Résumé: In aquaculture, fish are exposed to unavoidable stressors that can be detrimental for their health and welfare. However, welfare in farmed fish can be difficult to assess, and, so far, no standardized test has been universally accepted as a welfare indicator. This work contributes to the establishment of behavioural welfare indicators in a marine teleost in response to different water quality acute stressors. Groups of ten fish were exposed to high Total Ammonia Nitrogen concentration (High TAN, 18 mg.L-1), Hyperoxia (200 % O-2 saturation), Hypoxia (20 % O-2 saturation), or control water quality (100% O-2 saturation and TAN < 2.5 mg.L-1) over 1 hour. Fish were then transferred in a novel environment for a group behaviour test under the same water quality conditions over 2 hours. Videos were recorded to assess thigmotaxis, activity and group cohesion. After this challenge, plasma cortisol concentration was measured in a subsample, while individual behavioural response was measured in the other fish using novel tank diving test. Prior to this study, the novel tank diving test was validated as a behavioural challenge indicative of anxiety state, by using nicotine as anxiolytic drug. Overall, all stress conditions induced a decrease in activity and thigmotaxis and changes in group cohesion while only fish exposed to Hypoxia and High TAN conditions displayed elevated plasma cortisol concentrations. In post-stress condition, activity was still affected but normal behaviour was recovered within the 25 minutes of the test duration. Our work suggests that the activity, thigmotaxis and group cohesion are good behavioural indicators of exposure to degraded water quality, and could be used as standardized measures to assess fish welfare.

Résumé: Beginning in the 1990's, Chile implemented an extensive Territorial User Rights for Fisheries (TURFs) network that now comprises nearly 1,000 TURFs. This network provides a rare opportunity to examine spatial and temporal trends in TURF use and impacts on surrounding open access areas (OAAs). In this analysis, landings of keyhole limpet (Fissurella spp.), kelp (Lessonia spp.) and red sea urchin (Loxechinus albus) were used to estimate catch-per-unit effort (CPUEs) and catch-per-unit area (CPUAs) indices inside and outside TURFs by fishing cove. For these species, CPUEs and CPUAs in 2015 were significantly higher inside TURFs. However, temporal trends analyzed with a linear mixed effects model indicate that CPUAs inside TURFs have been significantly decreasing since 2000 for keyhole limpet, red sea urchin and for loco (Concholepas concholepas), while in OAAs this measure only decreased for limpet. An elastic net regression was used to better explain catches in OAAs during 2015, including a variety of variables related to the characteristics and activity of proximal TURFs. Results indicate that exogenous factors unrelated to TURF management were the primary drivers of catches in OAAs during 2015 but that factors related to proximal TURFs appear to have a slight negative impact that grows over time. Collectively, these results indicate that while TURFs are associated with higher catch rates than surrounding OAAs, catch rates appear to be decreasing over time and, though limited, the impact of TURFs on surrounding OAAs may be negative. These findings suggest a need for a more nuanced and dynamic approach to spatial management on benthic resources in Chile.

Résumé: Coral reef fisheries depend on reef fish biomass to support ecosystem functioning and sustainable fisheries. Here, we evaluated coral reefs across 4,000 km of the Indonesian archipelago to reveal a large gradient of biomass, from 17,000 kg/ha. Trophic pyramids characterized by planktivore dominance emerged at high biomass, suggesting the importance of pelagic pathways for reef productivity. Total biomass and the biomass of most trophic groups were higher within gear restricted and no-take management, but the greatest biomass was found on unmanaged remote reefs. Within marine protected areas (MPAs), 41.6% and 43.6% of gear restricted and no-take zones, respectively, met a global biomass target of 500 kg/ha, compared with 71.8% of remote sites. To improve conservation outcomes for Indonesia's biodiverse and economically important coral reef fisheries, our results suggest to: (1) strengthen management within Indonesia's existing MPAs and (2) precautionarily manage remote reefs with high biomass.

Résumé: 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.

Résumé: Thau lagoon is a large Mediterranean coastal lagoons and it supports traditional shellfish farming activities. It has been subject to eutrophication leading to major anoxic events associated with massive mortalities of shellfish stocks. Since the 1970s, improvements have been made to wastewater treatment systems, which have gradually led to oligotrophication of the lagoon. The aim of our study was to determine how the decrease in nutrient inputs resulted in major ecological changes in Thau lagoon, by analysing five decades of time-series (1970–2018) of observations on pelagic and benthic autotrophic communities. We were able to identify two periods during the oligotrophication process. Period 1 (1970–1992) was considered a eutrophic period, characterised by the shift from seagrass dominance to dominance of red macroalgae. Period 2 (1993–2018), characterised by improved eutrophication status, was further divided into three: a transition phase (1993–2003) during which the water column continued to recover but the benthic community lagged behind in recovery and in partial resilience; a regime shift (2003–2006), after which the water column became oligotrophic and seagrass began to recover (2007–2018). Considering anoxia crises as indicators of ecosystem resilience and resistance, we used a generalised linear model to analyse meteorological and environmental data with the aim of identifying the triggers of summer anoxia over the study period. Among the meteorological variables studied, air temperature had the strongest positive effect, followed by the period and wind intensity (both negative effects) and by rainfall in July (positive effect). The risk of triggering anoxia was lower in period 2, evidence for the increasing resistance of the ecosystem to climatic stress throughout the oligotrophication process. At the ecosystem scale and in the long term perspective, the ecological gains related to oligotrophication are especially important in the context of climate change, with more frequent and severe heat waves predicted.

Résumé: Tetraodontiformes fishes play a critical role in benthic and demersal communities and are facing threats due to anthropogenic impacts and climate change. However, they are poorly studied worldwide. To improve knowledge on the socio-ecological significance and conservation of Tetraodontiformes a review of literature addressing the diversity, ecology, use and trade, conservation, and main threats of Tetraodontiformes combined with a comprehensive in situ dataset from two broad-range multidisciplinary oceanographic surveys performed along the Tropical Brazilian Continental Shelf was undertaken. Twenty-nine species were identified, being primarily found on coral reefs and algal ecosystems. At these habitats, tetraodontids present highly diversified trophic categories and might play an important role by balancing the marine food web Coral reef ecosystems, especially those near to the shelf break, seem to be the most important areas of Tetraodontiformes fishes, concentrating the highest values of species richness, relative abundance and the uncommon and Near Threatened species. Ninety per cent of species are commonly caught as bycatch, being also used in the ornamental trade (69%) and as food (52%), serving as an important source of income for artisanal local fisheries. Tetraodontiformes are threatened by unregulated fisheries, overexploitation, bycatch, and habitat loss due to coral reef degradation and the potential effects of climate change. These factors are more broadly impacting global biodiversity, food security, and other related ecosystem functions upon which humans and many other organisms rely. We recommend the following steps that could improve the conservation of Tetraodontiformes along the tropical Brazilian Continental shelf and elsewhere: (i) data collection of the commercial, incidental, ornamental and recreational catches; (ii) improvement of the current legislation directed at the marine ornamental harvesting; (iii) increase efforts focused on the education and conservation awareness in coastal tourism and communities; and, most important, (iv) creation of marine reserves networks in priority areas of conservation, protecting either the species and key habitats for its survival.

Résumé: Understanding the life cycle strategies and predatory impact of alien jellyfish species is critical to mitigate the impact that these organisms may have on local populations, biodiversity, and ultimately on the functioning of food webs. In the Mediterranean Sea, little is known about the dynamics of alien jellyfish, despite this biodiversity hotspot being one of the most threatened areas by increasing numbers of alien jellyfish. Here, we investigated the population dynamics and predatory impact of a non-indigenous scyphomedusa, Aurelia solida Browne 1905, in the Bizerte Lagoon, Tunisia. The study was based on bimonthly surveys performed over two consecutive years, from November 2012 to August 2014. Field observations showed that the planktonic phase of A. solida occurs from winter to early summer. Prey composition was investigated by means of gut content and field zooplankton analyses. Calanoid copepods, mollusc larvae, and larvaceans represented the main food items of A. solida. To determine the jellyfish feeding rate and their predatory impact on zooplankton populations, the digestion time for zooplankton prey was assessed at three different temperatures: 13, 18, and 23 degrees C in laboratory conditions, corresponding to the average range of temperatures encountered by A. solida in the Bizerte Lagoon. We found that A. solida consumed 0.5-22.5% and 0.02-37.3% of the daily zooplankton standing stock in 2013 and 2014, respectively. These results indicate a non-negligible but restricted seasonal grazing impact on some mesozooplankton groups, explained by the relatively short lifespan of the medusa stage (5-6 months).

