The tall sea pen Funiculina quadrangularis (Pallas, 1766), a widespread octocoral species found in Mediterranean soft-bottom habitats, is recognized by the Food and Agriculture Organization of the United Nations as a vulnerable marine ecosystem indicator due to its sensitivity to bottom trawling. Adapted to stable environments, its distribution could be affected by the combined impacts of climate change, particularly warming bottom waters, and trawling activities. Records from the Mediterranean International Trawl Survey program and other sources were used in an ensemble species distribution modelling approach to predict current habitat suitability and project potential habitat shifts under the intermediate IPCC climate scenario SSP2–4.5 for 2050 and 2100. Results indicated a widespread distribution across the Mediterranean continental shelf and slope, with the species typically found between 100 and 750 m depth (occasionally as shallow as 20 m) and tolerating temperatures between 12°C and 16°C. By 2050, over 80% of the current habitat was projected to remain suitable. However, only 50% were expected to serve as climate refugia by 2100, likely due to warming bottom waters and increased salinity. Some habitat gains were projected (e.g., Ligurian Sea, Corsican waters, deep Eastern Mediterranean), but uncertainties persist regarding the species’ ability to colonize these new areas. Despite its presence in trawled areas, suggesting a relatively lower fishing pressure sensitivity than other VME taxa, significant habitat shifts were projected under future climate conditions. Therefore, it is essential to prioritize conservation efforts in areas projected to remain suitable over time. The climate refugia identified through this study offer critical guidance for future climate-smart VME management plans, helping to ensure the long-term survival of F. quadrangularis in the Mediterranean Sea.

Partitioning of the Mediterranean basin has so far mainly focused on surface waters, relying on biogeochemical and hydrological data while the Mediterranean seafloor has received much less attention. Bioregions are essential units for conservation planning, as they provide a framework for designing representative networks of protected areas. Therefore, seafloor-specific bioregions are needed to support the management and conservation of benthic ecosystems. While benthic habitat mapping is generally based on macrofaunal patterns, we propose the first mesoscale partitioning of the Mediterranean seabed based on epibenthic megainvertebrate communities. Benthic records from the MEDITS programme (International Mediterranean Bottom Trawl Survey) were used to partition the Mediterranean soft bottoms. Using k-means clustering combined with Random Forest modelling, we grouped sites according to similarities in biotic composition and predicted their distribution in relation to environmental variables. The analysis was conducted independently across four sub-basins: the Western Mediterranean, the Central Mediterranean, the Adriatic Sea, and the Aegean Sea. This approach identified 16 distinct bioregions, each characterized by unique epibenthic megainvertebrate communities. The partitioning revealed a pronounced bathymetric gradient, with deep-sea bioregions showing a more homogeneous set of indicator taxa and greater similarity across regions compared to the more distinct communities found on the shelf and slope. These coherent bioregions can serve as spatial units to enhance the representativeness of conservation priority networks and provide a valuable complement to the existing EUNIS seabed habitat classification, which does not explicitly account for vulnerable epibenthic megainvertebrate communities.

Sustainable harvesting of marine resources relies on effective assessment and management plans, which in turn depend on accurately identifying stock structure. Interdisciplinary studies are increasingly recommended, with otolith chemistry and shape analyses among the most widely used tools for this purpose, providing complementary insights. In this study, we seek to shed light on the intra-stock structure of a metapopulation system of one of the Mediterranean key fishery resources, the red mullet (Mullus barbatus), by integrating otolith trace element analysis -specifically focusing on elements whose concentrations are directly influenced by ambient water chemistry- with wavelet-based contour analysis across three spatial scales. A high (>70%) classification success was achieved for specimens grouped following the spatial scale of the current assessment framework, and a moderate classification (up to 60%) was achieved when specimens were grouped following the more biologically realistic spatial ecoregions. Unsupervised classification based on trace elements revealed two distinct natal sources, while wavelet-based analysis identified seven morphotypes within the metapopulation system. Our findings are primarily explained by the high dispersal during early life stages, the overall spatial uniformity of environmentally influenced chemical markers, and the presence of distinct, environmental- and diet-driven spatial units. Our results align with the spatially complex structure of Mediterranean demersal stocks and emphasize the need for spatially explicit assessments and multi-marker approaches-combining tagging, simulations, and otolith data-to resolve fine-scale population structure and connectivity to inform on the complex population dynamics. The growing recognition of complex intra-stock structure worldwide makes our study of broad application for modern fisheries management.

