Résumé: In an increasingly anthropogenic world, the scientific community and managers have to take interactions between the drivers of ecosystems into consideration. Tools like ecological network analysis (ENA) indices offer the opportunity to study those interactions at the ecosystem level. However, ENA indices have never been used to test the incidence of cumulative drivers. The present study uses models combining the effects of (i) the reef caused by the future offshore wind farm of Courseulles-sur-Mer and (ii) climate change on species distribution, to test the response of multiple ENA indices. ENA indices proved sensitive to this cumulative impact, displaying a wide variety of cumulative effects. They were also very powerful to characterize the role of the cumulative impact on ecosystem functioning. These results demonstrate the capacity of ENA indices to describe and understand cumulative effects at the ecosystem scale. Using a sensitivity analysis approach, this study shows that ENA indices could be viable tools for managers. To help them in their tasks, the next step could be to link ecosystem services to ENA indices for a more practical use.

Résumé: The spectre of increasing impacts on exploited fish stocks in consequence of warmer climate conditions has become a major concern over the last decades. It is now imperative to improve the way we project the effects of future climate warming on fisheries. While estimating future climate-induced changes in fish distribution is an important contribution to sustainable resource management, the impacts on European small pelagic fish-representing over 50% of the landings in the Mediterranean and Black Sea between 2000 and 2013-are yet largely understudied. Here, we investigated potential changes in the spatial distribution of seven of the most harvested small pelagic fish species in Europe under several climate change scenarios over the 21st century. For each species, we considered eight Species Distribution Models (SDMs), five General Circulation Models (GCMs) and three emission scenarios (the IPCC Representative Concentration Pathways; RCPs). Under all scenarios, our results revealed that the environmental suitability for most of the seven species may strongly decrease in the Mediterranean and western North Sea while increasing in the Black and Baltic Seas. This potential northward range expansion of species is supported by a strong convergence among projections and a low variability between RCPs. Under the most pessimistic scenario (RCP8.5), climate-related local extinctions were expected in the south-eastern Mediterranean basin. Our results highlight that a multi-SDM, multi-GCM, multi-RCP approach is needed to produce more robust ecological scenarios of changes in exploited fish stocks in order to better anticipate the economic and social consequences of global climate change.

Résumé: The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed toward small fragments, we evaluated the effect of removing short DNA fragments via size selection and ethanol reconcentration using eDNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by eDNA and environmental RNA (eRNA) co-extracted from similar to 2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using eRNA. With ribosomal loci, eRNA, while resolving similar spatial patterns than co-extracted eDNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to overabundance of rRNA and RNA release. With the mitochondrial locus, eRNA detected lower metazoan richness and resolved fewer spatial patterns than co-extracted eDNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (>= 10 g) for accurately surveying eukaryotic diversity. We conclude that eDNA should be favored over eRNA for logistically realistic, repeatable, and reliable surveys and confirm that large sediment samples (>= 10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.

Résumé: In the context of parentage assignment using genomic markers, key issues are genotyping errors and an absence of parent genotypes because of sampling, traceability or genotyping problems. Most likelihood-based parentage assignment software programs require a priori estimates of genotyping errors and the proportion of missing parents to set up meaningful assignment decision rules. We present here the R package APIS, which can assign offspring to their parents without any prior information other than the offspring and parental genotypes, and a user-defined, acceptable error rate among assigned offspring. Assignment decision rules use the distributions of average Mendelian transmission probabilities, which enable estimates of the proportion of offspring with missing parental genotypes. APIS has been compared to other software (CERVUS, VITASSIGN), on a real European seabass (Dicentrarchus labrax) single nucleotide polymorphism data set. The type I error rate (false positives) was lower with APIS than with other software, especially when parental genotypes were missing, but the true positive rate was also lower, except when the theoretical exclusion power reached 0.99999. In general, APIS provided assignments that satisfied the user-set acceptable error rate of 1% or 5%, even when tested on simulated data with high genotyping error rates (1% or 3%) and up to 50% missing sires. Because it uses the observed distribution of Mendelian transmission probabilities, APIS is best suited to assigning parentage when numerous offspring (>200) are genotyped. We have demonstrated that APIS is an easy-to-use and reliable software for parentage assignment, even when up to 50% of sires are missing.

Résumé: Ecosystem-based management of fisheries aims to allow sustainable use of fished stocks while keeping impacts upon ecosystems within safe ecological limits. Both the FAO Code of Conduct for Responsible Fisheries and the Aichi Biodiversity Targets promote these aims. We evaluate implementation of ecosystem-based management in six case-study fisheries in which potential indirect impacts upon bird or mammal predators of fished stocks are well publicized and well studied. In particular, we consider the components needed to enable management strategies to respond to information from predator monitoring. Although such information is available in all case-studies, only one has a reference point defining safe ecological limits for predators and none has a method to adjust fishing activities in response to estimates of the state of the predator population. Reference points for predators have been developed outside the fisheries management context, but adoption by fisheries managers is hindered a lack of clarity about management objectives and uncertainty about how fishing affects predator dynamics. This also hinders the development of adjustment methods because these generally require information on the state of ecosystem variables relative to reference points. Nonetheless, most of the case-studies include precautionary measures to limit impacts on predators. These measures are not used tactically and therefore risk excessive restrictions on sustainable use. Adoption of predator reference points to inform tactical adjustment of precautionary measures would be an appropriate next step towards ecosystem-based management.

