time span widely used in the global climate modeling community but where the skill level assessments of MEMs are in their infancy. This is mostly due to technical hurdles that prevent the global MEM community from performing large ensemble simulations with which to undergo systematic skill assessments. Here, we developed a novel distributed execution framework constructed of low-tech and freely available technologies to enable the systematic execution and analysis of linked ESM/MEM prediction ensembles. We apply this framework on the seasonal-to-decadal time scale, and assess how retrospective forecast uncertainty in an ensemble of initialized decadal ESM predictions affects a mechanistic and spatiotemporal explicit global trophodynamic MEM. Our results indicate that ESM internal variability has a relatively low impact on the MEM variability in comparison to the broad assumptions related to reconstructed fisheries. We also observe that the results are also sensitive to the ESM specificities. Our case study warrants further systematic explorations to disentangle the impacts of climate change, fisheries scenarios, MEM internal ecological hypotheses, and ESM variability. Most importantly, our case study demonstrates that a simple and free distributed execution framework has the potential to empower any modeling group with the fundamental capabilities to operationalize marine ecosystem modeling, JS acknowledges institutional support from the Polytechnic University of Catalunya (UPC), Barcelona, Spain. RB, VC, MC, EE, NK, PO, DR and JS acknowledge the European Union's Horizon 2020 research and innovation programme under Grant 817578 (TRIATLAS). VC and JS acknowledge the European Commission's Horizon 2020 Research and Innovation programme under Grant 101000302 (EcoScope). JS and MC acknowledge the European Commission's Horizon 2020 Research and Innovation programme under Grant 101060072 (ACTNOW) and the Spanish Ministry of Science and Innovation Grant PID2020-118097RB-I00 (ProOceans). MC acknowledges institutional support of the “Severo Ochoa Centre of Excellence” accreditation CEX2019-000928-S, Peer reviewed

16 pages, 9 figures, 1 table, supplementary data https://doi.org/10.1093/icesjms/fsad213.-- Data availability: The data underlying this article will be shared on reasonable request to the corresponding author, Ecosystem models, such as Ecopath with Ecosim (EwE), provide a platform to simulate intricate policy scenarios where multiple species, pressures, and ecosystem services interact. Complex questions often return complex answers, necessitating evidence and advice to be communicated in terms of trade-offs, risks, and uncertainty. Calibration procedures for EwE, which can act as a source of uncertainty and bias in model results, have yet to be explored in a comprehensive way that communicates how sensitive model outputs are to different calibration approaches. As the EwE community has grown, multiple divergent approaches have been applied to calibrate models through the estimation of vulnerability multipliers: parameters that augment the consumption rate limits of predators. Here we explore the underlying principles of vulnerability multipliers as well as existing calibration approaches and their justification. Two case studies are presented: the first explores how vulnerability multipliers emerge based on the chosen calibration approach using simulated data, while the second takes two operational EwE models (Irish Sea and Northwest Atlantic Continental Shelf) and compares their outputs when calibrated following alternate calibration approaches. We show how calibration approaches can impact model-derived advice and provide a list of best practice recommendations for EwE calibration, J.B. would like to acknowledge the EU Horizon project OceanICU (grant agreement no. 101083922). J.J.H. and V.C. would like to acknowledge the EU Horizon 2020 project EcoScope: ecocentric management for sustainable fisheries and healthy marine ecosystems project (grant agreement no. 101000302). M.C. would like to acknowledge EU Horizon project Ges4Seas (grant agreement no. 101059877), the Spanish project ProOceans (Plan Estatal de Investigación Científica, Técnica y de Innovación 2020, PID2020-118097RB-I00), and the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S). V.C. also acknowledges NSERC Discovery Grant RGPIN-2019–04901, Peer reviewed

Despite the high diversity of elasmobranch fishes in the Balearic Islands, knowledge of their biology and population dynamics is still scarce. A recent mark-and-recapture experiment off the Balearic Islands tagged 3738 individuals of 23 shark and batoid species during MEDITS and CANAL bottom trawl scientific surveys from June 2021 to August 2023. Retrieval was reported for the sharks Scyliorhinus canicula and Mustelus mustelus, revealing relatively small home ranges for these species (0.2–38.5 km and 7.8–15.3 km for S. canicula and M. mustelus, respectively). Recapture efficiency was higher from scientific surveys than from commercial catches, highlighting potential challenges in collaboration with fishermen and recapture reports. Density estimates obtained from the MEDITS bottom trawl survey suggest a much larger population for S. canicula than estimates from the mark–recapture data, indicating MEDITS density estimates for this species may be overestimated due to its scavenger behavior perhaps favoring individuals searching for discards aggregated in the fishing grounds. This study emphasizes the importance of monitoring, collaborative efforts, and improved reporting mechanisms to enhance our understanding of elasmobranch populations and provide support for sustainable management of these vulnerable marine species., This research was partly funded by the European Union’s Horizon 2020 Research and Innovation Program (H2020-BG-10-2020-2) grant 101000302—EcoScope (Ecocentric management for sustainable fisheries and healthy marine ecosystems). F.F.-P. was supported by the Ministry of European Funds, University and Culture of the Balearic Islands through grants for the training of research personnel 2021., Peer reviewed