Achieving sustainable management of marine resources and implementing biologically realistic assessment depend on accurate identification of stock structure. Most harvested marine species are currently assessed under the common and long-standing assumption of "stock unit" within designated spatiotemporally invariant polygons known as assessment units, despite evidence of passive and/or active dispersal across multiple scales. Our objective here is to investigate the connectivity and spatial structure of red mullet (Mullus barbatus) metapopulation system in the Northwestern Mediterranean Sea and compare the delineation of assessment units with biological units. To achieve this, we integrate simulated larval dispersal modelling with tissue stable isotope analysis, encompassing the entire life cycle. We observe misalignment between the present "closed" assessment units and the identified biologically informed units. The identified metapopulation system comprises northern and southern subpopulations with dissimilar demographic roles. This principally stems from the Northern Current mediated larval transport from high-density persistent spawning grounds and, secondarily, likely from the regional differences in the isotopic baseline associated with different productivity regimes. Such an interdisciplinary approach is of elevated importance for species with stark differences across their life history, such as red mullet. Moreover, larval connectivity diagnostics successfully capture the interannual variability of recruitment dynamics of this complex stock, evidencing the capacity of biophysical models to inform fisheries assessment and management. This study highlights the importance of implementing spatial stock assessment frameworks that rely on critical, yet still largely disregarded, ecological information.

The need for an ecosystem-based approach to fisheries management is widely recognized. Designing ecosystem models for management purposes requires the identification of key interactions and environmental forcing that drive the dynamics of fish stocks. This can be a very challenging task given the complexity of interactions, which determine the evolution of marine ecosystems. To overcome this difficulty, this study proposes a statistical approach based on multivariate time series analysis to identify the main biotic and abiotic interactions using as a case study of a complex and exploited marine ecosystem, the Gulf of Lions (GOL) in the Mediterranean Sea. To do so, first, pairwise Granger causality tests were performed to detect and select the strongest interactions and drivers, then followed by Multivariate Auto-Regressive (MAR) modelling techniques to evaluate the relevance of the selected causal relationships in a multivariate system. The results led to the identification of three statistical interaction networks (SINs) of moderated complexity. The first showed statistical interactions between blackbellied angler (Lophius budegassa), hake (Merluccius merluccius), grey gurnard (Eutrigla gurnardus), and John dory (Zeus faber), as well as the influence of phosphate concentration. The second focused on blackbellied angler, red mullet (Mullus barbatus), anchovy (Engraulis encrasicolus), under the combined influence of demersal trawlers, Sea Surface Temperature (SST) and nitrate concentration. Horned octopus (Eledone cirrhosa), capelan (Trisopterus capelanus), and sardine (Sardina pilchardus) were also investigated under the influence of nitrate concentration. These SINs can serve as a basis to build models of intermediate complexities to describe the dynamics of the main fish stocks of the GOL.