Résumé: By relating observed changes to the pressures suffered, the Marine Strategy Framework Directive intends to better control the factors of environmental degradation and to manage their consequences in European waters. Several descriptors are defined within the framework of the MFSD and in particular descriptor 1 relating to the biological diversity of the seabed and descriptor 6 relating to the seabed integrity (i.e. the quality of their structures and functions). For each descriptor, indicators and threshold values must be defined and a novel conceptual approach to define and detect seabed integrity thresholds is proposed here. Bottom trawling being the main source of shelf continental disturbance, it is important to evaluate its impact on benthic habitat. The goal of this study is to propose a methodology to determine “Good Ecological Status” threshold values for each habitat type present in three contrasted MFSD sub-region (North Sea, English Channel and Mediterranean Sea). Trawling impacts are dependent of the spatial and temporal distribution of the fishing effort, fishing gears, intensity of natural disturbances and habitat types. Benthic community structures present in these areas were studied using by-catch non-commercial benthic invertebrates data collected during French scientific bottom trawl surveys. Swept area ratios derived from VMS data were used to quantify the intensity of fishery induced abrasion on the seabed. A modeling approach was used to determine abrasion threshold values on each EUNIS level 4 habitat. The values, beyond which trawling has an adverse effect on benthic communities, have been determined for each habitat. This made it possible to assess and map the ecological status of each of the habitats and to determine the percentage of each habitat impacted by trawling. The method proposed here to evaluate the impact of trawling on benthic communities highlighted that the vast majority of the investigated sub-regions were adversely impacted or lost as a result of seabed impacting trawling.

Résumé: Shellfish aquaculture has the potential to alter benthic assemblage composition with subsequent modifications of ecosystem functioning. While the impacts of aquaculture on the taxonomic structure of macro- and — to a lesser extent — meiofauna, have been widely studied, the functional changes of these communities remain relatively unknown. The recent development of biological trait analysis (BTA) has made it possible to produce information about how ecosystem functioning could change across specific terrestrial or aquatic system. In the present study, we used a BTA in parallel with standard taxonomic analysis to evaluate how well the two approaches detected the potential influence of juvenile oyster culture on the benthic community in the French Mediterranean Thau Lagoon. Two sites were sampled under farm structures and compared with two reference sites beyond the influence of farming. This study is the first detailed parallel description of macro- and meiofauna (nematodes). A total of 118 and 41 taxa were determined for macrofauna and nematodes respectively. Some taxa were more abundant or exclusively observed under farm structures such as Chaetozone gibber and Neanthes acuminata for macrofauna and Daptonema fallax and Anticoma eberthi for nematodes. Overall, our results indicate that biological traits and functional indices both detected the impact of shellfish culture on benthic assemblages, whereas macrofauna taxonomic indices revealed no difference. Our results thus suggest that trophic and ecological groups are particularly good indicators of the effects of shellfish culture. This study confirms the relevance of the functional approach, and more generally of multi-index approaches, to detect the influence of aquaculture on benthic communities. Further work is required to test multiple traits in different regions and under different systems, but this work paves the way for environmental impact assessment using a trait based approach.

Résumé: Circulation patterns in the North Atlantic Ocean have changed and re-organized multiple times over millions of years, influencing the biodiversity, distribution, and connectivity patterns of deep-sea species and ecosystems. In this study, we review the effects of the water mass properties (temperature, salinity, food supply, carbonate chemistry, and oxygen) on deep-sea benthic megafauna (from species to community level) and discussed in future scenarios of climate change. We focus on the key oceanic controls on deep-sea megafauna biodiversity and biogeography patterns. We place particular attention on cold-water corals and sponges, as these are ecosystem-engineering organisms that constitute vulnerable marine ecosystems (VME) with high associated biodiversity. Besides documenting the current state of the knowledge on this topic, a future scenario for water mass properties in the deep North Atlantic basin was predicted. The pace and severity of climate change in the deep-sea will vary across regions. However, predicted water mass properties showed that all regions in the North Atlantic will be exposed to multiple stressors by 2100, experiencing at least one critical change in water temperature (+2 degrees C), organic carbon fluxes (reduced up to 50%), ocean acidification (pH reduced up to 0.3), aragonite saturation horizon (shoaling above 1000 m) and/or reduction in dissolved oxygen (> 5%). The northernmost regions of the North Atlantic will suffer the greatest impacts. Warmer and more acidic oceans will drastically reduce the suitable habitat for ecosystem-engineers, with severe consequences such as declines in population densities, even compromising their long-term survival, loss of biodiversity and reduced biogeographic distribution that might compromise connectivity at large scales. These effects can be aggravated by reductions in carbon fluxes, particularly in areas where food availability is already limited. Declines in benthic biomass and biodiversity will diminish ecosystem services such as habitat provision, nutrient cycling, etc. This study shows that the deep-sea VME affected by contemporary anthropogenic impacts and with the ongoing climate change impacts are unlikely to withstand additional pressures from more intrusive human activities. This study serves also as a warning to protect these ecosystems through regulations and by tempering the ongoing socio-political drivers for increasing exploitation of marine resources.