12 pages, 5 figures, 3 tables, supporting information https://doi.org/10.1073/pnas.2412845122.-- Data, Materials, and Software Availability: R codes developed to conduct the present study are made available in the following Zenodo repository (136). The analyses presented in the manuscript build up from data and products previously published in various publications: (56–59), Ocean giants shape the structure and functioning of marine food webs via trophic top–down controls, landscapes of fear, vertical and horizontal redistribution of nutrients, energy, and matter. Yet, they face threats from overfishing, pollution, habitat degradation, and climate change, and one-third of marine megafauna species are at risk of extinction, ultimately endangering the resilience of entire ecosystems. In such a context, knowing when and where megafauna find resources to balance their substantial energy requirements is critical for their management. Through an energyscape approach integrating abundance censuses, diet, and energy requirements, we investigated the prey consumption patterns of Mediterranean marine megafauna during the summer. We thereby shed light on a diverse guild of species composed of fishes, mammals, reptiles, and birds and estimated that 4.1 million individuals consume 1.6 million tons of prey each summer, pelagic cephalopods being the primary food resource and cetaceans and tunas being key players in the community. Spatial patterns in prey consumption reflected the diverse distribution and needs of the megafauna species and underlined the critical importance of the western Mediterranean for the megafauna community. Conservation strategies should prioritize spatial and biological diversity to safeguard megafauna and ecosystem functions across the Mediterranean basin, This work was funded by the European Horizon 2020 Program EcoScope project under the grant agreement number 101000302, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Peer reviewed

R scripts to replicate the analyses from "Energyscapes pinpoint marine megafauna feeding hotspots in the Mediterranean"., European Commission
EcoScope — Ecocentric management for sustainable fisheries and healthy marine ecosystems: 101000302, With funding form the Spanish government through the "Severa Ochoa Centre of Excellence" accreditation (CEX2019-000928-S)., Peer reviewed

Understanding the functioning and resilience of marine ecosystems requires identifying the main energy flow pathways. Key trophic groups occupy strategic positions in the trophic interactions network, acting as hubs that control the energy distribution across the ecosystem. This study examines the Bay of Biscay’s pelagic food web using stable isotope analysis with stomach content data, creating a network of 38 trophic groups and 125 interactions. Both annual-weighted and seasonal (spring and late summer) networks were constructed. The analysis of unweighted and weighted annual networks found that low-trophic level epipelagic fish (European anchovy, Engraulis encrasicolus; sardine, Sardina pilchardus; and sprat, Sprattus sprattus) is a key trophic group displaying higher scores in many centrality indices. These forage fish play a central role in facilitating energy transfer across trophic levels, thus representing a critical link between the planktonic food web and higher trophic level predators and fisheries. Overall, annual networks showed that phytoplankton-dominated grazing chains support a higher diversity of predators compared to chains originating from particulate organic matter (POM). The analysis of weighted networks accounting for seasonal variations in trophic interactions revealed that, during late summer, predators occupy more vulnerable positions than in spring. Changes in feeding preferences cause blue whiting to shift from mostly depending on grazing chains during spring to occupying a position along POM-dominated chains in late summer. These findings highlight the need for fisheries management strategies to prioritize the conservation of key trophic groups supplying energy to predators while considering seasonal shifts in the structure of the energy flow network., We would like to thank the crew of the R/V ‘Ángeles Alvariño’, R/V ‘Vizconde de Eza’ and R/V ‘Emma Bardán’, as well as the AZTI and IEO-CSIC staff who took part in the BIOMAN and JUVENA surveys, allowing the collection of the samples used in this study. We also thank AZTI’s scientific observers and others who contributed to the sample collection, including members of the French stranding scheme (RNE) for their continuous effort in collecting data on stranded cetaceans. The study was supported under the EPELECO project funded by the Spanish Government, and partially by the PETFISH project funded by the Basque Government and the BIOcean5D project (Horizon Europe grant agreement 10109915). BI was funded by a PhD fellowship from the Department of Economic Development, Sustainability and Environment of the Basque Government. ML was funded by a Ramón y Cajal contract (RYC-2012-09897) from the Spanish Government. The authors are grateful to Gaël Guillou for his assistance with stable isotope analyses. Thank you to Adrien Lambrechts, who made it possible to obtain the data on Balearic shearwaters. Thanks are also due to the CPER (Contrat de Projet Etat-Région) and the FEDER (Fonds Européen de Développement Régional) for funding the IRMS of LIENSs laboratory. Pelagis is funded by the French ministry in charge of the environment, the French Office for Biodiversity (Office Française de la Biodiversité—OFB), and by the “Communauté d’Agglomération de la Ville de La Rochelle.” PB is an honorary member of the IUF (Institut Universitaire de France). MSco acknowledges the German Federal Agency for Nature Conservation (Bundesamt für Naturschutz, BfN), which provided financial support with funds from the Federal Ministry of the Environment, Nature Conservation, and Nuclear Safety (BMU) under grant agreement FKZ: 3521532201. MI and MSco are grateful to the support from the EcoScope Project, funded by the European Commission's Horizon 2020 Research and Innovation Programme under grant agreement Nº 101000302. This is contribution number 1273 from AZTI, Marine Research, Basque Research and Technology Alliance (BRTA)., Peer reviewed

