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The aim of this paper is to provide evidence of the species-specific export of adult fishes for some species or group of species from six well-enforced Mediterranean marine protected areas (MPAs): Cerbère-Banyuls and Carry-le-Rouet in France and Medes, Cabrera, Tabarca, and Cabo de Palos in Spain. We estimated the distance at which spillover of those individual or groups of species occur by directly assessing the existence of gradients of biomass across the MPA boundaries by means of underwater visual census, asuming that such gradients will be specifics in terms of structure (sharpness, slope, and intercept) for every species and group of species. A significant “reserve effect” was observed for biomass of some of the individual and grouped species in all MPAs. Decreasing gradients of biomass differ among taxons and are not related with the insular nature of the location. Different gradients of biomass resulted from the interaction between species characteristics and some ecological and structural drivers, and we did not find regular patterns for each taxa among MPAs, even though the same species can exhibit different gradient structure and/or spillover distances in the same MPA depending on the orientation. Habitat patch distribution and continuity seems the most important environmental factor explaining the existence and pattern of gradients at species level, interacting with fish home range and fishing pressure close to the limits of the MPAs. Managers should take in account the surrounding distribution of habitats in terms of complexity and quality in order to optimize the spillover capacity of the MPAs.

Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across spatial scales. As such, they are likely to insure against future uncertainty arising from climate change and the ever-increasing anthropogenic pressures on ecosystems. Our results call for a more detailed understanding of the role of rarity and functional vulnerability in ecosystem functioning.

Understanding species’ roles in food webs requires an accurate assessment of their trophic niche. However, it is challenging to delineate potential trophic interactions across an ecosystem, and a paucity of empirical information often leads to inconsistent definitions of trophic guilds based on expert opinion, especially when applied to hyperdiverse ecosystems. Using coral reef fishes as a model group, we show that experts disagree on the assignment of broad trophic guilds for more than 20% of species, which hampers comparability across studies. Here, we propose a quantitative, unbiased, and reproducible approach to define trophic guilds and apply recent advances in machine learning to predict probabilities of pairwise trophic interactions with high accuracy. We synthesize data from community-wide gut content analyses of tropical coral reef fishes worldwide, resulting in diet information from 13,961 individuals belonging to 615 reef fish. We then use network analysis to identify 8 trophic guilds and Bayesian phylogenetic modeling to show that trophic guilds can be predicted based on phylogeny and maximum body size. Finally, we use machine learning to test whether pairwise trophic interactions can be predicted with accuracy. Our models achieved a misclassification error of less than 5%, indicating that our approach results in a quantitative and reproducible trophic categorization scheme, as well as high-resolution probabilities of trophic interactions. By applying our framework to the most diverse vertebrate consumer group, we show that it can be applied to other organismal groups to advance reproducibility in trait-based ecology. Our work thus provides a viable approach to account for the complexity of predator–prey interactions in highly diverse ecosystems.

The link between climate-driven river runoff and sole fishery yields observed in the Gulf of Lions (NW Mediterranean) was analysed using carbon- and nitrogen stable isotopes along the flatfish food webs. Off the Rhone River, the main terrestrial (river POM) and marine (seawater POM) sources of carbon differed in$\\delta^{13} {\\rm{C}}$(-26.11‰ and -22.36‰, respectively). Surface sediment and suspended POM in plume water exhibited low$\\delta^{13} {\\rm{C}}$(-24.38‰ and -24.70‰, respectively) that differed more from the seawater POM than from river POM, demonstrating the dominance of terrestrial material in those carbon pools. Benthic invertebrates showed a wide range in$\\delta^{15} {\\rm{N}}$(mean 4.30‰ to 9.77‰) and$\\delta^{13} {\\rm{C}}$(mean -23.81‰ to -18.47‰), suggesting different trophic levels, diets and organic sources. Among the macroinvertebrates, the surface (mean$\\delta^{13} {\\rm{C}}$-23.71‰) and subsurface (mean$\\delta^{13} {\\rm{C}}$-23.81‰) deposit-feeding polychaetes were particularly$^{13}{\\rm{C}}$depleted, indicating that their carbon was mainly derived from terrestrial material. In flatfish,$\\delta^{15} {\\rm{N}}$(mean 9.42 to 10.93‰) and$\\delta^{13} {\\rm{C}}$(mean -19.95‰ to -17.69‰) varied among species, indicating differences in food source and terrestrial POM use. A significant negative correlation was observed between the percentage by weight of polychaetes in the diet and the$\\delta^{13} {\\rm{C}}$of flatfish white muscle. Solea solea (the main polychaete feeder) had the lowest mean$\\delta^{13} {\\rm{C}}$, Arnoglossus laterna and Buglossidium luteum (crustacean, mollusc and polychaete feeders) had intermediate values, and Solea impar (mollusc feeder) and Citharus linguatula (crustacean and fish feeder) exhibited the highest$\\delta^{13} {\\rm{C}}$. Two different benthic food webs were thus identified off the Rhone River, one based on marine planktonic carbon and the other on the terrestrial POM carried by the river. Deposit-feeding polychaetes were responsible for the main transfer of terrestrial POM to upper trophic levels, linking sole population dynamics to river runoff fluctuations.