Résumé: In Europe, implementation of sustainable fisheries management has been reinforced in the latest common fisheries policy, and presently marine fish stocks are mostly managed through assessment of their exploitation and ecological status compared to reference points such as Maximum Sustainable Yield (MSY). However, MSY and its associated fishing mortality rate F-MSY are sensitive to both stock characteristics and environment conditions. In parallel, climate change impacts are increasingly affecting fish stocks directly and indirectly but might also change the exploitation reference points and the associated level of catch. Here we explored the variability of MSY reference points under climate change by using a multi-species model applied to the Eastern English Channel, a highly exploited semi-continental sea. The spatial individual-based OSMOSE explicitly represents the entire fish life cycle of 14 species interacting through size-based opportunistic predation. The model was first parameterized and run to fit the historical situation (2000-2009) and then used to assess the ecosystem state for the 2050-2059 period, using two contrasting climate change scenarios (RCP 4.5 and RCP 8.5). For each condition, a monospecific MSY estimation routine was performed by varying species fishing mortality independently and allowed estimation of reference points for each species. The F-MSY estimated with OSMOSE were mostly in accordance with available values derived from stock assessment and used for fishing advice. Evolution of reference points with climate change was compared across species and highlighted that overexploited cold-water species are likely to have both MSY and F-MSY declining with climate warming. Considering all species together, MSY under RCP scenarios was expected to be higher than historical MSY for half of them, with no clear link with species temperature preferences, exploitation status or trophic level, but in relation with expected change of species biomass under climate change. By contrast, for 80% of cases F-MSY projections showed consistent decreasing pattern as climate conditions changed from historical to RCP scenarios in the Eastern English Channel. This result constitutes a risk for fisheries management, and anticipation of climate change impacts on fish community would require targeting a smaller fishing mortality than F-MSY to ensure sustainable exploitation of marine stocks.

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: Seafloor litter has been studied both on the continental shelves (by trawling during 24 years) and in canyons (by ROV) of the French Mediterranean sea Water (FMW). On the continental shelf, mean densities range from 49.63 to 289.01 items/km(2). The most abundant categories were plastic, glass/ceramics, metals and textiles. Trend analysis shows a significant increase in plastic quantities during the study period. Plastics accumulate at all depths, with heavier items being found in deeper areas, while the continental slope-break appears as a clean area. The spatial distribution of litter revealed the influence of geomorphologic factors, anthropic activities, shipping route, river inputs. All the canyons are affected by debris but coastal canyons (Ligurian Sea and Corsica) were more impacted than offshore canyons in the Gulf of Lion. The FMW appears to be highly polluted with regard to values found in other areas, but lower than those observed in the Eastern Mediterranean.

Résumé: Trait-based ecology strives to better understand how species, through their bio-ecological traits, respond to environmental changes, and influence ecosystem functioning. Identifying which traits are most responsive to environmental changes can provide insight for understanding community structuring and developing sustainable management practices. However, misinterpretations are possible, because standard statistical methods (e.g., principal component analysis and linear regression) for identifying and ranking the responses of different traits to environmental changes ignore interspecific differences. Here, using both artificial data and real-world examples from marine fish communities, we show how considering species-specific responses can lead to drastically different results than standard community-level methods. By demonstrating the potential impacts of interspecific differences on trait dynamics, we illuminate a major, yet rarely discussed issue, highlighting how analytical misinterpretations can confound our basic understanding of trait responses, which could have important consequences for biodiversity conservation.

Résumé: Understanding how inter-specific variation in functional traits affects native and non-native species responses to stream disturbances, is necessary to inform management strategies, providing tools for biomonitoring, conservation and restoration. This study used a functional trait approach to characterise the responses of macrophyte assemblages to reach-scale disturbances (measured by lack of riparian shading, altered hydromorphology and eutrophication), from 97 wadeable stream sites in an agriculturally impacted region of New Zealand. To determine whether macrophyte assemblages differed due to disturbances, we examined multidimensional assemblage functional structure in relation to eleven functional traits and further related two functional diversity indices (entropy and originality) to disturbances. Macrophyte assemblages showed distinct patterns in response to disturbances, with riparian shading and hydromorphological conditions being the strongest variables shaping macrophyte functional structure. In the multidimensional space, most of the non-native species were associatedwith disturbed conditions. These species had traits allowing faster colonisation rates (higher number of reproductive organs and larger root-rhizome system) and superior competitive abilities for resources (tall and dense canopy, heterophylly and greater preferences for light and nitrogen). In addition, lack of riparian shading increased the abundance of functionally distinct species (i.e. entropy), and eutrophication resulted in the growth of functionally unique species (i.e. originality). We demonstrated that stream reach-scale habitat disturbances were associated to a dominance of more productive species, equating to a greater abundance of non-native species. This, can result in a displacement of native species, habitat alterations, and changes to higher trophic level assemblages. Our results suggests that reachscale management efforts such as the conservation and restoration of riparian vegetation that provides substantial shading and hydromorphologically diverse in-stream habitat, would have beneficial direct and indirect effects on ecosystem functioning, and contribute to the mitigation of land-use impacts. (C) 2018 Published by Elsevier B.V.

Résumé: Marine litter is one of the main sources of anthropogenic pollution in the marine ecosystem, with plastic representing a global threat. This paper aims to assess the spatial distribution of plastic macro-litter on the seafloor, identifying accumulation hotspots at a northern Mediterranean scale. Density indices (items km(-2)) from the MEDITS trawl surveys (years 2013-2015) were modelled by generalized additive models using a Delta-type approach and several covariates: latitude, longitude, depth, seafloor slope, surface oceanographic currents and distances from main ports. To set thresholds for the identification of accumulation areas, the percentiles (85th, 90th and 95th) of the plastic spatial density distribution were computed on the raster data. In the northern Mediterranean marine macro-litter was widespread (90.13% of the 1279 surveyed stations), with plastic by far the most recurrent category. The prediction map of the plastic density highlighted accumulation areas (85th, 90th and 95th percentiles of the distribution, respectively, corresponding to 147, 196 and 316 items km(-2)) in the Gulf of Lions, eastern Corsica. the eastern Adriatic Sea, the Argo-Saronic region and waters around southern Cyprus. Maximum densities were predicted in correspondence to the shallower depths and in proximity to populated areas (distance from the ports). Surface currents and local water circulation with cyclonic and anticyclonic eddies were identified as drivers likely facilitating the sinking to the bottoms of floating debris