This review evaluates the current knowledge of essential biological traits (diet, fecundity, maturity, length-weight relationships, spawning, growth, lifespan, and natural mortality) of marine fishes across European and adjacent waters. These traits are crucial for ecosystem modeling and stock assessments. Using data from FishBase, the largest and most comprehensive database on fishes, a gap analysis was performed to identify areas of research focus and the corresponding gaps that require further study. Biological data coverage is strong in the Baltic and North Seas but moderate in the Adriatic, Aegean, Biscay, Celtic, Levantine, and western Mediterranean Seas. Well-documented species include the European conger (Conger conger), thornback ray (Raja clavata), and transparent goby (Aphia minuta) which are reported from all areas. The narrowest knowledge gaps concern length-weight relationships, followed by spawning and growth, while natural mortality and fecundity are the least studied biological characteristics. Regional variations exist, particularly for protected species. Future research should focus on filling gaps by addressing overlooked species (bycatch and discarded species) and traits such as natural mortality and fecundity, with special attention to vulnerable groups like sharks and rays. Expanding biological data coverage will reduce uncertainties in stock assessments and improve ecosystem models, two widely used tools for sustainable fisheries management and marine conservation., The present work was supported by the Horizon 2020 Framework Programme funded project “EcoScope” [Contract No. 101000302]., Peer reviewed

This review evaluates the current knowledge of essential biological traits (diet, fecundity, maturity, length-weight relationships, spawning, growth, lifespan, and natural mortality) of marine fishes across European and adjacent waters. These traits are crucial for ecosystem modeling and stock assessments. Using data from FishBase, the largest and most comprehensive database on fishes, a gap analysis was performed to identify areas of research focus and the corresponding gaps that require further study. Biological data coverage is strong in the Baltic and North Seas but moderate in the Adriatic, Aegean, Biscay, Celtic, Levantine, and western Mediterranean Seas. Well-documented species include the European conger (Conger conger), thornback ray (Raja clavata), and transparent goby (Aphia minuta) which are reported from all areas. The narrowest knowledge gaps concern length-weight relationships, followed by spawning and growth, while natural mortality and fecundity are the least studied biological characteristics. Regional variations exist, particularly for protected species. Future research should focus on filling gaps by addressing overlooked species (bycatch and discarded species) and traits such as natural mortality and fecundity, with special attention to vulnerable groups like sharks and rays. Expanding biological data coverage will reduce uncertainties in stock assessments and improve ecosystem models, two widely used tools for sustainable fisheries management and marine conservation., The present work was supported by the Horizon 2020 Framework Programme funded project “EcoScope” [Contract No. 101000302]., Peer reviewed

[Data availability statement]
The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation., The complex relationships among ecological sustainability, economic viability, and employment opportunities within the fishing industry emphasize the importance of adopting a holistic analytical framework for fishery management. The evaluation of a comprehensive fisheries management policy becomes increasingly critical when an ecosystem, such as the eastern Mediterranean Sea, undergoes large changes. In this study, we analyzed the fishery sector in the Mediterranean region of Israel using the Ecopath with Ecosim (EwE) suite of ecological models, which are influenced by climate change and the influx of nonindigenous species (NIS) both, which alter the ecological and economic balance in the region. We identified key components within the fish supply chain that contribute significantly to the national economy and assessed their performance under several scenarios involving changes in the biomass of NIS within the ecosystem. Our findings indicate that while NIS contributes considerably to the local economy, most of the revenue is derived from native species, particularly large pelagics. Furthermore, the fishery sector in Israel exhibits a financial multiplier of four; that is, for every Israeli Shekel (ILS) earned by fishers, three additional ILS are generated through subsequent transactions along the fish supply chain. Within the supply chain, the restaurant sector is the primary employer, accounting for 41% of all employment. Furthermore, a considerable proportion of those engaged in fishing are recreational fishers who, despite not usually selling their catch, contribute indirectly to local economies and community well-being while deriving substantial cultural, psychological, and recreational value. The results of this study reveal the structure of the Israeli fisheries value chain, which is mostly determined by the moderately small scale of local commercial fisheries. However, the economic contribution of the value chain to the local economy is substantial and should not be overlooked when defining fishery management measures. This study emphasizes the need to examine the entire value chain, from fishing practices to the end consumer, to understand the broader implications of management actions on employment and income distribution, and to inform sustainable policymaking., The author(s) declared that financial support was received for this work and/or its publication. This article was written as part of the project “Ecocentric management for sustainable fisheries and healthy marine ecosystems -EcoScope”, which received funding from the European Commission’s Horizon 2020 Research and Innovation programme under Grant agreement no. 101000302.Data., Peer reviewed