Résumé: Changes in ocean water temperature associated with global climate change are bound to enormously affect fish populations, with potential major economic consequences in the aquaculture and fisheries industries. A link between temperature fluctuations and changes in fish stress response is well established. In this study, we aimed to assess the effects of a short- (4 days) or a long-term (4 months) exposure to warm temperature in the stress physiology of European sea bass (Dicentrarchus labrax) larvae and juveniles. First, cortisol (i.e. the main stress hormone in fishes) analysis was used to confirm that a steady and short-term elevation of temperature acts as a physiological stressful event in these fish, and cortisol release is indeed above a metabolic increase linked to temperature. Moreover, our results verified that measurement of cortisol released into the water can be reliably employed as a non-invasive indicator of acute thermal stress in experimental conditions. Secondly, the different effects on the genetic cascade underlying the stress response between long-term low or high thermal treatments were evaluated at two larval development stages via candidate-gene and whole-transcriptome approaches. Interestingly, opposite expression for some key stress genes (nr3c1, nr3c2 and hsd11b2) were observed between developmental stages, highlighting the distinct adaptive mechanisms controlling the primary and secondary responses to a stressor. Surprising expression patterns for some understudied genes involved in the stress axis were also revealed, including crhr1, mc2r, mc5r, trh or trhr, which should be further explored. Finally, evaluation of cortisol content in scales was successfully used as a biomarker of chronic thermal stress, with 10x more cortisol in fish kept at 21 °C vs 16 °C after 4 months, supporting the gene expression results observed. The use of such a method as a proxy of long-term stress, unprecedented in the literature, holds a vast array of applications in further research, in particular, in the investigation of the impact of global warming on wild fish populations.

Résumé: Harmful Algal Blooms (HAB) events may have serious economic consequences for shellfish farmers. When toxic algae blooms threaten human health, public authorities may decide to shut down the farming business for a while, i.e. ranging from a few days to several weeks or months, according to the severity of risks. The impact of closures being temporally and spatially distributed, shellfish farmers can avoid the risky zones or develop adaptive strategies to mitigate the economic consequences and therefore reduce significantly their business sensitivity to HABs. A sequential approach by optimal matching analysis is applied to an original data set of shellfish area closure decrees between April 2004 and December 2018 in Southern Brittany and Pays de la Loire (France) to build a typology of 79 aquaculture zones affected by various HAB and microbiological hazards (ASP, DSP, Norovirus, E. Coli, oil spills). The hypothesis is that the degree of exposure to the HAB hazard assessed by zonal closures may not be correlated to the level of sensitivity revealed by the economic results of the shellfish farming industry which can develop avoidance strategies.

Résumé: The capacity of fishes to cope with environmental variation is considered to be a main determinant of their fitness and is partly determined by their stress physiology. By 2100, global ocean temperature is expected to rise by 1-4 degrees C, with potential consequences for stress physiology. Global warming is affecting animal populations worldwide through chronic temperature increases and an increase in the frequency of extreme heatwave events. As ectotherms, fishes are expected to be particularly vulnerable to global warming. Although little information is available about the effects of global warming on stress physiology in nature, multiple studies describe the consequences of temperature increases on stress physiology in controlled laboratory conditions, providing insight into what can be expected in the wild. Chronic temperature increase constitutes a physiological load that can alter the ability of fishes to cope with additional stressors, which might compromise their fitness. In addition, rapid temperature increases are known to induce acute stress responses in fishes and might be of ecological relevance in particular situations. This review summarizes knowledge about effects of temperature increases on the stress physiology of fishes and discusses these in the context of global warming.

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: The stable carbon (delta C-13) and nitrogen (delta N-15) isotope values of soft tissues of micronekton (crustaceans, squid, mesopelagic fish) and zooplankton were measured from organisms collected on the RV Antea at two seamounts located in the south-western Indian Ocean: La Perouse (summit depth similar to 60 m) and “MAD-Ridge” (thus named in this study; summit depth similar to 240 m). Surface particulate organic matter (POM-Surf) showed higher delta C-13 at the more productive MAD-Ridge than at the oligotrophic La Perouse seamount. Particulate organic matter and zooplankton were depleted in N-15 at La Pemuse pinnacle compared with MAD-Ridge. Gelatinous organisms and crustaceans occupied the lowest and intermediate tmphic levels (TL similar to 2 and 3 respectively) at both seamounts. Mesopelagic fish and smaller-sized squid sampled at both seamounts occupied TL similar to 3 to 4, whereas the large nektonic squid, Ommastrephes bartramii, collected at MAD-Ridge only, exhibited a TL of similar to 5. The delta N-15 values of common open-water mesopelagic taxa were strongly influenced by specimen size and feeding habits at both seamounts, with an increase in delta N-15 values with increasing size. Carnivorous fish species sampled exclusively over the seamounts' flanks and summits exhibited TL values of similar to 4, irrespective of their wide size ranges. The work could not demonstrate any differences in delta C-13 values of mesopelagic fish between the seamounts and the surrounding oceanic areas. The study segregated clusters of mesopelagic organisms according to their delta C-13 and delta N-15 values, with variations in stable isotope values reflecting a complex range of processes possibly linked to productivity as well as biological and ecological traits of the species (size and feeding mode).