Résumé: Wilderness areas offer unparalleled ecosystem conditions. However, growing human populations and consumption are among factors that drive encroachment on these areas. Here, we explore the threat of small-scale fisheries to wilderness reefs by developing a framework and modeling fluctuations in fishery range with fuel costs and fish prices. We modeled biomass of four fishery groups across the New Caledonian archipelago, and used fish and fuel prices from 2005 to 2020 to estimate the extent of exploited reefs across three fishing scenarios. From 2012 to 2018, maximum profitable range increased from 15 to over 30 hr from the capital city, expanding to reefs previously uneconomic to fish, including a UNESCO heritage site. By 2020, over half of New Caledonian (similar to 17% global) wilderness reefs will become profitable to fish. Our results demonstrate that remoteness from humans should not be considered protection for wilderness coral reefs in the context of rising fish prices.

Résumé: Coastal benthic ecosystems may be impacted by numerous human activities, including aquaculture, which continues to expand rapidly. Indeed, today aquaculture worldwide provides more biomass for human consumption than do wild fisheries. This rapid development raises questions about the interactions the practice has with the surrounding environment. In order to design strategies of sustainable ecosystem exploitation and marine spatial planning, a better understanding of coastal ecosystem functioning is needed so that tools to quantify impacts of human activities, including aquaculture, may be developed. To achieve this goal, some possible directions proposed are integrated studies leading to new concepts, model development based on these concepts and comparisons of various ecosystems on a global scale. This review draws on existing literature to (i) briefly summarize the major ecological interactions between off-bottom shellfish aquaculture and the environment, (ii) introduce research on the influence of benthic diversity on ecosystem functioning (BEF relationships) and (iii) propose a holistic approach to conduct aquaculture–environment studies using a BEF approach, highlighting the need for integrated studies that could offer insights and perspectives to guide future research efforts and improve the environmental management of aquaculture.

Résumé: Terrestrial plants seeds, spores and pollen are often dispersed by wind. Likewise, most eggs and larvae of marine organisms are dispersed by oceanic currents. It was historically believed that the spatial scale at which dispersal occurs was orders of magnitude smaller for plants than for fish. However, recent empirical estimates of seed and larval dispersal suggest that these dispersal scales are more alike than previously thought. The modeling approaches used to simulate aerial and aquatic dispersal are also converging. Similar biophysical models are developed, in which outputs of Eulerian models simulating the main physical forcing mechanism (wind or currents) are used as inputs to Lagrangian models that include biological components (such as seed terminal velocity or larval vertical migration). These biophysical models are then used to simulate trajectories of the biological entities (seeds, larvae) in three dimensions. We reflect on these converging trends by first putting them into an historical perspective, and then by comparing the physical and biological processes represented in marine larva vs. terrestrial seed dispersal models, the data used for the models output corroboration, and the tools available to perform simulations. We conclude that this convergence offers the opportunity to bridge the gap between two scientific communities which are currently largely disconnected. More broadly, we also see our comparison across systems as a useful way to strengthen the links between aquatic and terrestrial ecology by sharing knowledge, methods, tools, and concepts.

Résumé: Hypoxia and mercury contamination often co-occur in tropical freshwater ecosystems, but the interactive effects of these two stressors on fish populations are poorly known. The effects of mercury (Hg) on recorded changes in the detailed form of the electrocardiogram (ECG) during exposure to progressive hypoxia were investigated in two Neotropical freshwater fish species, matrinxa, Brycon amazonicus and traira, Hoplias malabaricus. Matrinxa were exposed to a sublethal concentration of 0.1 mg L-1 of HgCl2 in water for 96 h. Traira were exposed to dietary doses of Hg by being fed over a period of 30 days with juvenile matrinxas previously exposed to HgCl2, resulting in a dose of 0.45 mg of total Hg per fish, each 96 h. Both species showed a bradycardia in progressive hypoxia. Hg exposure impaired cardiac electrical excitability, leading to first-degree atrioventricular block, plus profound extension of the ventricular action potential (AP) plateau. Moreover, there was the development of cardiac arrhythmias and anomalies such as occasional absence of QRS complexes, extra systoles, negative Q-, R- and S-waves (QRS complex), and T wave inversion, especially in hypoxia below O-2 partial pressures (PO2) of 5.3 kPa. Sub-chronic dietary Hg exposure induced intense bradycardia in normoxia in traira, plus lengthening of ventricular AP duration coupled with prolonged QRS intervals. This indicates slower ventricular AP conduction during ventricular depolarization. Overall, the data indicate that both acute waterborne and sub-chronic dietary exposure (trophic level transfer), at sublethal concentrations of mercury, cause damage in electrical stability and rhythm of the heartbeat, leading to myocardial dysfunction, which is further intensified during hypoxia. These changes could lead to impaired cardiac output, with consequences for swimming ability, foraging capacity, and hence growth and/or reproductive performance.

Résumé: The decrease of microbial and nutrient inputs from the watershed has long dominated lagoon ecosystem management objectives. Phytoplankton biomass and abundance have drastically decreased for more than a decade and Zostera meadow have gradually recovered, expressing lagoon ecosystem restoration such as Thau lagoon. Do the progressive achievement of the good ecological status of the Thau lagoon possibly threatens the shellfish industry in terms of production and oyster quality, by reducing the carrying capacity? To provide answers about the right balance to be achieved between conservation and exploitation, a new numerical tool was developed to help in decision-making. We hereby propose to incorporate a Dynamic Energy Budget type shellfish production model to an existing lagoon ecosystem box-model. The influence of different scenarios of nutrient inputs (related to projections of population growth or improvement of treatment plants) and shellfish stocks were tested on oyster performances (production, oyster condition index), carrying capacity of the lagoon and ecological status indices used within the EU Water Framework Directive. Model outputs demonstrated that shellfish production was mainly controlled by nutrient inputs, which depend on hydro-meteorological variability, and specifically by phosphorus and N:P ratios of nutrient inputs. Scenarios tested, however, demonstrated smaller differences of oyster production in comparison to inter-annual variability. The overall ecological status of the lagoon remained in a “good” status with acceptable lagoon-scale phytoplankton depletion, regardless of scenarios, setting the carrying capacity of this ecosystem to be sustainable.

Résumé: The distribution of marine organisms is strongly influenced by climatic gradients worldwide. The ecological niche (sensu Hutchinson) of a species, i.e. the combination of environmental tolerances and resources required by an organism, interacts with the environment to determine its geographical range. This duality between niche and distribution allows climate change biologists to model potential species’ distributions from past to future conditions. While species distribution models (SDMs) have been intensively used over the last years, no consensual framework to parametrise, calibrate and evaluate models has emerged. Here, to model the contemporary (1990–2017) spatial distribution of seven highly harvested European small pelagic fish species, we implemented a comprehensive and replicable numerical procedure based on 8 SDMs (7 from the Biomod2 framework plus the NPPEN model). This procedure considers critical issues in species distribution modelling such as sampling bias, pseudo-absence selection, model evaluation and uncertainty quantification respectively through (i) an environmental filtration of observation data, (ii) a convex hull based pseudo-absence selection, (iii) a multi-criteria evaluation of model outputs and (iv) an ensemble modelling approach. By mitigating environmental sampling bias in observation data and by identifying the most ecologically relevant predictors, our framework helps to improve the modelling of fish species’ environmental suitability. Not only average temperature, but also temperature variability appears as major factors driving small pelagic fish distribution, and areas of highest environmental suitability were found along the north-western Mediterranean coasts, the Bay of Biscay and the North Sea. We demonstrate in this study that the use of appropriate data pre-processing techniques, an often-overlooked step in modelling, increase model predictive performance, strengthening our confidence in the reliability of predictions.