Chlordecone is a persistent organochlorine pesticide used in the banana fields of the French West Indies from 1972 to 1993. Three marine habitats (mangroves, seagrass beds and coral reefs) of two study sites located downstream contaminated rivers were chosen to evaluate the level of contamination of marine food webs. On each habitat, the food chain collected included suspended organic matter, primary producers (macroalgae, algal turf, seagrass), zooplankton, symbiotic organisms (corals, sea anemones), primary consumers (herbivores, suspension feeders, biofilm feeders), omnivores and detritivores (lobsters, fish), secondary consumers (carnivores 1: invertebrate feeders, planktivores) and tertiary consumers (carnivores 2: invertebrate and fish feeders, piscivores). Log-linear regressions of the concentrations of chlordecone versus nitrogen isotopic ratios (δ15N) were used to assess the bioaccumulation of chlordecone along trophic food webs. At each site, bioconcentration and bioamplification take part on the transfer of chlordecone in marine organisms. In mangroves (i.e. close to the source of pollution), lower trophic magnification factors (TMF) indicated that bioconcentration prevailed over bioamplification phenomenon. The opposite phenomenon appeared on coral reefs in which bioconcentration processes were less important and bioamplification pathway became dominant. Far from the source of pollution, molecules of chlordecone seemed to be transfered to organisms mostly via trophic interactions rather than water contact.

Coastal zones are ecosystems of high economic value but exposed to numerous disturbances, while they represent nurseries for many fish species, raising the issue of the preservation of their functions and services. In this context, the juvenile fish assemblages of all types of habitats present in shallow coastal zones were studied on the south-east coast of France using underwater visual censuses in warm (June–July 2014) and cold (April 2015) periods. A total of fourteen habitat types were characterized, which could be grouped into three broad categories, rocky substrates (natural and artificial), sedimentary bottoms with all levels of granulometry, and seagrass beds including Cymodocea nodosa and Posidonia oceanica meadows; the ecotones or interfaces between the three broad habitat categories were individualized as particular habitat types. The abiotic and biotic descriptors of the 14 habitat types individualized did not vary with time, except for a higher cover percentage and canopy height of macrophytes in the warm period, which increased the three-dimensional structure of some habitats. The taxonomic composition and density of juvenile fish assemblages were analyzed using both multivariate and univariate descriptors, after grouping the 57 fish species recorded into 41 well-individualized taxa. Juvenile fishes were recorded in all habitat types, with higher mean species richness and abundance during the warm than the cold period. The richest habitats in terms of both fish species richness and abundance were the natural rocky substrates and the interfaces between Posidonia beds and the other habitats. Although juvenile fish assemblage composition differed among habitat types and between periods, the most abundant fish species were Atherina sp., Sarpa salpa , Gobiidae, Symphodus spp., Pagellus spp. and several Diplodus species, which colonized 7 up to 14 different habitat types (depending on taxa) during their juvenile life. Most species settled in one or a few specific habitats but rapidly colonized adjacent habitats when growing. This study provided evidence of the role of all types of shallow coastal habitats as fish nurseries and their varying pattern of occupation in space and time by the different juvenile stages. It highlighted the importance of the mosaic of habitats and interfaces for the complete development of all juvenile life stages of fishes, and for the preservation of a high diversity of coastal fish assemblages and fisheries resources in the Mediterranean Sea.