Résumé: Bivalve production is an important aquaculture activity worldwide, but few environmental assessments have focused on it. In particular, bivalves' ability to extract nutrients from the environment by intensely filtering water and producing a shell must be considered in the environmental assessment. LCA of blue mussel bouchot culture (grown out on wood pilings) in Mont Saint-Michel Bay (France) was performed to identify its impact hotspots. The chemical composition of mussel flesh and shell was analyzed to accurately identify potential positive effects on eutrophication and climate change. The fate of mussel shells after consumption was also considered. Its potential as a carbon-sink is influenced by assumptions made about the carbon sequestration in wooden bouchots and in the mussel shell. The fate of the shells which depends on management of discarded mussels and household waste plays also an important role. Its carbon-sink potential barely compensates the climate change impact induced by the use of fuel used for on-site transportation. The export of N and P in mussel flesh slightly decreases potential eutrophication. Environmental impacts of blue mussel culture are determined by the location of production and mussel yields, which are influenced by marine currents and the distance to on-shore technical base. Bouchot mussel culture has low environmental impacts compared to livestock systems, but the overall environmental performances depend on farming practices and the amount of fuel used. Changes to the surrounding ecosystem induced by high mussel density must be considered in future LCA studies.

Résumé: Life cycle assessment (LCA) is the normed and international framework for assessing the environmental impacts of most human activities. LCA is commonly used to assess various aspects of fisheries but is only at the onset for estimating impacts of fish removal. This study proposes original characterization factors (CFs) to quantify impacts on biotic resources using the mass of fish caught. This mid-point assessment occurs in impact pathways leading to natural resources, one of the three areas of protection in LCA, and thus fisheries can be compared according to the depleted stock fraction. CFs are defined by the marginal approach applied to the Schaefer model, representing the dynamics of the stocks. They combine catches, current biomass and maximum intrinsic growth rates, determined from the application of the CMSY algorithm (Froese etal. (2017), Fish Fish, 18, 506) with FAO and FishBase data. A multistock CF is also proposed and used for multispecies-stocks. CFs for the 4,993 stocks defined from global FAO areas are obtained and sorted according to the robustness of the model hypotheses. CF values among stocks generally tend to decrease when fish catches increase because high catches are generally associated with abundant stocks. Multispecies-stocks CFs for the northeast Atlantic Ocean are compared to ICES-based CFs and are reliable for the main fished stocks. With this simple and generic structure, this operational fish resource depletion potential could be extended to other biotic resources.

Résumé: Determining whether many functionally complementary species or only a subset of key species are necessary to maintain ecosystem functioning and services is a critical question in community ecology and biodiversity conservation. Identifying such key species remains challenging, especially in the tropics where many species co-occur and can potentially support the same or different processes. Here, we developed a new community-wide scan CWS) approach, analogous to the genome-wide scan, to identify fish species that significantly contribute, beyond the socio-environmental and species richness effects, to the biomass and coral cover on Indo-Pacific reefs. We found that only a limited set of species (51 out of approx. 400, = approx. 13%), belonging to various functional groups and evolutionary lineages, are strongly and positively associated with fish biomass and live coral cover. Many of these species have not previously been identified as functionally important, and thus may be involved in unknown, yet important, biological mechanisms that help sustain healthy and productive coral reefs. CWS has the potential to reveal species that are key to ecosystem functioning and services and to guide management strategies as well as new experiments to decipher underlying causal ecological processes.

Résumé: In the highly productive Northern Humboldt Current System, 3 seabird species, the Guanay cormorant Phalacrocorax bougainvillii, the Peruvian booby Sula variegata and the Peruvian pelican Pelecanus thagus, commence breeding in austral spring, coinciding with the lowest availability of their prey, the Peruvian anchovy Engraulis ringens. This strategy ensures the matching of increased prey availability when young achieve independence in summer. This pattern was observed during the last decade when anchovy was abundant. However, over the last century, the abundance of anchovy has varied widely due to contrasting interdecadal regimes in oceanographic conditions and fishing activity. We hypothesized that these regime shifts affected the abundance and availability of prey and may have conditioned the breeding seasonality of seabirds. We examined the timing and magnitude of the onset of breeding using dynamic occupancy models and related these parameters to the seasonality of oceanographic conditions, abundance of anchovy and fishing pressure. During a regime of lower anchovy abundance (1977-1990), cormorants showed the highest flexibility, adjusting the timing of breeding from spring to winter and skipping reproduction in the worst conditions. Boobies showed the lowest flexibility, maintaining the same magnitude and timing of onset of breeding in spring. Pelicans showed intermediate flexibility, foregoing breeding during the worst conditions, but maintaining the onset of breeding in spring. The 3 species used sea surface temperature as a cue for the initiation of breeding. Furthermore, given their better diving abilities, cormorants could monitor prey availability changes associated with the reversion in the seasonality of the oxycline depth.

Résumé: The effects of environmental change on biodiversity are still poorly understood. In particular, the consequences of shifts in species composition for marine ecosystem function are largely unknown. Here we assess the loss of functional diversity, i.e. the range of species biological traits, in benthic marine communities exposed to ocean acidification (OA) by using natural CO2 vent systems. We found that functional richness is greatly reduced with acidification, and that functional loss is more pronounced than the corresponding decrease in taxonomic diversity. In acidified conditions, most organisms accounted for a few functional entities (i.e. unique combination of functional traits), resulting in low functional redundancy. These results suggest that functional richness is not buffered by functional redundancy under OA, even in highly diverse assemblages, such as rocky benthic communities.