Crinoid beds of Leptometra phalangium (Müller, 1841) have been identified as sensitive habitats by the General Fisheries Commission for the Mediterranean (GFCM) due to their high vulnerability to bottom trawl fisheries. Poorly resilient to physical damage, L. phalangium has been listed as a potential indicator of Vulnerable Marine Ecosystems (VMEs) in the Mediterranean Sea. If fishing activities represent the main cause of habitat destruction for this species, the ongoing changes in climate conditions may rapidly exacerbate the process. In this study, we developed an ensemble Species Distribution Modeling framework to predict the potential habitat of L. phalangium for present-days in the Mediterranean Sea, and used the model to infer potential changes in its spatial distribution by 2050 under two different climate scenarios (IPCC Representative Concentration Pathways RCP2.6 and RCP8.5). True presence-absence records were used and correlated to a parsimonious set of environmental predictors considered as important drivers of benthic species distribution. In present conditions, L. phalangium seems to be widely distributed along the continental slopes of the western and central Mediterranean. This crinoid is often described as confined to the continental shelf-break (100–200 m), but our results show that it can be found over a wider depth range, between 100 and 500 m. Our predictions obtained for the mid-21st century indicate an important habitat loss for L. phalangium under future climate conditions, mainly in the central and southern basins. Declines of 50 to 70 % in its suitable habitat were predicted under RCP2.6 and RCP8.5 compared to present-day predictions. Climate refugia (i.e., areas where environmental conditions remain suitable for the species in the future) were restricted to the northwestern basin (e.g., Gulf of Lion, the Catalan Sea, the Balearic Sea, Ligurian Sea) and in the southern Adriatic Sea. Provided by a robust statistical framework, climate refugia predictions, along with uncertainty assessments, must support the identification of priority areas for the conservation of VME indicator species by governmental bodies and regional management organizations.

The bamboo-coral Isidella elongata is a key habitat-forming species in the deep Mediterranean Sea. This alcyonacean is listed as an indicator of Vulnerable Marine Ecosystems (VMEs) and as Critically Endangered due to bottom trawling impacts. In this work, a modeling approach was used to predict and map the habitat suitability of I. elongata in the Mediterranean Sea under current environmental conditions. Occurrence data were modeled as a function of environmental parameters. Using climate change scenarios and fishing effort data, the risk of climate change and fisheries impacts on habitat suitability were estimated, and climate refugia were identified. A drastic loss of habitat is predicted, and climate change scenarios suggest a loss of 60% of suitable habitats by 2100. In the central Mediterranean, climate refugia overlapped with active fishing grounds. This study represents the first attempt to identify hot spots for the protection of soft bottom Vulnerable Marine Ecosystems for the entire Mediterranean Sea, and highlights areas most at risk from trawling. This work is relevant to the objectives of the EU Marine Strategy Framework and Maritime Spatial Planning Directives, the Biodiversity Strategy for 2030 regarding priority areas for conservation.

Increasing impacts of both fisheries and climate change have resulted in shifts in the structure and functioning of marine communities. One recurrent observation is the rise of cephalopods as fish recede. This is generally attributed to the removal of main predators and competitors by fishing, while mechanistic evidence is still lacking. In addition, climate change may influence cephalopods due to their high environmental sensitivity. We aim to unveil the effects of different anthropogenic and environmental drivers at different scales focusing on the cephalopod community of the Western Mediterranean Sea. We investigate several ecological indicators offering a wide range of information about their ecology, and statistically relating them with environmental, biotic and fisheries drivers. Our results highlight non-linear changes of indicators along with spatial differences in their responses. Overall, the environment drivers have greater effects than biotic and local human impacts with contrasting effects of temperature across the geographic gradient. We conclude that cephalopods may be impacted by climate change in the future while not necessary through positive warming influence, which should make us cautious when referring to them as generalized winners of current changes.

Accounting for marine stocks spatiotemporal complexity has become one of the most pressing improvements that should be added to the new generation of stock assessment. Disentangling persistent and dynamic population subcomponents and understanding their main drivers of variation are still stock-specific challenges. Here, we hypothesized that the spatiotemporal variability of density in two adjacent fish stocks is associated with spatially structured environmental processes across multiple spatiotemporal scales. To test this, we applied a generalized empirical orthogonal function and dynamic factor analysis to fishery-independent and -dependent data of red mullet, a highly commercial species, in the Western Mediterranean Sea. Areas with persistent and dynamic high aggregations were detected for both stock units. A large-scale climatic index and local open-ocean convection were associated with both stocks, while other variables exhibited stock-specific effects. We also revealed spatially structured density dynamics within the examined management units. This suggests a metapopulation structure and supports the future implementation of a spatial stock assessment. Considering the common—generally unrealistic—assumptions of panmictic structure and absence of connectivity with neighbouring stock units, our methodology can be applied to other species and systems with putative spatial complexity to inform more accurate population dynamics and structure.