Résumé: Several pelagic fish species are known to regularly associate with floating objects in the open ocean, including commercially valuable species. The tuna purse seine industry takes advantage of this associative behavior and has been increasingly deploying free-drifting man-made floating objects, also known as fish aggregating devices (FADs). Using passive acoustic telemetry, this study describes the associative dynamics of the main targeted tropical tuna species (Thunnus albacores, T. obelus and Katsuwonus pelamis), as well as three major bycatch species, silky shark (Carcharhinus falciformis), rainbow runner (Elagatis bipinmdata) and oceanic triggerfish (Canthidermis maculata). Short-term excursions away from the FADs were frequently performed by all tuna species as well by silky sharks. These excursions were characterized by a marked diel pattern, mainly occurring during nighttime. Rainbow runners and oceanic triggerfish were much more present at the FADs and rarely performed excursions. Average continuous residence times (CRTs) ranged from 6 days, for silky shark, up to 25 days for bigeye tuna. Similar to silky shark, average CRTs for skipjack tuna and oceanic triggerfish were less than 10 days. For yellowfin tuna and rainbow runner, CRTs averaged 19 and 16 days, respectively. Bigeye and yellowfin tuna remained associated to a single drifting FAD for a record of 55 days and 607 km traveled.

Résumé: Micronekton distributions and assemblages were investigated at two shallow seamounts of the south-western Indian Ocean using a combination of trawl data and a multi-frequency acoustic visualisation technique. La Pa rouse seamount (summit depth similar to 60 m) is located on the outskirts of the oligotrophic Indian South Subtropical Gyre (ISSG) province with weak mesoscale activities and low primary productivity all year round. The “MAD-Ridge” seamount (thus termed in this study; similar to 240 m) is located in the productive East African Coastal (EAFR) province with high mesoscale activities to the south of Madagascar. Higher micronekton species richness was recorded at MAD-Ridge compared to La Perouse. Resulting productivity at MAD-Ridge seamount was likely due to the action of mesoscale eddies advecting productivity and larvae from the Madagascar shelf rather than local dynamic processes such as Taylor column formation. Mean micronekton abundance/biomass, as estimated from mesopelagic trawl catches, were lower over the summit compared to the vicinity of the seamounts, due to net selectivity and catchability and depth gradient on micronekton assemblages. Mean acoustic densities in the night shallow scattering layer (SSL: 10-200 m) over the summit were not significantly different compared to the vicinity (within 14 nautical miles) of MAD-Ridge. At La Perouse and MAD-Ridge, the night and day SSL were dominated by common diel vertically migrant and non-migrant micronekton species respectively. While seamount-associated mesopelagic fishes such as Diaphus suborbitalis (La Perouse and MAD-Ridge) and Benthosema fibula= performed diel vertical migrations (DVM) along the seamounts' flanks, seamount-resident benthopelagic fishes, including Cookeolus japonicus (MAD-Ridge), were aggregated over MAD-Ridge summit. Before sunrise, mid-water migrants initiated their vertical migration from the intermediate to the deep scattering layer (DSL, La Perouse: 500-650 m; MAD-Ridge: 400-700 m) or deeper. During sunrise, the other taxa contributing to the night SSL exhibited a series of vertical migration events from the surface to the DSL or deeper until all migrants have reached the DSL before daytime. Possible mechanisms leading to the observed patterns in micronekton vertical and horizontal distributions are discussed. This study contributes to a better understanding of how seamounts influence the DVM, horizontal distribution and community composition of micronekton and seamount-associated/resident species at two poorly studied shallow topographic features in the south-western Indian Ocean.

Résumé: An end-to-end model named OSMOSE-GoL has been built for the Gulf of Lions, the main French Mediterranean fishing area. This spatialized dynamic model links the coupled hydrodynamic and biogeochemical model Eco3M-S/SYMPHONIE (LTL – low trophic level model) to OSMOSE (HTL – high trophic level model). It includes 15 compartments of living organisms, five from the LTL model (i.e. nanophytoplankton, microphytoplankton, nanozooplankton, microzooplankton and mesozooplankton) and ten from the HTL model (northern krill, southern shortfin squid, European pilchard, European anchovy, European sprat, Atlantic horse mackerel, Atlantic mackerel, blue whiting, European hake and Atlantic bluefin tuna). With the exception of northern krill and European sprat, all HTL species are commercially exploited and undergo fisheries mortality pressure. The modeled species represent more than 70% of annual catches in this area. This paper presents the parameterization, calibration and evaluation of this model with satellite data for phytoplankton and with biomass, landings, diet and trophic level data for HTL groups. For most species, the diets in output of OSMOSE-GoL are similar to field and literature data in terms of dominant prey groups and species. However, some differences were observed. Various reasons may explain the mismatch between the modeled diet and field data. Benthic prey sometimes observed in the stomach content of the HTL predators were not modeled in OSMOSE-GoL. Field studies were carried out at specific periods and locations, while our data concern the period 2001–2004 and the entire modeled domain. Inter- and intra-annual variations in spatial distribution and density of prey may also explain these differences. The model estimates trophic level values similar to those cited in the literature for all the HTL compartments. These values are also close to the trophic levels estimated by a previous Ecopath model for the same area and period. Even though some improvements are still possible, this model may already be of use to explore fishery or Marine Protected Areas scenarios for socio-ecosystem management issues.

Résumé: The state of marine systems subject to natural or anthropogenic impacts can be generally summarized by suites of ecological indicators carefully selected to avoid redundancy. Length-based indicators capture the status of fish community structure, fulfilling the Marine Strategy Framework Directive (MSFD) requirement for Descriptor 3 (status of commercial fish species). Although the MSFD recommends the development of regional indicators, a comparison among alternative length-based indicators is so far missing for the Mediterranean Sea. Using principal component analysis and dynamic factor analysis, we identified the most effective subset of length-based indicators, whether or not based on maximum length. Indicator trends and lime series of fishing effort and environmental variables are also compared in order to highlight the individual and combined capability of indicators to track system changes across geographical sub-areas. Two indicators, typical length and mean maximum length, constitute the smallest set of non-redundant indicators, capturing together 87.45% of variability. Only in combination can these indicators disentangle changes in the fish community composition from modifications of size structure. Our study supports the inclusion of typical length among the regional MSFD Descriptor 3 indicators for the Mediterranean Sea. Finally, we show dissimilarity between the western and eastern-central Mediterranean, suggesting that there are sub-regional differences in stressors and community responses.

Résumé: The uncertainty in age estimation by otolith reading may be at the root of the large variability in red mullet (Mullus barbatus) growth models in the Mediterranean. In the MEDITS survey, red mullet age data are produced following the same sampling protocol and otolith reading methodology. However, ageing is assigned using different interpretation schemes, including variations in theoretical birthdate and number of false rings considered, in addition to differences in the experience level of readers. The present work analysed the influence of these variations and the geographical location of sampling on red mullet ageing using a multivariate approach (principal component analysis). Reader experience was the most important parameter correlated with the variability. The number of rings considered false showed a significant effect on the variability in the first age groups but had less influence on the older ones. The effect of the theoretical birthdate was low in all age groups. Geographical location had a significant influence, with longitude showing greater effects than latitude. In light of these results. workshops, exchanges and the adoption of a common ageing protocol based on age validation studies are considered fundamental tools for improving precision in red mullet ageing.

Résumé: As wide-spread pollutants in the marine environment, microplastics (MPs) have raised public concern about potential toxic effects in aquatic organisms, and, among others, MPs were suspected to act as a vector for organic pollutants to biota. The purpose of the present study was to investigate effects by three model pollutants, oxybenzone (BP3), benzo[a] pyrene (BaP), and perfluorooctane sulfonate (PFOS) adsorbed to polyethylene MPs on the basis of a standard assay, the acute fish embryo toxicity test (FET; OECD TG 236) with zebrafish (Danio rerio) supplemented by additional endpoints such as induction of ethoxyresorufin-O-deethylase (EROD) activity, modification of cyp1a gene transcription and changes in larval swimming behavior. FET assays were performed in three laboratories using slightly different husbandry and exposure conditions, which, however, were all fully compatible with the limits defined by OECD TG 236. This allowed for testing of potential changes in the FET assay due to protocol variations. The standard endpoints of the FET (acute embryotoxicity) did not reveal any acute toxicity for both virgin MPs and MPs spiked with BP3, BaP, and PFOS. With respect to sublethal endpoints, EROD activity was increased after exposure to MPs spiked with BP3 (3 h pulse) and MPs spiked with BaP (96 h continuous exposure). Cyp1a transcription was increased upon exposure to MPs spiked with BP3 or BaP. For the selected combination of MPs particles and contaminants, the basic FET proved not sensitive enough to reveal effects of (virgin and spiked) MPs. However, given that the FET can easily be supplemented by a broad variety of more subtle and sensitive endpoints, an enhanced FET protocol may provide a relevant approach with developmental stages of a vertebrate animal model, which is not protected by current EU animal welfare legislation (Directive EU 2010/63).