Résumé: Pinnatoxins (PnTXs) are a group of emerging marine biotoxins produced by the benthic dinoflagellate Vulcanodinium rugosum, currently not regulated in Europe or in any other country in the world. In France, PnTXs were detected for the first time in 2011, in mussels from the Ingril lagoon (South of France, Mediterranean coast). Since then, analyses carried out in mussels from this lagoon have shown high concentrations of PnTXs for several months each year. PnTXs have also been detected, to a lesser extent, in mussels from other Mediterranean lagoons and on the Atlantic and Corsican coasts. In the French data, the main analog is PnTX G (low levels of PnTX A are also present in some samples). No cases of PnTXs poisoning in humans have been reported so far in France or anywhere else in the world. In mice, PnTXs induce acute neurotoxic effects, within a few minutes after oral administration. Clinical signs of toxicity include decreased mobility, paralysis of the hind legs, tremors, jumps and breathing difficulties leading to death by respiratory arrest at high doses. The French agency for food safety (ANSES) recently conducted a review of the state of knowledge related to PnTXs and V. rugosum. Based on (i) the clinical signs of toxicity in mice, (ii) the mode of action of PnTXs as nicotinic acetylcholine receptor competitive antagonists and (iii) knowledge on drugs and natural toxins with PnTX-related pharmacology, potential human symptoms have been extrapolated and proposed. In this work, a provisional acute benchmark value for PnTX G of 0.13 μg/kg bw per day has been derived from an oral acute toxicity study in mice. Based on this value and a large shellfish meat portion size of 400g, a concentration lower than 23 μg PnTX G/kg shellfish meat is not expected to result in adverse effects in humans. ANSES recommends taking into account PnTXs in the French official monitoring program for shellfish production and identified data gaps to refine health risk assessment.

Résumé: This work combines state-of-the-art methods (DNA metabarcoding) with classic approaches (visual stomach content characterization and stable isotope analyses of nitrogen (delta N-15) and carbon (delta C-13)) to investigate the trophic ecology of anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) at high taxonomic and spatial resolution in the Western Mediterranean Sea. Gut contents observed are in accordance with the dietary plasticity generally described for anchovy and sardine, suggesting a diet related to the opportunistic ingestion of available prey in a certain area and/or time. Genetic tools also showed modest inter-specific differences regarding ingested species. However, inter-specific and intra-specific differences in ingested prey frequencies and prey biomass reflected a latitudinal signal that could indicate a more effective predation on large prey like krill by anchovy versus sardine, as well as a generalized higher large prey ingestion by both species southwards. In fact, both species presented lower delta N-15 in the northernmost area. This latitudinal gradient indicates changes in the trophic ecology of anchovy and sardine that coincide with previously described better biological conditions for fish in the southern part of the study area as well as higher landings of both species in recent years.

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: Juvenile silky sharks (Carcharhinus falciformis)regularly associate with floating objects yet the reasons driving this behaviour remain uncertain. Understanding the proportion of time that silky sharks spend associated with floating objects is essential for assessing the impacts of the extensive use of fish aggregating devices (FADs) in the tropical tuna purse-seine fisheries, including increased probability of incidental capture and the potential of an ecological trap. Previous studies provided insight into the amount of time that silky sharks spent at an individual FAD but were unable to assess neither the time spent between two associations nor the proportion of time spent associated/unassociated. The percentage of time that juvenile silky sharks spend unassociated with floating objects was estimated through the analysis of horizontal movements of 26 silky sharks monitored with pop-up archival tags. Under the assumption that a high association rate with drifting FADs would align the trajectories of tracked sharks with ocean surface currents, a novel methodology is proposed, based on the comparison of shark trajectories with simulated trajectories of passively drifting particles derived using a Lagrangian model. Results revealed that silky shark trajectories were divergent from surface currents, and thus unassociated with FADs, for at least 30% of their time. The potential of the methodology and the results are discussed in the context of increasing FAD densities in the Indian Ocean.