Résumé: Marine reserves are viewed as flagship tools to protect exploited species and to contribute to the effective management of coastal fisheries. Yet, the extent to which marine reserves are globally interconnected and able to effectively seed areas, where fisheries are most critical for food and livelihood security is largely unknown. Using a hydrodynamic model of larval dispersal, we predict that most marine reserves are not interconnected by currents and that their potential benefits to fishing areas are presently limited, since countries with high dependency on coastal fisheries receive very little larval supply from marine reserves. This global mismatch could be reversed, however, by placing new marine reserves in areas sufficiently remote to minimize social and economic costs but sufficiently connected through sea currents to seed the most exploited fisheries and endangered ecosystems.

Résumé: 1. Seabirds and pinnipeds are vulnerable to reductions in prey availability, especially during the breeding season when spatial constraints limit their adaptive capacity. There are growing concerns about the effects of fisheries on prey availability in regions where large commercial fisheries target forage fish. 2. For breeding seabirds and pinnipeds, prey availability depends on a combination of abundance, accessibility, patchiness and distance from the colony. An understanding of the aspects of prey availability that determine foraging success is essential for the design of effective management responses. 3. We used a mechanistic individual-based foraging model based on observed data for two sea-bird species, the Peruvian Booby Sula variegata and Guanay Cormorant Phalacrocorax bougainvilliorum, to simulate the foraging patterns of seabirds feeding on schooling fish. We ran the model over simulated prey fields representing eight possible combinations of high or low prey abundance, shallow or deep prey, and broadly distributed or spatially concentrated prey. 4. The results highlight the importance of the accessibility of prey. Depth distribution was the primary factor determining modelled foraging success for both species, followed by abundance, and then spatial configuration. 5. Synthesis and applications. The individual-based foraging model provides a spatially explicit framework for assessing the effects of fisheries on the foraging success of seabirds and other central place foragers, and for evaluating the potential effectiveness of marine-protected areas and other fisheries management strategies for safeguarding central place foragers in dynamic ecosystems. Our analysis indicates that broad-scale fisheries management strategies that maintain forage fish above critical biomass levels are essential, but may need to be supplemented by targeted actions, such as time-area closures, when environmental conditions lead to low prey abundance or reduce prey accessibility for seabirds or pinnipeds of conservation concern. The individual-based foraging model is adaptable and could be reconfigured for application to other species and systems.

Résumé: The increase of anthropogenic pressures on the marine environment together with the necessity of a sustainable management of marine living resources have underlined the need to map and model coastal environments, particularly for the purposes of spatial planning and for the implementation of integrated ecosystem-based management approach. The present study compares outputs of a process-driven benthic habitat sensitivity (PDS) model to the structure, composition and distribution of benthic invertebrates in the Eastern English Channel and southern part of the North Sea. Trawl disturbance indicators (TDI) computed from species biological traits and benthic community composition were produced from samples collected with a bottom trawl. The TDI was found to be highly correlated to the PDS further validating the latter's purpose to identify natural process-driven pattern of sensitivity. PDS was found to reflect an environmental potential that may no longer be fully observable in the field and difference with in situ biological observations could be partially explained by the spatial distribution of fishery pressure on the seafloor. The management implication of these findings are discussed and we suggest that, used in conjunction with TDI approaches, PDS may help monitor management effort by evaluating the difference between the current state and the presumed optimal environmental status of marine benthic habitats.

Résumé: Productivity and Susceptibility Analysis (PSA) is a methodology for evaluating the vulnerability of a stock based on its biological productivity and susceptibility to fishing. In this study, we evaluated the vulnerability of 60 stocks of tuna, billfishes and other teleosts caught by the tuna longline fleets operating in the South Atlantic and Indian Ocean using a semi-quantitative PSA. We (a) evaluated the vulnerability of the species in the study areas; (b) compared the vulnerability of target and non-target species and oceans; (c) analyzed the sensitivity of data entry; and (d) compared the results of the PSA to other fully quantitative assessment methods. Istiophoridae exhibited the highest scores for vulnerability. The top 10 species at risk were: Atlantic Istiophorus albicans; Indian Ocean Istiompax indica; Atlantic Makaira nigricans and Thunnus alalunga; Indian Ocean Xiphias gladius; Atlantic T. albacares, Gempylus serpens, Ranzania laevis and X. gladius; and Indian Ocean T. alalunga. All species considered at high risk were targeted or were commercialized bycatch, except for the Atlantic G. serpens and R. laevis which.were discarded, and may be considered as a false positive. Those species and others at high risk should be prioritized for further assessment and/or data collection. Most species at moderate risk were bycatch species kept for sale. Conversely, species classified at low risk were mostly discarded. Overall, species at high risk were overfished and/or subjected to overfishing. Moreover, all species considered to be within extinction risk (Critically Endangered, Endangered and Vulnerable) were in the high risk category. The good concordance between approaches corroborates the results of our analysis. PSA is not a replacement for traditional stock assessments, where a stock is assessed at regular intervals to provide management advice. It is of importance, however, where there is uncertainty about catches and life history parameters, since it can identify species at risk, and where management action and data collection is required, e.g. for many species at high and most at moderate risk in the South Atlantic and Indian oceans.