Résumé: The end-to-end OSMOSE-GoL model parameterized, calibrated and evaluated for the Gulf of Lions ecosystem (Northwestern Mediterranean Sea) has been used to investigate the effects of introducing two-ways coupling between the dynamics of Low and High Trophic Level groups. The use of a fully dynamic two-ways coupling between the models of Low and High Trophic Levels organisms provided some insights in the functioning of the food web in the Gulf of Lions. On the whole microphytoplankton and mesozooplankton were found to be preyed upon by High Trophic Levels planktivorous groups at rates lower than 20% and 30% of their respective natural mortality rates, but these relatively low rates involved some important alterations in the infra-seasonal and annual cycles of both High and Low Trophic Levels groups. They induced significant changes in biomass, fisheries landings and food web interactions by cascading effects. Spatial differential impacts of High Trophic Levels predation on plankton are less clear except in areas in which primary productivity is high. Higher predation rates on plankton groups were encountered within the area of the Rhone river’s influence and in areas associated to the presence of mesoscale eddies in the Northwestern part of the Gulf of Lions, especially. Generally, the pressure of the High Trophic Levels predation was the highest in areas of highest biomass whatever the plankton group considered. The two-ways coupling between Low and High Trophic Levels models revealed both bottom-up and top-down controls in the ecosystem with effects on planktivorous species similar to those observed in the field. The use of the end-to-end model enabled to propose a set of potential mechanisms that may explain the observed decrease in small pelagic catches by the French Mediterranean artisanal fisheries over the last decade.

Résumé: In an ecosystem approach to fisheries management (EAFM) framework of the tuna purse-seine fishery, the assessment of target species, but also that of bycatch species, is essential. In the Atlantic and Indian oceans, purse-seine nets are sometimes set around tuna schools associated with whale sharks and baleen whales, although less frequently than around free-swimming tuna schools or those associated with fish aggregating devices (FAD). However, knowledge on the targeted catch and bycatch in these megafauna associated fishing sets is still relatively limited. Therefore, the aims of this study were to assess species and size composition of the target tuna species, as well as the diversity of bycatch species in whale and whale shark associated sets. Whale associated sets were found to be very similar to free school sets in terms of tuna catch (large yellowfin tuna), bycatch occurrence (presence in half the sets) and species assemblage (alpha and beta diversity). Whale shark associated sets were intermediate between FAD and free school sets, with tuna catch (skipjack and juvenile yellowfin) closer to FAD than to free school sets. However, the presence of large yellowfin, the bycatch composition (with almost no finfish, abundantly captured in FAD sets) and the species assemblage showed similarity with free school sets. This study highlights the need for an EAFM in the tuna purse-seine fishery by providing knowledge on pelagic multi-specific catches and bycatches.

Résumé: Thanks to the availability of the MEDITS survey data, a standardized picture of the occurrence and abundance of demersal Chondrichthyes in the northern Mediterranean has been obtained. During the spring-summer period between 2012 and 2015, 41 Chondrichthyes, including 18 sharks (5 orders and 11 families). 22 batoids (3 orders and 4 families) and 1 chimaera, were detected from several geographical sub-areas (GSAs) established by the General Fisheries Commission for the Mediterranean. Batoids had a preferential distribution on the continental shelf (10-200 m depth). while shark species were more frequent on the slope (200-800 m depth). Only three species, the Carcharhiniformes Galeus melastomus and Scyliorhinus canicida and the Torpediniformes Torpedo matmorata were caught in all GSAs studied. On the continental shelf, the Rajidae family was the most abundant, being represented in primis by Raja clavaia and then by R. miraleius, R. polystigma and R. asterias. The slope was characterized by the prevalence of G. melastomus in all GSAs, followed by S. canictda, E. spinax and Squalus blainville. Areas under higher fishing pressure, such as the Adriatic Sea and the Spanish coast (with the exception of the Balearic Islands), show a low abundance of chondrichthyans, but other areas with a high level of fishing pressure, such as southwestern Sicily, show a high abundance, suggesting that other environmental drivers work together with fishing pressure to shape their distribution. Results of generalized additive models highlighted that depth is one of the most important environmental drivers influencing the distribution of both batoid and shark species, although temperature also showed a significant influence on their distribution. The approach explored in this work shows the possibility of producing maps modelling the distribution of demersal chondrichthyans in the Mediterranean that are useful for the management and conservation of these species at a regional scale. However, because of the vulnerability of these species to fishing exploitation, fishing pressure should be further incorporated in these models in addition to these environmental drivers.

Résumé: We develop a spatially explicit model of diversification based on palaeohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the 'time-area', 'tropical niche conservatism', 'ecological limits' and 'evolutionary speed' livpotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are nonmutually exclusive and that their relative influence depends on the time scale considered. Simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating biodiversity patterns.

Résumé: Bycatch in fisheries can have profound effects on the abundance of species with relatively low resilience to increased mortality, can alter the evolutionary characteristics and concomitant fitness of affected populations through heritable trait-based selective removals, and can alter ecosystem functions, structure and services through food web trophic links. We challenge current piecemeal bycatch management paradigms, which reduce the mortality of one taxon of conservation concern at the unintended expense of others. Bycatch mitigation measures may also reduce intraspecific genetic diversity. We drew examples of broadly prescribed ‘best practice’ methods to mitigate bycatch that result in unintended cross-taxa conflicts from pelagic longline, tuna purse seine, gillnet and trawl fisheries. We identified priority improvements in data quality and in understanding ecological effects of bycatch fishing mortality to support holistic ecological risk assessments of the effects of bycatch removals conducted through semi-quantitative and model-based approaches. A transition to integrated bycatch assessment and management that comprehensively consider biodiversity across its hierarchical manifestations is needed, where relative risks and conflicts from alternative bycatch management measures are evaluated and accounted for in fisheries decision-making processes. This would enable managers to select measures with intentional and acceptable tradeoffs to best meet objectives, when conflicts are unavoidable.

Résumé: Most studies on European hake focus on the recruitment process and nursery areas, whereas the information is comparatively limited on the ecology of the juvenile stage (ca. second year of life)-the one most exploited by the Mediterranean trawl fisheries. Using information of the MEDITS programme, we provide a spatial and temporal assessment of the influence of body size and growth on hake survival from recruits (age 0) to juveniles (age 1), along with the impact of surface temperature and chlorophyll variability. At a biogeographic scale, size-dependent survival is supported, with areas with higher mean length of recruits and juveniles yielding higher survival. A similar pattern was observed at interannual level in some western Mediterranean areas, also mediated by a density-dependent effect on growth. However, the most recurrent inter-annual pattern was a negative effect of size on survival, which could be attributed to potential ontogenetic changes in catchability and underrepresentation of intra-annual recruitment pulses that are seasonally inaccessible to the MEDITS survey. Results also evidence that survival in the Alboran and Adriatic seas is dependent on the primary production variability, and that Corsica and Sardinia could be potential feeding grounds receiving juveniles from neighbouring areas. The present study reveals the importance of size- and growth-dependent survival in the juvenile stage of European hake in the Mediterranean Sea.