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: Taxonomic composition, abundance and biological features of micronektonic fish were investigated using pelagic trawls conducted near and over the summits of three seamounts located in the western Indian Ocean (La Perouse, MAD-Ridge and Walters Shoal). Mesopelagic fish from three families accounted for 80% by number of the total catch (5714 specimens, 121 taxa), namely myctophids (59%), gonostomatids (12%) and sternoptychids (9%). Whereas the gonostomatid Sigmops elongatus was the most abundant species around La Perouse seamount, myctophids were the most diverse and dominant group by number in all three studied areas. Most myctophids were high-oceanic species, which included the numerically dominant Benthosema suborbitale, Ceratoscopelus warmingii, Diaphus perspicillatus, Hygophum hygomii, and Lobianchia dofleini. The few remaining myctophids (Diaphus suborbitalis being the most abundant) were pseudoceanic fish, highlighting the association with landmasses. The study adds one myctophid species new to the Indian Ocean (Diaphus bertelseni), and a second record in the literature of the recently described sternoptychid Argyripnus hulleyi.

Résumé: Pelagic sharks are an important bycatch in pelagic fisheries, especially for drifting longlines targeting swordfish. In the Cabo Verde Archipelago (tropical NE Atlantic), pelagic shark catches can reach a significant proportion of the total catches. Due to the increased concern on the status of pelagic shark species, this study was developed to enhance the current knowledge of those sharks in the Cabo Verde region in comparison to the adjacent areas, especially associated with European Union (EU) pelagic longline fishing activity. Stock status indicators for the two main species, blue shark (Prionace glauca) and shortfin mako (Isurus oxyrinchus), were developed, based on fisheries data from logbooks and onboard scientific observers, including analysis of size frequency distributions and standardized catch-per-unit-of-effort (CPUE) indexes over time. The standardized CPUEs have been stable or increasing for both species in the past 10 years, indicating no signs of local depletion. In terms of sizes, the blue shark catch is composed mainly of adults, which can be a sign of a stable population. On the contrary, the catch of shortfin mako is composed mainly of juveniles, which in conjunction of a decrease of mean size might be a cause of concern, highlighting possible overfishing on the species in the region. Thirty satellite tags, 25 archival miniPATs and 5 SPOT GPS, were deployed in the Cabo Verde Exclusive Economic Zone (EEZ), showing that those species are highly mobile. The biomass and size distributions were modeled with spatial and seasonal models (GAMs) identifying locations where juveniles are predominantly concentrated and that should be prioritized for conservation. This work presents new information on the status of pelagic sharks in the Cabo Verde region in the context of those highly migratory species, and can now be used to promote more sustainable fisheries in the region.

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: Understanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain much debated, as they relate to contrasting mechanisms of speciation that are not yet fully understood. In the European sea bass (Dicentrarchus labrax), the genomic regions involved in RI between Atlantic and Mediterranean lineages are enriched for anciently diverged alleles of unknown origin. Here, we used haplotype-resolved whole-genome sequences to test whether divergent haplotypes could have originated from a closely related species, the spotted sea bass (Dicentrarchus punctatus). We found that an ancient admixture event between D. labrax and D. punctatus is responsible for the presence of shared derived alleles that segregate at low frequencies in both lineages of D. labrax. An exception to this was found within regions involved in RI between the two D. labrax lineages. In those regions, archaic tracts originating from D. punctatus locally reached high frequencies or even fixation in Atlantic genomes but were almost absent in the Mediterranean. We showed that the ancient admixture event most likely occurred between D. punctatus and the D. labrax Atlantic lineage, while Atlantic and Mediterranean D. labrax lineages were experiencing allopatric isolation. Our results suggest that local adaptive introgression and/or the resolution of genomic conflicts provoked by ancient admixture have probably contributed to the establishment of RI between the two D. labrax lineages.