Résumé: IndiSeas (“Indicators for the Seas”) is a collaborative international working group that was established in 2005 to evaluate the status of exploited marine ecosystems using a suite of indicators in a comparative framework. An initial shortlist of seven ecological indicators was selected to quantify the effects of fishing on the broader ecosystem using several criteria (i.e., ecological meaning, sensitivity to fishing, data availability, management objectives and public awareness). The suite comprised: (i) the inverse coefficient of variation of total biomass of surveyed species, (ii) mean fish length in the surveyed community, (iii) mean maximum life span of surveyed fish species, (iv) proportion of predatory fish in the surveyed community, (v) proportion of under and moderately exploited stocks, (vi) total biomass of surveyed species, and (vii) mean trophic level of the landed catch. In line with the Nagoya Strategic Plan of the Convention on Biological Diversity (2011–2020), we extended this suite to emphasize the broader biodiversity and conservation risks in exploited marine ecosystems. We selected a subset of indicators from a list of empirically based candidate biodiversity indicators initially established based on ecological significance to complement the original IndiSeas indicators. The additional selected indicators were: (viii) mean intrinsic vulnerability index of the fish landed catch, (ix) proportion of non-declining exploited species in the surveyed community, (x) catch-based marine trophic index, and (xi) mean trophic level of the surveyed community. Despite the lack of data in some ecosystems, we also selected (xii) mean trophic level of the modelled community, and (xiii) proportion of discards in the fishery as extra indicators. These additional indicators were examined, along with the initial set of IndiSeas ecological indicators, to evaluate whether adding new biodiversity indicators provided useful additional information to refine our understanding of the status evaluation of 29 exploited marine ecosystems. We used state and trend analyses, and we performed correlation, redundancy and multivariate tests. Existing developments in ecosystem-based fisheries management have largely focused on exploited species. Our study, using mostly fisheries independent survey-based indicators, highlights that biodiversity and conservation-based indicators are complementary to ecological indicators of fishing pressure. Thus, they should be used to provide additional information to evaluate the overall impact of fishing on exploited marine ecosystems.

Résumé: AimBiological invasions are major contributors to global change and native biodiversity decline. However, they are overlooked in marine conservation plans. Here, we examine for the first time the extent to which marine conservation planning research has addressed (or ignored) biological invasions. Furthermore, we explore the change of spatial priorities in conservation plans when different approaches are used to incorporate the presence and impacts of invasive species. LocationGlobal analysis with a focus on the Mediterranean Sea region. MethodsWe conducted a systematic literature review consisting of three steps: (1) article selection using a search engine, (2) abstract screening and (3) review of pertinent articles, which were identified in the second step. The information extracted included the scale and geographical location of each case study as well as the approach followed regarding invasive species. We also applied the software Marxan to produce and compare conservation plans for the Mediterranean Sea that either protect, or avoid areas impacted by invasives, or ignore the issue. One case study focused on the protection of critical habitats, and the other on endemic fish species. ResultsWe found that of 119 papers on marine spatial plans in specific biogeographic regions, only three (2.5%) explicitly took into account invasive species. When comparing the different conservation plans for each case study, we found that the majority of selected sites for protection (ca. 80%) changed in the critical habitat case study, while this proportion was lower but substantial (27%) in the endemic fish species case study. Main conclusionsBiological invasions are being widely disregarded when planning for conservation in the marine environment across local to global scales. More explicit consideration of biological invasions can significantly alter spatial conservation priorities. Future conservation plans should explicitly account for biological invasions to optimize the selection of marine protected areas.

Résumé: The identification and mitigation of adverse effects of the bycatch of tuna longline fishery have been mainly developed and implemented for seabirds, sharks and turtles and, the knowledge on teleost bycatch for this fishery, remains very poor. This paper contributes to a comprehensive assessment of life history traits and fishery attributes of target and bycatch species caught by the tuna longline fishery in the South Atlantic and Indian Oceans. Data was compiled on seven life history traits and three fishery attributes for 33 and 27 teleost stocks caught by longliners in South Atlantic and Indian Oceans, respectively. In addition, each species was assigned into four categories describing the fate of the catch: target species for commercial use, bycatch species kept for consumption, bycatch species kept for commercial use and discarded bycatch. Life history traits and fishery attributes did not differ between oceans. However, non-target but commercialized species were smaller in the Atlantic Ocean. Teleosts caught by the tuna longline fishery was segregated into three main groups: (1) the fast growing species represented mainly by dolphinfishes (Coryphaena hippurus and C. equisellis), skipjack tuna (Katsuwonus pelamis), kawakawa (Euthynnus affinis), bullet tuna (Auxis rochei), snoek (Thyrsites atun) and blackfin tuna (Thunnus atlanticus); (2) target tunas and most other bycatch species which were part of an intermediate group and (3) billfishes including swordfish representing the large and slow growing species with moderate to high market values and unknown or highly uncertain stock status. Investment in some key life history traits (such as growth coefficient) and the development of quantitative or semi-quantitative approaches (stock assessment and Ecological Risk Assessment) should be priorized as precautionary management measures for these species.

Résumé: Understanding how marine predators interact is a scientific challenge. In marine ecosystems, segregation in feeding habits has been largely described as a common mechanism to allow the coexistence of several competing marine predators. However, little is known about the feeding ecology of most species of chondrichthyans, which play a pivotal role in the structure of marine food webs worldwide. In this study, we examined the trophic ecology of 3 relatively abundant chondrichthyans coexisting in the Mediterranean Sea: the blackmouth catshark Galeus melastomus, the velvet belly lanternshark Etmopterus spinax and the rabbit fish Chimaera monstrosa. To examine their trophic ecology and interspecific differences in food habits, we combined the analysis of stomach content and stable isotopes. Our results highlighted a trophic segregation between C. monstrosa and the other 2 species. G. melastomus showed a diet composed mainly of cephalopods, while E. spinax preyed mainly on shrimps and C. monstrosa on crabs. Interspecific differences in the trophic niche were likely due to different feeding capabilities and body size. Each species showed different isotopic niche space and trophic level. Specifically, C. monstrosa showed a higher trophic level than E. spinax and G. melastomus. The high trophic levels of the 3 species highlighted their important role as predators in the marine food web. Our results illustrate the utility of using complementary approaches that provide information about the feeding behaviour at short (stomach content) and long-term scales (stable isotopes), which could allow more efficient monitoring of marine food-web changes in the study area.