Résumé: In teleosts, the regulation of hydromineral balance has a direct impact on several physiological functions, biochemical processes, and can influence behaviour, distribution and survival. As European sea bass Dicentrarchus labrax undertake seasonal migrations from seawater (SW) to brackish, estuarine and fresh water (FW) in their habitat, this study investigates their capacity to tolerate fresh water and explores intraspecific variations in physiological responses. Juvenile D. labrax were transferred from SW to FW at various ages. Freshwater-tolerant and non-tolerant phenotypes were discriminated according to behavioural and morphological characteristics. About 30% of the fish exposed to FW were identified as freshwater intolerant following FW challenges performed at different ages. Interestingly, intolerant fish exhibited the same phenotypic traits: erratic swimming, lower speed, isolation from the shoal and darker colour. Freshwater-intolerant fish were also characterised by a significant lower blood osmolality compared to tolerant fish, and significantly lower Na+/K+-ATPase alpha 1a expression in the posterior kidney. An imbalance in ion regulatory mechanisms was further confirmed by a blood Na+/Cl- ratio imbalance observed in some freshwater-intolerant fish. The analysis of glucocorticoid and mineralocorticoid receptor expression levels in gills and kidney revealed significant differences between freshwater-intolerant and -tolerant fish in both organs, suggesting differential stress-related responses. This study clearly shows an intraspecific difference in the responses following FW transfer with a decreased renal ion uptake capacity as a major cause for freshwater intolerance.

Résumé: To investigate dispersal and connectivity between spawning and lagoon nursery habitats of the gilthead seabream, Sparus aurata, in the Gulf of Lions (northwestern Mediterranean Sea), we modeled the potential transport of the species’ larvae between its supposed main spawning site in the region (the Planier Island) and two of its main local nursery areas (the coastal lagoons of Thau and Salses-Leucate). Passive larval drift simulations using a dispersal biophysical model showed a large variability in the possible trajectories from spawning to nursery areas and in the predicted ages for larvae arrival on the two nursery sites. The most common ages at arrival obtained in the simulations (20–60 days) are broadly consistent with previous modeling studies but contrast with the actual ages of the S. aurata post-larvae collected in 2016 and 2017 at time of the lagoon entrances (60–90 days, from otolith readings). The period between 25 and 70 days being critical for gilthead seabream larvae to acquire sufficient swimming, osmoregulatory, and olfactory abilities to enter coastal lagoons, we argue that ontogenic development plays a crucial role in the transport and local retention of S. aurata larvae in the studied region, explaining the discrepancy between simulation results and observed data.

Résumé: Long-distance (>40-km) dispersal from marine reserves is poorly documented; yet, it can provide essential benefits such as seeding fished areas or connecting marine reserves into networks. From a meta-analysis, we suggest that the spatial scale of marine connectivity is underestimated due to the limited geographic extent of sampling designs. We also found that the largest marine reserves (>1000 km(2)) are the most isolated. These findings have important implications for the assessment of evolutionary, ecological, and socio-economic long-distance benefits of marine reserves. We conclude that existing methods to infer dispersal should consider the up-to-date genomic advances and also expand the spatial scale of sampling designs. Incorporating long-distance connectivity in conservation planning will contribute to increase the benefits of marine reserve networks.

Résumé: Trait diversity is believed to influence ecosystem dynamics through links between organismal traits and ecosystem processes. Theory predicts that key traits and high trait redundancy-large species richness and abundance supporting the same traits-can buffer communities against environmental disturbances. While experiments and data from simple ecological systems lend support, large-scale evidence from diverse, natural systems under major disturbance is lacking. Here, using long-term data from both temperate (English Channel) and tropical (Seychelles Islands) fishes, we show that sensitivity to disturbance depends on communities' initial trait structure and initial trait redundancy. In both ecosystems, we found that increasing dominance by climatically vulnerable traits (e.g., small, fast-growing pelagics/corallivores) rendered fish communities more sensitive to environmental change, while communities with higher trait redundancy were more resistant. To our knowledge, this is the first study demonstrating the influence of trait structure and redundancy on community sensitivity over large temporal and spatial scales in natural systems. Our results exemplify a consistent link between biological structure and community sensitivity that may be transferable across ecosystems and taxa and could help anticipate future disturbance impacts on biodiversity and ecosystem functioning.

Résumé: While climate change is rapidly impacting marine species and ecosystems worldwide, the effects of climate warming on coastal fish nurseries have received little attention despite nurseries' fundamental roles in recruitment and population replenishment. Here, we used a 26-year time series (1987-2012) of fish monitoring in the Bay of Somme, a nursery in the Eastern English Channel (EEC), to examine the impacts of environmental and human drivers on the spatial and temporal dynamics of fish functional structure during a warming phase of the Atlantic Multidecadal Oscillation (AMO). We found that the nursery was initially dominated by fishes with r-selected life-history traits such as low trophic level, low age and size at maturity, and small offspring, which are highly sensitive to warming. The AMO, likely superimposed on climate change, induced rapid warming in the late 1990s (over 1 degrees C from 1998 to 2003), leading to functional reorganization of fish communities, with a roughly 80% decline in overall fish abundance and increased dominance by K-selected fishes. Additionally, historical overfishing likely rendered the bay more vulnerable to climatic changes due to increased dominance by fishing-tolerant, yet climatically sensitive species. The drop in fish abundance not only altered fish functional structure within the Bay of Somme, but the EEC was likely impacted, as the EEC has been unable to recover from a regime shift in the late 1990s potentially, in part, due to failed replenishment from the bay. Given the collapse of r-selected fishes, we discuss how the combination of climate cycles and global warming could threaten marine fish nurseries worldwide, as nurseries are often dominated by r-selected species.

Résumé: The manefishes of the family Caristiidae are rare, poorly known deep-sea species with broad geographical distribution. This study provides new information on the diversity and distribution of this family around the oceanic islands and seamounts off northeastern Brazil, reporting the first records of Paracaristius nudarcus, Platyberyx andriashevi, Platyberyx paucus and Platyberyx pietschi in Brazilian waters. Measurements and counts for all specimens examined are provided and compared with those available in the literature. In addition, the identity of caristiids previously reported from Brazil is discussed.

Résumé: The Mediterranean Sea is one of the main hotspots of marine biodiversity in the world. The combined pressures of fishing activity and climate change have also made it a hotspot of global change amidst increasing concern about the worsening status of exploited marine species. To anticipate the impacts of global changes in the Mediterranean Sea, more integrated modelling approaches are needed, which can then help policymakers prioritize management actions and formulate strategies to mitigate impacts and adapt to changes. The aim of this study was to develop a holistic model of marine biodiversity in the Mediterranean Sea with an explicit representation of the spatial, multispecies dynamics of exploited resources subject to the combined influence of climate variability and fishing pressure. To this end, we used the individual-based OSMOSE model (Object-oriented Simulator of Marine ecOSystEms), including 100 marine species (fish, cephalopods and crustaceans) representing about 95% of the total declared catch, at a high spatial resolution (400 km2) and a large spatial scale (the entire Mediterranean basin) – the first time such a resolution and scale have been modelled. We then combined OSMOSE with the NEMOMED 12 physical model and the Eco3M-S biogeochemical low trophic level model to build the end-to-end model, OSMOSE-MED. We fitted OSMOSE-MED model with observed or estimated biomass and commercial catch data using a likelihood approach and an evolutionary optimization algorithm. The outputs of OSMOSE-MED were then verified against observed biomass and catch data, and compared with independent datasets (MEDITS data, diet composition and trophic levels). The model results – at different hierarchical levels, from individuals to the scale of the ecosystem – were consistent with current knowledge of the structure, functioning and dynamics of the ecosystems in the Mediterranean Sea. While the model could be further improved in future iterations, all the modelling steps – the comprehensive representation of key ecological processes and feedback, the selective parameterization of the model, and the comparison with observed data in the validation process – strengthened the predictive performance of OSMOSE-MED and thus its relevance as an impact model to explore the future of marine biodiversity under scenarios of global change. It is a promising tool to support ecosystem-based fishery management in the Mediterranean Sea.

Résumé: Anticipating future changes in marine social-ecological systems (MSES) several decades into the future is essential in the context of accelerating global change. This is challenging in situations where actors do not share common understandings, practices, or visions about the future. We introduce a dedicated scenario method for the development of MSES scenarios in a participatory context. The objective is to allow different actors to jointly develop scenarios which contain their multiple visions of the future. The method starts from four perspectives: “fisheries management,” “ecosystem,” “ocean climate,” and “global context and governance” for which current status and recent trends are summarized. Contrasted scenarios about possible futures are elaborated for each of the four single perspectives before being integrated into multiple-perspective scenarios. Selected scenarios are then developed into storylines. Focusing on individual perspectives until near the end allows actors with diverse cultures, interests and horizons to confront their own notions of the future. We illustrate the method with the exploration of the futures of the Barents Sea MSES by 2050. We emphasize the following lessons learned: first, many actors are not familiar with scenario building and attention must be paid to explaining the purpose, methodology, and benefits of scenarios exercises. Second, although the Barents Sea MSES is relatively well understood, uncertainties about its future are significant. Third, it is important to focus on unlikely events. Fourth, all perspectives should be treated equally. Fifth, as MSES are continuously changing, we can only be prepared for future changes if we collectively keep preparing.