Environmentally driven changes in small pelagic fish condition and size have been observed in the Gulf of Lions (GOL) since 2008, leading to a significant fishery crisis. However, the effect of changes in environment and/or in the small pelagic community on the demersal community remain unknown. For the first time, this study examines the body condition (bc) and population density of 22 demersal species since 1994, using dynamic factor analysis (DFA). Most (but not all) of demersal species have shown a common shift between 2006 and 2009, which is synchronous with that observed in small pelagic species and the environmental conditions in the GOL. It had been concluded that the environmentally driven changes detected in the pelagic fish community also affected the demersal fish community, but with less drastic and lasting consequences. As the DFA revealed that the bc displayed important variations for several species, notably hake (Merlucius merluccius), the interaction between the bc and population density was investigated using the Multivariate Autoregressive (MAR) model on hake population at three life stages (recruits, juveniles, and adults). Results showed that adult bc, while negatively affected by density, had a positive effect on recruitment. So hake bc could have affected population dynamics by promoting higher recruitment at low densities. Further work is needed to ascertain whether such effects exist in other demersal species.

The Mediterranean Sea is a large marine ecosystem with high heterogeneity in both environmental and ecological characteristics. It presents clear gradients from north to south and west to east. It is also an important area in terms of biodiversity and conservation of vulnerable species, and it suffers from several cumulative human impacts, such as fishing and climate change. Previous studies have characterized spatial and temporal patterns of species distributions and biodiversity indicators. However, a comprehensive analysis combining a wide representation of biodiversity indicators is still missing. In this study, we examined spatial and temporal changes of marine communities along a latitudinal gradient over the continental shelf ecosystems (25–500 m depth) of the Western Mediterranean Sea, from the Gulf of Lion in the north to the Gibraltar Strait in the south. We used information from the MEDITS trawl scientific surveys from 1994 to 2018, and we calculated relevant indicators to investigate spatial and temporal patterns in the region. We selected several indicators measuring alpha (species richness, Shannon diversity index and Pielou evenness index) and beta (decomposing both turnover and nestedness) diversity, as well as previously studied indicators identified to be sensitive to fishing and climate change impacts (biomass-based and trophic-level based metrics). We assessed differences in these indicators for the surveyed community as a whole and for fish, crustaceans and cephalopods, separately, over five regions. Our results show clear latitudinal gradients in some indicators: we observe a reversed pattern between richness (decreasing from south to north) and biomass trends (increasing from south to north) for the demersal community. We also found a generalized increase in β-diversity in most regions with time, and a decline in the trophic level of the surveyed community. In addition, we identify a remarkable increase in several indicators when only considering the cephalopods group, and a general low environmental status for the North Catalan Sea. We discuss our results considering the differences between regions and taxa related to the fishing activity and environmental dynamics that can act at different scales. This in-depth analysis illustrates how to use a selection of indicators that combine the capacity to detect ecological changes from regional to sub-regional scales.

Uncommon fish records may reflect local or global changes of fish composition resulting from environmental changes or anthropog,enic activities. Significant records of uncommon marine fishes, including migrant, non-native, cryptic, rare and threatened species, collected in French waters or by French vessels in European waters, observed by scuba divers or beachgoers, are reported for the year 2019. They include first, new, rare and unusual records for the following 33 species: Tetronarce nobiliana, Gymnothorax unicolor, Maulisia mauli, Salmo trutta, Grammonus aler, Photostomias guernei, Ifintaia loppei, Echiodon drummondii, Holocentrus adscensionis, Nerophis lumbriciformis, Scorpaena scrofa, Lepidoirigla dieuzeidei, Eutelichthys leptochirus, Liparis montag tti, Mycteroperca rubra, Serranus cabrilla, Remora remora, Caram: crysos, Naucrates doctor, Trachurus picturatus, Seriola rivoliana, Argyrosomus regius, Parablennius pilicornis, Pseudoscopelus astronesthidens, Deltentosteus collonianus, Didogobius schlieweni, Didogobius splechinai, Gobius couchi, Gobius f.;asteveni, Lebetus guilleti, Synapturichthys kleinii, Lagocephalus lagocephalus and 21.1ola mola, among which I. loppei, H. adscensionis and P. astronesthidens represent first records for the French waters and additions to the Checklist of the marine fishes from metropolitan France. Photostomias guernei is a first record for the Bay of Biscay, found close the French ETV,.