Résumé: Species of the family Sternoptychidae (hatchetfishes) occur worldwide and play critical roles by sequestering carbon, recycling nutrients, and acting as a key trophic link between epipelagic primary consumers and higher trophic levels in marine ecosystems. Nevertheless, basic knowledge on their ecology is still lacking and their functional ecology remains understudied with respect to composition, organization, functions and environment interactions. Here we integrated comprehensive information collected in the western Tropical Atlantic on the diversity, abundance, distribution and trophic ecology of hatchetfishes, including physicochemical features of their habitats and extensive carbon and nitrogen stable isotope data on its main prey groups. On this basis we defined five functional groups of hatchetfishes with different diet preference, isotopic composition, and vertical abundance peaks and reveal a possible high resource partitioning. Additionally, these species might have a different feeding tie chronology. Hence, hatchetfishes segregate in different ecological groups responding differently to environmental constraints including oxygen concentration and presenting diverse functional roles. As deep-sea species that migrate to epipelagic waters, hatchetfishes may play a key role in the transfer of subsurface photoassimilated carbon to deeper waters, a pathway through which the effects of climate change at the surface are transferred to the deep ocean. Moreover, as consumers of gelatinous organisms, these species convert “gelatinous energy” into “fish energy” readily usable by higher trophic levels, including endangered and commercially important species. This is a crucial trophic relationship that has been historically underestimated due to methodology limitations (e.g., quickly digested gelatinous organisms were probably underestimated in previous studies, based solely on stomach contents). Considering in ecosystem models this trophic relationship, as well as the functional organization of hatchetfishes, is important to properly answer key ecological questions including resource use, carbon transportation, and influence of mesopelagic community in climate change process.

Résumé: Length-weight relationship parameters were calculated for twelve mesopelagic fish species from the western Tropical Atlantic:Diretmus argenteus, Melamphaes polylepis, Bolinichthys distofax, Diaphus lucidus, Diaphus splendidus, Electrona risso, Hygophum taaningi, Taaningichthys bathyphilus, Melanolagus bericoides, Winteria telescopa, Diplophos taenia, Astronesthes similus.Data was collected off northeastern Brazil from April 9th to May 6th, 2017. Hauls were conducted during day and night at 47 stations by using a micronekton trawl (body mesh: 40 mm, cod-end mesh: 10 mm) from 10 to 1,113 m depth. The material was fixed in a 4% formalin solution for 1 month and then preserved in a 70% alcohol solution for proximally 6 months before processing for length (nearest 0.1 cm of standard length) and weight (nearest 0.01 g of total weight). A new maximum standard length forWinteria telescopais also provided.

Résumé: An important decrease in small pelagic fish condition and size has been observed in the most productive ecosystem of the Mediterranean Sea, the Gulf of Lions, since 2008, leading to an important fishery crisis. Previous studies suggested bottom-up control to be the most probable cause for these changes. Here, we investigate whether an environmental change might have caused such a situation. In the absence of zooplankton time series, this study aims at describing temporal changes in key abiotic factors for the planktonic and fish production of the Gulf of Lions, such as SST, meso-scale fronts, wind-induced coastal upwelling, river discharge, water stratification and deep convection and then at understanding potential link on Chl-a concentration as well as small pelagic fish populations. Our results indicate that the environmental conditions have broadly changed in the Gulf of Lion, with a major change in the mid-2000s, affecting the Chla concentration (which showed a regime shift in 2007), but also the SST, the upwelling and frontal activities, the Rhone river discharge (and particularly the N and P nutrients inputs) as well as the deep winter convection. Those changes could have affected the plankton production and consequently the small pelagic fish community that displayed similar patterns of variations as the environmental conditions.

Résumé: The marine ecosystem off British Columbia (BC), Canada, has experienced various changes in the last two decades. Understanding how stressors interactively and cumulatively affect commercially important fish species is key to moving towards ecosystem-based fisheries management. Because it is challenging to assess the cumulative effects of multiple stressors by using empirical data alone, a dynamic, individual-based spatially-explicit ecosystem modeling platform such as OSMOSE represents a valuable tool to simulate ecological processes and comprehensively evaluate how stressors cumulatively impact modelled species. In this study, we employed OSMOSE to investigate the cumulative effects of fishing, plankton biomass change, and marine mammal consumption on the dynamics of some fish species and the BC marine ecosystem as a whole. We specifically simulated ecosystem dynamics during the last 20 years under two sets of scenarios: (1) unfavorable conditions from the perspective of commercial fish species (i.e., doubling fishing rates, halving plankton biomass, and doubling marine mammal biomass, acting individually or collectively); and (2) favorable conditions with the three factors having opposite changes (i.e., halving fishing rates, doubling plankton biomass, and halving marine mammal biomass, acting individually or collectively). Our results indicate that, under unfavorable conditions, the degree to which species biomass was reduced varied among species, and that negative synergistic and negative dampened effects were dominant under historical and doubled fishing mortality rates, respectively. Under favorable conditions, species biomasses did not increase as much as expected due to the existence of complex predator-prey interactions among fish species, and positive synergistic and positive dampened effects were prevailing under historical and halved fishing mortality rates, respectively. The ecosystem total biomass and the biomass to fisheries yield ratio were found to be good ecological indicators to represent ecosystem changes and track the impacts from the multiple drivers of change. Our research provides insights on how fisheries management should adapt to prepare for potential future impacts of climate change.