Résumé: Bisphenol A (BPA) in eggs prior to fertilization was found to induce long-term metabolic disturbances in juvenile rainbow trout (Oncorhynchus mykiss). Here we describe these imprinting effects in a Dynamic Energy Budget (DEB) framework, which allows interpretation of the data in an energy allocation context. First, DEB parameters for control rainbow trout were optimized using data extracted from 12 studies in the literature. Several modes of action on DEB parameters were then tested in order to correctly predict weight differences observed in rainbow trout in response to 5 different concentrations of BPA in eggs prior to fertilization. Reduced energy conductance (v) over dot at day 0, followed by an exponential recovery, was found to closely fit the experimental data. Effects on (v) over dot lasted beyond the disappearance of the chemical from the body, suggesting an imprinting effect of BPA on energy mobilization from the reserve. Our model predicts that early changes in DEB parameters lead to permanent and irreversible impairment of the metabolic growth acceleration in rainbow trout.

Résumé: Around 2008, an ecosystem shift occurred in the Gulf of Lions, highlighted by considerable changes in biomass and fish mean weight of its two main small pelagic fish stocks (European anchovy, Engraulis encrasicolus; European sardine, Sardina pilchardus). Surprisingly these changes did not appear to be mediated by a decrease in fish recruitment rates (which remained high) or by a high fishing pressure (exploitation rates being extremely low). Here, we review the current knowledge on the population's dynamics and its potential causes. We used an integrative ecosystem approach exploring alternative hypotheses, ranging from bottom-up to top-down control, not forgetting epizootic diseases. First, the study of multiple population characteristics highlighted a decrease in body condition for both species as well as an important decrease in size resulting from both a slower growth and a progressive disappearance of older sardines. Interestingly, older sardines were more affected by the decrease in condition than younger ones, another sign of an unbalanced population structure. While top-down control by bluefin tuna or dolphins, emigration and disease were mostly discarded as important drivers, bottom-up control mediated by potential changes in the plankton community appeared to play an important role via a decrease in fish energy income and hence growth, condition and size. Isotopic and stomach content analyses indicated a dietary shift pre- and post-2008 and modeled mesozooplankton abundance was directly linked to fish condition. Despite low energy reserves from 2008 onwards, sardines and anchovies maintained if not increased their reproductive investment, likely altering the life-history trade-off between reproduction and survival and resulting in higher natural mortality. The current worrying situation might thus have resulted from changes in plankton availability/diversity, which remains to be thoroughly investigated together with fish phenotypic plasticity.

Résumé: The present study provides updated information on the occurrence, abundance and biomass distribution patterns and length frequencies of Merluccius merluccius in the Mediterranean Sea, by analysing a time series of data from the Mediterranean International Trawl Surveys (MEDITS) from 1994 to 2015. The highest values of abundance and biomass were observed in the Sardinian Seas. The use of a generalized additive model, in which standardized biomass indices (kg km(-2)) were analysed as a function of environmental variables, explained how ecological factors could affect the spatio-temporal distribution of European hake biomass in the basin. High biomass levels predicted by the model were observed especially at 200 m depth and between 14 degrees C and 18 degrees C, highlighting the preference of the species for colder waters. A strong reduction of biomass was observed since the year 2009, probably due to the strengthening of the seasonal thermocline that had greatly reduced the availability of food. The general decrease in biomass of several stocks of anchovy and sardine, preys of European hake, might be indirectly connected to the decreasing biomass detected in the present study. The length analysis shows median values lower than 200 mm total length of most of the investigated areas.

Résumé: Biological traits of Oreochromis niloticus were studied in order to identify potential differences between the population of the Nam Theun 2 Reservoir and other populations in Asia and in Africa. The study also aimed to characterize the demographic structure of the exploited population by fisheries in the reservoir. Toluidine-stained transverse section of otoliths from 322 specimens, collected between November 2015 and January 2017, were analysed to identify the periodicity of annulus formation and to age individuals. Length, weight, sex and sexual maturity stage were recorded. Life history traits were characterized by length-weight and length age relationships. The periodicity of annulus formation was annual, with complete formation of the translucent zone at the beginning of the warm and wet season (June and July). The length-age key has been established and was composed of 9 age classes, ranging from 0 to 8 years old. Males showed positive allometric growth whereas juveniles and females exhibited isometric growth. The study showed an asymptotic standard length of 658 mm and a low growth rate (K = 0.08 year(-1)). The sex ratio was equilibrated, and first maturity of females was at 277 mm standard length. The population was composed of individuals aged 3 years old and older, and 60% of the landings were composed of individuals aged 5 years and older. The growth rate was lower than for Asian and African populations, and the age-length key provided was specific to the studied reservoir. However, some biological traits of the O. niloticus population were similar to those found for other population in the world: (i) formation of an annual annulus during the reproduction period, at the beginning of the warm and wet season like populations from subtropical countries, and (ii) an isometric or a positive allometric growth as seen in populations that were not overexploited and were living in favourable environmental conditions. Therefore, the present study suggests that the O. niloticus population of the NT2 Reservoir was not overexploited at the time of the survey.

Résumé: Partial migration is a key adaptive strategy, increasingly observed across multiple taxa. To investigate partial migration and life-cycle diversity of Merluccius australis in northwestern Patagonia, we analysed isotopic (delta C-13, delta O-18) and elemental (B-11, Na-23, Mg-24, Mn-55, Sr-86, Ba-138) compositions of otoliths from juveniles, sub-adults, and adults to identify nursery origins, habitats used, and migratory behaviours of multiple cohorts (1990-2005). Influence of early size upon migration was assessed by comparing back-calculated sizes at demersal recruitment between resident and migratory adults. Although partial migration occurred at both estuarine and oceanic nursery habitats, migratory behaviour was more frequent in fish of estuarine origin (59%) than in fish of oceanic origin (17%). Adults of estuarine origin dominated both estuarine (92%) and oceanic (77%) sampling areas. Although we found no significant differences in size at demersal recruitment between oceanic-resident and oceanic-migratory fish, a strong relationship between size at demersal recruitment and migratory behaviour appeared in fish of estuarine origin, whose probability of migration increased from 5% to 95% as demersal recruitment size increased from 18.8 to 23.6cm. Further research on M. australis life cycle is required to incorporate sub-population processes into the stock assessment and management models being used for this overexploited species.

Résumé: Cultural and recreational values of biodiversity are considered as important dimensions of nature's contribution to people. Among these values, the aesthetics can be of major importance as the appreciation of beauty is one of the simplest forms of human emotional response. Using an online survey, we disentangled the effects of different facets of biodiversity on aesthetic preferences of coral reef fish assemblages that are among the most emblematic assemblages on Earth. While we found a positive saturating effect of species' richness on human preference, we found a net negative effect of species abundance, no effect of species functional diversity and contrasting effects of species composition depending on species' attractiveness. Our results suggest that the biodiversity-human interest relationship is more complex than has been previously stated. By integrating several scales of organization, our study is a step forward in better evaluating the aesthetic value of biodiversity.