The otolith, found in both inner ears of bony fish, has mainly been used to estimate fish age. Another application that has been developing significantly in recent years, however, is the use of otolith shape as a tool for stock identification. Often, studies have directly used the shape asymmetry between the right and left otoliths. We tested the magnitude of directional asymmetry between the sagittal otoliths (left vs. right) of 2991 individuals according to their catch locations, and we selected species to evaluate whether directional asymmetry may itself be a tool to evaluate stock boundaries. Elliptical Fourier descriptors were used to describe the otolith shape. We used a flatfish, the common sole (Solea solea, n = 2431), from the eastern English Channel and the southern North Sea as well as a roundfish, the bogue (Boops boops, n = 560), from the Mediterranean Sea. Both species showed significant levels of directional asymmetry between the testing locations. The bogue otoliths showed significant asymmetry for only 5 out of 11 locations, with substantial separation between two large areas: the Algerian coast and the western part of the Italian coast. The sole otoliths showed significant asymmetry in the shape analysis (3.84%–6.57%), suggesting a substantial separation between two large areas: the English and French parts of the English Channel and the southern North Sea. Consequently, directional bilateral asymmetry in otolith shape is a potential new method for stock identification.

Independence of science and best available science are fundamental pillars of the UN-FAO code of conduct for responsible fisheries and are also applied to the European Union (EU) Common Fishery Policy (CFP), with the overarching objective being the sustainable exploitation of the fisheries resources. CFP is developed by DG MARE, the department of the European Commission responsible for EU policy on maritime affairs and fisheries, which has the Scientific, Technical and Economic Committee for Fisheries (STECF) as consultant body. In the Mediterranean and Black Sea, the General Fisheries Commission for the Mediterranean (FAO-GFCM), with its own Scientific Advisory Committee on Fisheries (GFCM-SAC), plays a critical role in fisheries governance, having the authority to adopt binding recommendations for fisheries conservation and management. During the last years, advice on the status of the main stocks in the Mediterranean and Black Sea has been provided both by GFCM-SAC and EU-STECF, often without a clear coordination and a lack of shared rules and practices. This has led in the past to: i) duplications of the advice on the status of the stocks thus adding confusion in the management process and, ii) a continuous managers’ interference in the scientific process by DG MARE officials hindering its transparency and independence. Thus, it is imperative that this stalemate is rapidly resolved and that the free role of science in Mediterranean fisheries assessment and management is urgently restored to assure the sustainable exploitation of Mediterranean marine resources in the future.

Many deep-water fish populations, being K-selected species, have little resilience to overexploitation and may be at serious risk of depletion as a consequence. Sea warming represents an additional threat. In this study, the condition, or health, of several populations of common ling (Molva molva), blue ling (Molva dypterygia) and Mediterranean or Spanish ling (Molva macrophthalma) inhabiting different areas in the North Atlantic and the Mediterranean was evaluated, to shed light on the challenges these deep-water species are facing in the context of fishing activity and a warming climate. The data on the condition of Molva populations which are analysed here have been complemented with data on abundance and, for the southernmost species (Mediterranean ling), with two other health indicators (parasitism and hepato-somatic index). Despite some exceptions (e.g., common ling in Icelandic waters), this study shows that the condition of many populations of Molva species in the northeastern Atlantic and the Mediterranean Sea has worsened, a trend which, in recent decades, has usually been found to be accompanied by a decline in their abundance. In addition, the poor health status of most populations of common ling, blue ling and Mediterranean ling considered in this analysis points to a lower sustainability of these populations in the future. Overall, the health status and abundance of Molva populations in the northeastern Atlantic and the Mediterranean suggest that only some populations located in the North Atlantic may be able to rebuild, whereas the populations in southern North Atlantic and the Mediterranean, which are probably most at risk from sea warming, are facing serious difficulties in doing so. In the context of fisheries and global warming, this study's results strongly indicate that management bodies need to consider the health status of many of the populations of Molva species, particularly in southern European waters, before implementing their decisions.