Biotic indices, which reflect the quality of the environment, are widely used in the marine realm. Sometimes, key species or ecosystem engineers are selected for this purpose. This is the case of the Mediterranean seagrass Posidonia oceanica, widely used as a biological quality element in the context of the European Union Water Framework Directive (WFD). The good quality of a water body and the apparent health of a species, whether or not an ecosystem engineer such as P. oceanica, is not always indicative of the good structure and functioning of the whole ecosystem. A key point of the recent Marine Strategy Framework Directive (MSFD) is the ecosystem-based approach. Here, on the basis of a simplified conceptual model of the P. oceanica ecosystem, we have proposed an ecosystem-based index of the quality of its functioning, compliant with the MSFD requirements. This index (EBQI) is based upon a set of representative functional compartments, the weighting of these compartments and the assessment of the quality of each compartment by comparison of a supposed baseline. The index well discriminated 17 sites in the northwestern Mediterranean (French Riviera, Provence, Corsica, Catalonia and Balearic Islands) covering a wide range of human pressure levels. The strong points of the EBQI are that it is easy to implement, non-destructive, relatively robust, according to the selection of the compartments and to their weighting, and associated with confidence indices that indicate possible weakness and biases and therefore the need for further field data acquisition.

The Rhone river is the most important input to the Mediterranean Sea, responsible for 50% of the primary productivity of the Gulf of Lions. A highly variable amount of$1-23\\times 10^{6}$t year-1of terrestrial material is exported to the sea by the Rhone and stocked on the continental shelf for the most part. Soft-bottom communities off the Rhone delta were dominated by polychaetes both in species richness and abundance, and exhibited strong temporal fluctuations mainly related to flooding events. Floods caused pulses of organic matter followed, with different time lags, by peaks of polychaetes. Opportunistic, short-lived species, such as Mediomastus sp. and Aricidea claudiae, exhibited high short-term peaks in density and biomass a few months after flooding events. Conversely, long-lived species, such as Laonice cirrata and Sternaspis scutata, peaked in density and biomass with a time lag of 1-3 years, and their population increase lasted for a few years. The common sole, Solea solea, is a voracious predator of polychaetes which represent >80% of its prey. A positive correlation was found between the mean annual discharge of the Rhone river and the annual commercial landings of S. solea with a time lag of 5 years in the two fishing harbours (Sete and Martigues) located close to the Rhone delta. The long-term increase in food (i.e. polychaete density and biomass) after flooding events might favour the different stages of the sole life cycle, enhancing its population size for several years. Fluctuations of sole fishery yields in the Gulf of Lions could be influenced by climate, as the Rhone river flow is related to the North Atlantic Oscillation that drives precipitation over Western Europe.

Groupers species are extremely vulnerable to overfishing and many species are threatened worldwide. In recent decades, Mediterranean groupers experienced dramatic population declines. Marine protected areas (MPAs) can protect populations inside their boundaries and provide individuals to adjacent fishing areas through the process of spillover and larval export. This study aims to evaluate the effectiveness of six marine reserves in the Western Mediterranean Sea to protect the populations of three species of grouper, Epinephelus marginatus, Epinephelus costae and Mycteroperca rubra, and to understand in which circumstances MPAs are able to export biomass to neighbouring areas. All the studied MPAs, except one where no grouper was observed, were able to maintain high abundance, biomass and mean weight of groupers. Size classes were more evenly distributed inside than outside MPAs. In two reserves, biomass gradients could be detected through the boundaries of the reserve as an indication of spillover. In some cases, habitat structure appeared to exert a great influence on grouper abundance, biomass and mean individual weight, influencing the gradient shape. Because groupers are generally sedentary animals with a small home range, we suggest that biomass gradients could only occur where groupers attain sufficient abundance inside MPA limits, indicating a strongly density-dependent process.

The European hake, Merluccius merluccius, is an important resource for Mediterranean fisheries. This study focuses on juvenile and adult hake feeding ecology in the Gulf of Lions, using information from scientific surveys carried out during two seasons and three years (2004-2006). Stomach content and stable isotope (δ15N, δ13C) analyses were performed, and the main factors explaining variations in δ15N were investigated using GLMs. In the Gulf of Lions, hake mostly fed on crustaceans and fish and a dominant piscivorous regime was reached at 15 cm total length. Pelagic fish (sardine, anchovy and small blue whiting) were the main source of prey (40%-80%) and cannibalism was low (< 5%). The results confirmed that hake is an opportunistic feeder and also showed that the size and diversity of prey vary among hake size classes, probably as a result of the different spatial distribution and/or foraging migrations. The present study finally postulates that the unbalanced sex ratio (80% female against 20% male) observed at the adult stage could be related to the combination of growth pattern differences, diet and exploitation rate on the continental shelf, where the males spend a longer period of time.