Résumé: Fillet yield, the proportion of edible fillet relative to body weight, is a major trait to improve in fish sold processed, as it has a direct impact on profitability and can simultaneously decrease the environmental impact of producing a given amount of fillet. However, it is difficult to improve by selective breeding, because it cannot be measured on live breeding candidates, its phenotypic variation is low, and, as a ratio, it is not normally distributed and a same change in fillet yield can be the result of different changes in fillet weight and body weight. Residual headless gutted carcass weight (rHGCW) is heritable and highly genetically correlated to Fillet% in rainbow trout, and can be predicted by the ratio of abdominal wall thickness to depth of the peritoneal cavity (E8/E23), measured on live fish by ultrasound tomography. We selected broodstock based on rHGCW, measured on sibs of the selection candidates, on ultrasound measurements (E8/E23) measured on the selection candidates, or a combination of both. Seven broodstock groups were selected: fish with 15% highest (rHGCW+) or lowest (rHGCW-) EBV for rHGCW, with 15% highest (E8/E23+) or lowest (E8/E23-) EBV for E8/E23, with both rHGCW+ and E8/E23+ (Both+) or rHGCW- and E8/E23- (Both-), or with close to zero EBVs for both traits (Mid). Seven corresponding groups of offspring were produced and reared communally. At harvest size (1.5 kg mean weight), 1,561 trout were slaughtered, measured for the traits of interest, and pedigreed with DNA fingerprinting. Offspring from groups Both+, rHGCW+ and E8/E23+ had a higher EBV for rHGCW than the control group, while down-selected groups had a lower EBV. Looking at the phenotypic mean for Fillet% (correlated response), up-selected fish had more fillet than down-selected fish. The highest difference was between Both+ (69.36%) and Both- (68.20%), a 1.16% units difference in fillet percentage. The change in Fillet% was explained by an opposite change in Viscera%, while Head% remained stable. Selection using sib information on rHGCW was on average more efficient than selection using the candidates' own E8/E23 phenotypes, and downward selection (decreasing Fillet%) was more efficient than upward selection.

Résumé: Quantifying changes in functional diversity, the facet of biodiversity accounting for the biological features of organisms, has been advocated as one of the most integrative ways to unravel how communities are affected by human-induced perturbations. The present study assessed how functional diversity patterns varied among communities that differed in the degree to which non-native species dominated the community in temperate lake fish communities and whether accounting for intraspecific functional variability could provide a better understanding of the variation of functional diversity across communities. Four functional diversity indices were computed for 18 temperate lake fish communities along a gradient of non-native fish dominance using morphological functional traits assessed for each life-stage within each species. First, we showed that intraspecific variability in functional traits was high and comparable to interspecific variability. Second, we found that non-native fish were functionally distinct from native fish. Finally, we demonstrated that there was a significant relationship between functional diversity and the degree to which non-native fish currently dominated the community and that this association could be better detected when accounting for intraspecific functional variability. These findings highlighted the importance of incorporating intraspecific variability to better quantify the variation of functional diversity patterns in communities facing human-induced perturbations.

Résumé: Spatial distribution, community composition and trophic roles of micronekton (crustaceans, fishes and squids) were investigated in the Indian South Subtropical Gyre (ISSG) province and the East African Coastal province (EAFR), by combining acoustic surveys, mid-water trawls and stable isotope analyses from scientific cruises conducted in 2009 and 2010. Mesopelagic micronekton performed diel vertical migrations in both provinces, from deep (400-740 m) to surface (0-200 m) layers at dusk and in the opposite direction at dawn, with some species migrating below 740 m. The EAFR province was more dynamic than the oligotrophic ISSG province, with enhanced eddy activity and enhanced yearly productivity. The active enrichment mechanisms in the EAFR, in terms of available primary production, led to high micronekton acoustic density (as a proxy of micronekton abundance) and large micronekton weight and abundance estimates from trawl data. Particulate organic matter in the EAFR exhibited greater enrichment in C-13 and N-15 compared to the ISSG and, consequently, tissues of selected micronekton organisms in the EAFR were more enriched in N-15 (higher delta N-15 values). In both provinces, micronekton encompassed a wide range of isotopic niches, with large overlaps between species. Micronekton and swordfish in the EAFR had an overlapping range of delta N-15 values, contrasting with the ISSG province where swordfish were two trophic levels higher than the sampled micronekton. Our results provide some evidence that the combined action of riverine input and the dynamics of eddies might influence productivity in the EAFR, and hence the abundance of micronekton and the enrichment of tissues in N-15, compared to the oligotrophic ISSG province.

Résumé: For the first time in Senegal, assessments based on both stochastic and deterministic production models were used to draw a global diagnosis of the fishing impact on coastal demersal stocks. Based one national fisheries databases and scientific trawl surveys data: (i) trends in landings since 1971 were examined, (ii) abundance indices of 10 stocks were estimated using linear models fitted to surveys data and commercial catch per unit efforts, and (iii) stock assessments were carried out using pseudo-equilibrium Fox and Pella-Tomlinson models and a Biomass dynamic production model fitted in a Bayesian framework to abundance indices. Most stocks have seen their abundance sharply declining over time. All stocks combined, results of stock assessments suggest a 63% reduction compared to virgin state. Three fifth of demersal stocks are overexploited and excess in fishing effort was estimated until 75% for the worst case. We conclude by suggesting that the fishing of such species must be regulated and an ecosystem approach to fisheries management should be implemented in order to monitor the whole ecosystem.

Résumé: The performance of a combined catch quota and habitat credit system was explored to manage the sustainable exploitation of a mix of demersal fish species and reduce the benthic impacts of bottom trawl fisheries using a dynamic state variable model approach. The model was parameterised for the Eastern English Channel demersal mixed fishery using otter trawls or dredges. Target species differed in their association with habitat types. Restricting catch quota for plaice and cod had a limited effect on benthic impact, except when reduced to very low values, forcing the vessels to stay in port. Quota management had a minimal influence on fishing behaviour and hence resulted in a minimal reduction of benthic impact. Habitat credits may reduce the benthic impacts of the trawl fisheries at a minimal loss of landings and revenue, as vessels are still able to reallocate their effort to less vulnerable fishing grounds, while allowing the fishery to catch their catch quota and maintain their revenue. Only if they are reduced to extremely low levels can habitat credits potentially constrain fishing activities to levels that prevent the fisheries from using up the catch quota for the target species.

Résumé: Preliminary studies conducted on the human gastro-intestinal tract have revealed that enteric viral communities play a preponderant role in microbial homeostatis. However to date, such communities have never been investigated in the fish gut. Herein, we examined the main ecological traits of viruses in the digestive tract of a euryhaline fish, the tilapia Sarotherodon melanotheron. Individuals were collected at 8 different sites in Senegal covering a salinity gradient from 3 to 104 parts per thousand, and showing large disparities in their organic pollutant concentrations. Results showed that the gut of S. melanotheron is home to a highly abundant viral community (0.2-10.7 x 10(9) viruses ml(-1)), distinct from the surrounding water, and essentially composed of phages of which a substantial proportion is temperate (the fraction of lysogenized cells-FLC ranging from 8.1 to 33.0%). Also, a positive and significant correlation was detected between FLC and the concentrations of polycyclic aromatic hydrocarbon in sediment, while no clear relationships were found between salinity and any of the microbial parameters considered. Finally, our data suggest that virus-bacteria interactions within the fish intestine are likely sensitive to the presence of particular xenobiotics, which may compromise the balance in the gut microbiota, and subsequently affect the health of their host.

Résumé: High abundances of juvenile fish in certain ports suggest they might provide alternative nursery habitats for several species. To further investigate this possibility, post-settlement growth, metal uptake and body condition were estimated in 127 juveniles of two seabream species, collected in 2014–15, inside and outside the highly polluted ports of the Bay of Toulon. This showed that differences in local pollution levels (here in Hg, Cu, Pb and Zn) are not consistently mirrored within fish flesh. Muscle metal concentrations, below sanitary thresholds for both species, were higher in ports for Cu, Pb and V only. Otherwise, fish muscle composition principally differed by species or by year. Juvenile growth and condition were equivalent at all sites. Higher prey abundance in certain ports might therefore compensate the deleterious effects of pollution, resulting in similar sizes and body conditions for departing juvenile fish than in nearby natural habitats.

Résumé: Coral reefs provide ecosystem goods and services for millions of people in the tropics, but reef conditions are declining worldwide. Effective solutions to the crisis facing coral reefs depend in part on understanding the context under which different types of conservation benefits can be maximized. Our global analysis of nearly 1,800 tropical reefs reveals how the intensity of human impacts in the surrounding seascape, measured as a function of human population size and accessibility to reefs (“gravity”), diminishes the effectiveness of marine reserves at sustaining reef fish biomass and the presence of top predators, even where compliance with reserve rules is high. Critically, fish biomass in high-compliance marine reserves located where human impacts were intensive tended to be less than a quarter that of reserves where human impacts were low. Similarly, the probability of encountering top predators on reefs with high human impacts was close to zero, even in high-compliance marine reserves. However, we find that the relative difference between openly fished sites and reserves (what we refer to as conservation gains) are highest for fish biomass (excluding predators) where human impacts are moderate and for top predators where human impacts are low. Our results illustrate critical ecological trade-offs in meeting key conservation objectives: reserves placed where there are moderate-to-high human impacts can provide substantial conservation gains for fish biomass, yet they are unlikely to support key ecosystem functions like higher-order predation, which is more prevalent in reserve locations with low human impacts.