The Marine Strategy Framework Directive (MSFD), introduced in June 2008, was adopted to achieve a Good Environmental Status (GES) in the Ell's marine waters and to protect resources of socio-economic interest. The MSFD exerts to the marine area over which a Member State exercises jurisdictional rights in accordance with the United Nations Convention on the Law of the Sea (UNCLOS), including the deep-sea waters, seafloor and subseafloor of the Exclusive Economic Zones (EEZ). However, currently the MSFD focuses on coastal habitats and the shallow-water seafloor to the detriment of the deeper habitats. Despite the huge dimension of the deep sea (below 200 m of depth) covering more than 65% of the Earth's surface and including >95% of the global biosphere, the relevance of the dark portion of the seas and oceans is still almost completely neglected. Given the important bi-directional links between shallow and deep ecosystems, there is a clear need for extending the implementation of the MSFD into the deep sea, to define a sound ecosystem-based approach for the management and protection of deep-sea ecosystems and attain GES. We assembled data on drivers, anthropogenic pressures and impacts concerning the MSFD descriptors pertaining to the Mediterranean deep sea. We list deep-sea monitoring activities and the main sources providing benchmark conditions, and discuss knowledge and geographic coverage gaps. MSFD descriptors apply to the deep sea as to coastal waters, and ought to be monitored contemporaneously. We provide recommendations for guidelines for future deep-sea monitoring in the Mediterranean Sea.

Investigating the drivers of fish assemblage trophic structure is a critical question, in order to better understand ecosystem functioning, predict the effects of perturbations and implement integrated management of exploited marine ecosystems. Ecosystemic surveys enabled the determination of the trophic structure of the fish assemblages in three French marine ecosystems, namely the Eastern English Channel, the Bay of Biscay and the Gulf of Lions, through the simultaneous collection of qualitative (stable isotopes and energy content) and quantitative (biomass) data. In the Bay of Biscay and in the Gulf of Lions, pelagic primary production supported at least 80% of the fish biomass production, and explained the dominance of pelagic species, but with differences resulting from the different productivity. The lower productivity in the oligotrophic Gulf of Lions led to a lower total biomass, energy density as well as the predominance of zooplankton-feeders. In contrast, fluxes in the Bay of Biscay were sufficient to support a higher biomass of pelagic piscivores, and of species with higher energy content. In the shallow Eastern English Channel, the respective contributions of pelagic and benthic sources were similar. Bentho-demersal species of higher trophic level dominated this assemblage, because of their ability to exploit both pathways. Results of the present study confirmed that fisheries-focused surveys can be used as efficient platforms to address questions about ecosystem functioning. Here, it confirmed the expected differences between ecosystems and the importance of primary production and environment as drivers of fish assemblage structure and functioning. Future studies should nevertheless develop new methods to better assess the paramount role of low trophic level consumers.

This work combines state-of-the-art methods (DNA metabarcoding) with classic approaches (visual stomach content characterization and stable isotope analyses of nitrogen (δ15N) and carbon (δ13C)) to investigate the trophic ecology of anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) at high taxonomic and spatial resolution in the Western Mediterranean Sea. Gut contents observed are in accordance with the dietary plasticity generally described for anchovy and sardine, suggesting a diet related to the opportunistic ingestion of available prey in a certain area and/or time. Genetic tools also showed modest inter-specific differences regarding ingested species. However, inter-specific and intra-specific differences in ingested prey frequencies and prey biomass reflected a latitudinal signal that could indicate a more effective predation on large prey like krill by anchovy versus sardine, as well as a generalized higher large prey ingestion by both species southwards. In fact, both species presented lower δ15N in the northernmost area. This latitudinal gradient indicates changes in the trophic ecology of anchovy and sardine that coincide with previously described better biological conditions for fish in the southern part of the study area as well as higher landings of both species in recent years.