Résumé: Thirty years of progress using the Ecopath with Ecosim (EwE) approach in different fields such as ecosystem impacts of fishing and climate change, emergent ecosystem dynamics, ecosystem-based management, and marine conservation and spatial planning were showcased November 2014 at the conference “Ecopath 30 years-modelling dynamic ecosystems: beyond boundaries with EwE”. Exciting new developments include temporal-spatial and end-to-end modelling, as well as novel applications to environmental impact analyses, in both aquatic and terrestrial domains. A wide range of plug-ins have been added to extend the diagnostic capabilities of EwE, and the scientific community is applying EwE to a diversified range of topics besides fishing impact assessments, such as the development of scientific advice for management, the analysis of conservation issues, and the evaluation of cumulative impacts of environmental and human activities in marine food webs (including habitat modification and the invasion of alien species). Especially promising is the new potential to include the EwE model in integrated assessments with other models such as those related to climate change research. However, there are still many challenges, including the communication of scientific results in management procedures. In addition, other important scientific issues are how to improve model result validation and perform model quality control. During the conference, the Ecopath International Research and Development Consortium was presented as a way for the EwE user community to become involved in the long-term sustainability of the EwE approach. Overall, exciting times are facing the ecosystem modelling scientific community, and as illustrated by the conference: synergistic cooperation is the future path for the EwE approach.

Résumé: The EcoTroph modeling approach was applied to five Mediterranean marine ecosystems to characterize their food webs and investigate their responses to several simulated fishing scenarios. First, EcoTroph was used to synthesize the outputs of five pre-existing heterogeneous Ecopath models in a common framework, and thus to compare different ecosystems through their trophic spectra of biomass, catch, and fishing mortalities. This approach contributes to our understanding of ecosystem functioning, from both ecological and fisheries perspectives. Then, we assessed the sensitivity of each ecosystem to fishery, using EcoTroph simulations. For the five ecosystems considered, we simulated the effects of increasing or decreasing fishing mortalities on both the biomass and the catch per trophic class. Our results emphasize that the Mediterranean Sea is strongly affected by the depletion of high trophic level organisms. Results also show that fisheries impacts, at the trophic level scale, differ between ecosystems according to their trophic structure and exploitation patterns. A top-down compensation effect is observed in some simulations where a fishing-induced decrease in the biomass of predators impacts their prey, leading to an increase in the biomass at lower trophic levels. The results of this comparative analysis highlight that ecosystems where top-down controls are observed are less sensitive to variations in fishing mortality in terms of total ecosystem biomass. This suggests that the magnitude of top-down control present in a system can affect its stability.

Résumé: The impact of human activities on marine environments is poorly addressed by the scope of life cycle impact assessment (LCIA). The aim of this study is to provide characterization factors to assess impacts of sea use such as fishing activities or seafloor destruction and transformation on the life support functions of marine ecosystems. The consensual framework of land use for ecosystem services damage potential assessment was applied, according to the recent United Nations Environment Programme-Society for Environmental Toxicology and Chemistry (UNEP-SETAC) guidelines, using the free net primary production as a quality index of life support functions. The impact of shading, biomass removal, seafloor destruction, and artificial habitat creation on the available quantity of organic biomass for the ecosystem functioning was quantified at the midpoint level with a common unit (kg of organic carbon equivalent). It included effects of human interventions on both the ecosystem production potential and the stock of biomass present within the ecosystem. Characterization factors (CF) for biomass removal vary from 0.1 kg(Ceq) kg(-1) for seaweed to 111.1 kg(Ceq) kg(-1) for tunas, bonitos, and billfishes. CF for seafloor destruction range from 0.164 kg(Ceq) m(-2) for a temperate seagrass ecosystem to 0.342 kg(Ceq) m(-2) for an intertidal tropical rocky habitat. This study provides an operational method in order to compute sea use impact assessment.

Résumé: Bycatch of endangered marine turtles is a growing issue for the management of all fisheries, including the oceanic purse-seine fishery. The aim of this study was to assess the spatial and temporal variation in bycatch rates of these species in the entire European purse-seine fishery operating in the Atlantic and Indian oceans. The study was based on data collected through observer programs from 1995 to 2011. During that period, a total of 15 913 fishing sets were observed, including 6 515 on Drifting Fish Aggregating Devices (DFADs) and 9 398 on free swimming schools, representing a global coverage of 10.3% and 5.1% of the total fishing activity in the Atlantic and Indian Ocean, respectively. Moreover, from 2003 to 2011, 14 124 specific observations were carried out on DFADs to check turtle entanglement in the net covering DFADs. We found that the purse-seine fishery has a very low impact on marine turtles. We estimated that the annual number of individuals incidentally captured was 218 (SD = 150) and 250 (SD = 157) in the Atlantic and Indian Ocean, respectively, with more than 75% being released alive. The present study also investigated the impact of DFADs; which is considered a key conservation issue for this fishery. Drifting objects may play a key role in aggregating juveniles of marine turtles, implying the need for improving their construction to avoid entanglement (e.g. avoiding nets in the structure); however, based on our study it is not the main source of incidental captures of marine turtles in this fishery.