Résumé: Trail-based ecology has been developed for decades lo infer ecosystem responses to stressors based on the functional structure of communities, yet its value in species-poor systems is largely unknown. Here, we used an extensive clataset in a Spanish region highly prone to non-native fish invasions (15 catchments, N 389 sites) to assess for the first time how species-poor communities respond to large-scale environmental gradients using a taxonomic and functional trait-based approach in riverine fish. We examined total species richness and three functional trait-based indices available when many sites have <= 3 species (specialization, FSpe; onginaliy, FOri and entropy, FEnt). We assessed the responses of these taxonomic and functional indices along gradients of altitude, water pollution, physical habitat degradation and non-native fish biomass. Whilst species richness was relatively sensitive to spatial effects, functional diversity indices were responsive across natural and anthropogenic gradients. All four diversity measures declined with altitude but this decline was modulated by physical habitat degradation (richness, FSpe and FEnt) and the non-native total fish biomass ratio (FSpe and FOri) in ways that varied between indices. Furthermore, FSpe and FOri were significantly correlated with Total Nitrogen. Non-native fish were a major component of the taxonomic and functional structure of fish communities, raising concerns about potential misdiagnosis between invaded and environmentally-degraded river reaches. Such misdiagnosis was evident in a regional fish index widely used in official monitoring programs. We recommend the application of FSpe and FOri to extensive clatasets from monitoring programs in order to generate valuable cross-system information about the impacts of non-native species and habitat degradation, even in species-poor systems. Scoring non-native species apart from habitat degradation in the indices used to determine ecosystem health is essential to develop better management strategies. (C) 2013 Elsevier B.V. All rights reserved.

Résumé: Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on single nucleotide polymorphism (SNP) allele frequencies. We used Moran's eigenvector maps (db-MEMs) and asymmetric eigenvector maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (>1,000km), while larval dispersal was the major predictor at smaller spatial scale (<1,000km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history, or multigenerational stepping-stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected area network that would efficiently enhance protection and persistence capacity of marine species.

Résumé: Aim: The importance of quantifying the contribution of historical processes in shaping current biodiversity patterns is now recognized, but quantitative approaches that explicitly link speciation, extinction and dispersal processes to palaeo-environmental changes are currently lacking. Here, we propose a spatial diversification model of lineages through time (SPLIT) based on the reconstruction of palaeo-environments. We illustrate our approach using mangroves as a case study and evaluate whether habitat changes caused by plate tectonics explain the current biodiversity patterns of this group. Innovations: The SPLIT model allows one to simulate the evolutionary dynamics of species ranges by spatially linking speciation, extinction and dispersal processes to habitat changes over geological time periods. The SPLIT model provides a mechanistic expectation of speciation and extinction assuming that species are ecologically identical and not interacting. The likelihood of speciation and extinction is equivalent across species and depends on two dispersal parameters interacting with habitat dynamics (d a maximum dispersal distance and ds a distance threshold beyond which gene flow is absent). Beyond classical correlative approaches, this model tracks biodiversity dynamics under palaeo-environmental changes and provides multiple expectations (i.e., alpha-, beta-diversity, phylogenies) that can be compared to empirical patterns. Main conclusions: The SPLIT model allows a better understanding of the origin of biodiversity by explicitly accounting for habitat changes over geological times. The simulations applied to the mangrove case study reproduced the observed longitudinal gradient in species richness, the empirical pattern of beta-diversity and also provided inference on diversification rates. Future developments may include niche evolution and species interactions to evaluate the importance of non-neutral mechanisms. The method is fully implemented in the InsideDNA platform for bioinformatics analyses, and all modelling results can be accessed via interactive web links.

Résumé: There is an increasing need to understand community-level or whole-ecosystem responses to multiple stressors since the impacts of multiple stressors on marine systems depend not only on species-level responses, but also on species interactions and ecosystem structure. In this study, we used a multi-model ecosystem simulation approach to explore the combined effects of fishing and primary productivity on different components of the food-web across a suite of ecosystems and a range of model types. Simulations were carried out under different levels of primary productivity and various fishing scenarios (targeting different trophic levels). Previous work exploring the effects of multiple stressors often assumed that the combined effects of stressors are additive, synergistic or antagonistic. In this study, we included a fourth category “dampened”, which refers to less negative or to less positive impacts on a given ecosystem component compared to additive effects, and in contrast to previous studies, we explicitly considered the direction of the combined effects (positive or negative). We focused on two specific combined effects (negative synergism and positive dampened) associated with the ecological risk of resultant lower fish biomass than expected under additive effects. Through a meta-analysis of the multi-models’ simulation results, we found that (i) the risk of negative synergism was generally higher for low-trophic-level (LTL) taxa, implying that following an increase of fishing pressure on a given LTL stock, the subsequent decrease of biomass under low primary productivity would be higher than expected when fishing is the sole driver and (ii) the risk of positive dampened effects was generally higher for high-trophic-level (HTL) taxa, implying that given a management measure aimed at reducing the impact of fishing on HTL stocks, the subsequent rebuilding of these stocks would be slower than expected if only fishing were considered. Our approach to categorizing and exploring cumulative risk can be applied to evaluate other community properties and indicators and our findings could provide guidance in fisheries management.

Résumé: 1. Periodically harvested closures (PHCs) are one of the most common forms of fisheries management in Melanesia, demonstrating multiple objectives, including sustaining fish stocks and increasing catch efficiency to support small-scale fisheries. No studies have comprehensively assessed their ability to provide short-term fisheries benefits across the entire harvest regime. 2. We present a novel analytical framework to guide a meta-analysis and assist future research in conceptualizing and assessing the potential of PHCs to deliver benefits for multiple fisheries-related objectives. 3. Ten PHCs met our selection criteria and on average, they provided a 48% greater abundance and 92% greater biomass of targeted fishes compared with areas open to fishing prior to being harvested. 4. This translated into tangible harvest benefits, with fishers removing 21% of the abundance and 49% of the biomass within PHCs, resulting in few post-harvest protection benefits. 5. When PHCs are larger, closed for longer periods or well enforced, short-term fisheries benefits are improved. However, an increased availability of fish within PHCs leads to greater removal during harvests. 6. Synthesis and applications. Periodically harvested closures (PHCs) can provide short-term fisheries benefits. Use of the analytical framework presented here will assist in determining long-term fisheries and conservation benefits. We recommend PHCs be closed to fishing for as long as possible, be as large as possible, that compliance be encouraged via community engagement and enforcement, and strict deadlines/goals for harvesting set to prevent overfishing.

Résumé: Accurate information on the growth rates of fish is crucial for fisheries stock assessment and management. Empirical life history parameters (von Bertalanffy growth) are widely fitted to cross-sectional size-at-age data sampled from fish populations. This method often assumes that environmental factors affecting growth remain constant over time. The current study utilized longitudinal life history information contained in otoliths from 412 juveniles and adults of gilthead seabream, Sparus aurata, a commercially important species fished and farmed throughout the Mediterranean. Historical annual growth rates over 11 consecutive years (2002–2012) in the Gulf of Lions (NW Mediterranean) were reconstructed to investigate the effect of temperature variations on the annual growth of this fish. S. aurata growth was modelled linearly as the relationship between otolith size at year t against otolith size at the previous year t-1. The effect of temperature on growth was modelled with linear mixed effects models and a simplified linear model to be implemented in a cohort Integral Projection Model (cIPM). The cIPM was used to project S. aurata growth, year to year, under different temperature scenarios. Our results determined current increasing summer temperatures to have a negative effect on S. aurata annual growth in the Gulf of Lions. They suggest that global warming already has and will further have a significant impact on S. aurata size-at-age, with important implications for age-structured stock assessments and reference points used in fisheries.