Résumé: This work has two major objectives: (1) to perform an attributional life cycle assessment (LCA) of a complex mean of production, the main Peruvian fishery targeting anchoveta (anchovy) and (2) to assess common assumptions regarding the exclusion of items from the life cycle inventory (LCI). Data were compiled for 136 vessels of the 661 units in the fleet. The functional unit was 1 t of fresh fish delivered by a steel vessel. Our approach consisted of four steps: (1) a stratified sampling scheme based on a typology of the fleet, (2) a large and very detailed inventory on small representative samples with very limited exclusion based on conventional LCI approaches, (3) an impact assessment on this detailed LCI, followed by a boundary-refining process consisting of retention of items that contributed to the first 95 % of total impacts and (4) increasing the initial sample with a limited number of items, according to the results of (3). The life cycle impact assessment (LCIA) method mostly used was ReCiPe v1.07 associated to the ecoinvent database. Some items that are usually ignored in an LCI's means of production have a significant impact. The use phase is the most important in terms of impacts (66 %), and within that phase, fuel consumption is the leading inventory item contributing to impacts (99 %). Provision of metals (with special attention to electric wiring which is often overlooked) during construction and maintenance, and of nylon for fishing nets, follows. The anchoveta fishery is shown to display the lowest fuel use intensity worldwide. Boundary setting is crucial to avoid underestimation of environmental impacts of complex means of production. The construction, maintenance and EOL stages of the life cycle of fishing vessels have here a substantial environmental impact. Recommendations can be made to decrease the environmental impact of the fleet.

Résumé: The Gulf of Lions ecosystemwas described using the Ecopath mass-balancemodel to characterise its structure and functioning and to examine the effects of themultispecific fisheries operating in this area. The model is composed of 40 compartments, including 1 group of seabirds, 2 groups of etaceans, 18 groups of fish, 12 groups of invertebrates, 5 groups of primary producers, detritus and discards. Input datawere based on several recurrent scientific surveys, two alternative datasets for fishing data, stock assessment outputs, stomach content analyses and published information. Results showed that the functional groups were organised into five trophic levels with the highest one represented by dolphins, anglerfish, Atlantic bluefin tuna, European hake and European conger. European pilchard and European anchovy dominated in terms of fish biomass and catch. Other fish with high biomass such as Atlantic mackerel and blue whiting were highly important in the food web. Seabirds, dolphins and cuttlefish–squids represented keystone species. Important coupled pelagic–demersal–benthic interactions were described. The 7 different fisheries analysed were operating at mean trophic levels situated between 2.6 for small artisanal boats, and 4.1 for purse seines (>24 m) targeting large pelagic fish, indicating an intensively exploited ecosystem. Large trawlers (24–40 m) had the highest impact on most of the groups considered; while purse seines (12–24 m) targeting small pelagic fish had the lowest impact. Preliminary results highlighted the importance of data sources for further ecosystem and fisheries analyses and management scenarios.

Résumé: Ecosystem engineers change abiotic conditions, community assembly and ecosystem functioning. Consequently, their loss may modify thresholds of ecosystem response to disturbance and undermine ecosystem stability. This study investigates how loss of the bioturbating lugworm Arenicola marina modifies the response to macroalgal detrital enrichment of sediment biogeochemical properties, microphytobenthos and macrofauna assemblages. A field manipulative experiment was done on an intertidal sandflat (Oosterschelde estuary, The Netherlands). Lugworms were deliberately excluded from 1x m sediment plots and different amounts of detrital Ulva (0, 200 or 600 g Wet Weight) were added twice. Sediment biogeochemistry changes were evaluated through benthic respiration, sediment organic carbon content and porewater inorganic carbon as well as detrital macroalgae remaining in the sediment one month after enrichment. Microalgal biomass and macrofauna composition were measured at the same time. Macroalgal carbon mineralization and transfer to the benthic consumers were also investigated during decomposition at low enrichment level (200 g WW). The interaction between lugworm exclusion and detrital enrichment did not modify sediment organic carbon or benthic respiration. Weak but significant changes were instead found for porewater inorganic carbon and microalgal biomass. Lugworm exclusion caused an increase of porewater carbon and a decrease of microalgal biomass, while detrital enrichment drove these values back to values typical of lugworm-dominated sediments. Lugworm exclusion also decreased the amount of macroalgae remaining into the sediment and accelerated detrital carbon mineralization and CO2 release to the water column. Eventually, the interaction between lugworm exclusion and detrital enrichment affected macrofauna abundance and diversity, which collapsed at high level of enrichment only when the lugworms were present. This study reveals that in nature the role of this ecosystem engineer may be variable and sometimes have no or even negative effects on stability, conversely to what it should be expected based on current research knowledge.

Résumé: We show that the EcoTroph model based on trophic spectra is an efficient tool to build ecosystem diagnoses of the impact of fishing. Using the Southern Benguela case study as a pretext, we present the first thorough application of the model to a real ecosystem. We thus review the structure and functioning of EcoTroph and we introduce the user to the steps that should be followed, showing the various possibilities of the model while underlining the most critical points of the modelling process. We show that EcoTroph provides an overview of the current exploitation level and target factors at the ecosystem scale, using two distinct trophic spectra to quantify the fishing targets and the fishing impact per trophic level. Then, we simulate changes in the fishing mortality, facilitating differential responses of two groups of species within the Southern Benguela ecosystem to be distinguished. More generally, we highlight various trends in a number of indicators of the ecosystem's state when increasing fishing mortality and we show that this ecosystem is moderately exploited, although predatory species are at their MSY. Finally, trophic spectra of the fishing effort multipliers EMSY and E(0.1) are proposed as tools for monitoring the ecosystem effects of fishing.

Résumé: Shannon, L. J., Coll, M., Yemane, D., Jouffre, D., Neira, S., Bertrand, A., Diaz, E., and Shin, Y-J. 2010. Comparing data-based indicators across upwelling and comparable systems for communicating ecosystem states and trends. – ICES Journal of Marine Science, 67: 807-832.