Résumé: Fisheries can profoundly affect bycatch species with 'slow' life history traits. Managing bait type offers one tool to control species selectivity. Different species and sizes of marine predators have different prey, and hence bait, preferences. This preference is a function of a bait's chemical, visual, acoustic and textural characteristics and size, and for seabirds the effect on hook sink rate is also important. We conducted a global meta-analysis of existing estimates of the relative risk of capture on different pelagic longline baits. We applied a Bayesian random effects meta-analytic regression modelling approach to estimate overall expected bait-specific catch rates. For blue shark and marine turtles, there were 34% (95% HDI: 4-59%) and 60% (95% HDI: 44-76%) significantly lower relative risks of capture on forage fish bait than squid bait, respectively. Overall estimates of bait-specific relative risk were not significantly different for seven other assessed taxa. The lack of a significant overall estimate of relative capture risk for pelagic shark species combined but significant effect for blue sharks suggests there is species-specific variability in bait-specific catch risk within this group. A qualitative literature review suggests that tunas and istiophorid billfishes may have higher catch rates on squid than fish bait, which conflicts with reducing marine turtle and blue shark catch rates. The findings from this synthesis of quantitative and qualitative evidence support identifying economically viable bycatch management measures with acceptable tradeoffs when multispecies conflicts are unavoidable, and highlight research priorities for global pelagic longline fisheries.

Résumé: The great scallop (Pecten maximus) is a commercially important bivalve in Europe, particularly in the English Channel, where fisheries are managed at regional and local scales through the regulation of fishing effort. In the long term, knowledge about larval dispersal and gene flow between populations is essential to ensure proper stock management. Yet, previous population genetic studies have reported contradictory results. In this study, scallop samples collected across the main fishing grounds along the French and English coasts of the English Channel (20 samples with temporal replicates for three sites,n= 1059 individuals), and the population genetic structure was analysed using 13 microsatellite loci. Coupling empirical genetic data with demogenetic modelling based on a biophysical model simulating larval exchanges among scallop beds revealed a subtle genetic differentiation between south-west English populations and the rest of the English Channel, which was consistent with larval dispersal simulations. The present study provides a step forward in the understanding of great scallop population biology in the English Channel, underlining the fact that even in a context of potentially high gene flow and recent divergence times since the end of the last glacial maximum, weak but significant spatial genetic structure can be identified at a regional scale.

Résumé: Amazonian goliath catfishes are widespread in the Amazon Basin. Recently, otolith Sr-87:Sr-86 analyses using laser ablation-multi-collector-inductively coupled plasma mass spectrometry (LA-MC-ICPMS) revealed a >8,000 km trans-Amazonian natal homing in Brachyplatystoma rousseauxii among fish caught and hatched in the largest Amazon River tributary, the upper Madeira basin. Although also suspected for fish in the upper Amazon, homing could not be demonstrated owing to less distinct environmental Sr-87:Sr-86 gradients along the Amazon mainstem. Using scanning X-ray fluorescence microscopy (SXFM), a separate study provided evidence that Se:Ca and Sr:Ca are useful markers for identifying migration into Andean headwaters and the estuarine environment. We analysed otoliths of known Sr-87:Sr-86 profiles using SXFM mapping to test if Sr:Ca and Se:Ca patterns could demonstrate natal homing for three fish caught in the upper Amazon, using as reference two individuals that were natal homers and two forced residents (hatched after the construction of hydroelectric dams on the Madeira River) from the upper Madeira River. As hypothesised, although the Sr isotope profiles of the upper Amazon individuals were uninformative, two of them presented similar alternating mirror patterns of Sr:Ca and Se:Ca to those of the upper Madeira natal homers, indicating migrations out of the Andean region and into the estuary area. Both were therefore natal homers from the upper Amazon. The third individual from the upper Amazon presented similar Sr:Ca and Se:Ca patterns to those of the upper Madeira residents, suggesting it was a natural resident from the upper Amazon. By combining the results of Sr-87:Sr-86 analyses (LA-MC-ICPMS) and Sr:Ca and Se:Ca mappings (SXFM) that are completely independent of one another, we demonstrated that B. rousseauxii also performs natal homing in the upper Amazon. Our results indicate that the life cycle of B. rousseauxii is more complex than previous literature hypothesised, with the existence of partial migration, even in absence of physical barriers. Quantifying the relative importance of these different life-history strategies will have important implications for fisheries management. Our results also lay the groundwork for conservation efforts in the context of hydropower development in the Amazon Basin and set testable hypotheses of the potential impacts of the Madeira River dams.

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: Acclimation to low salinities is a vital physiological challenge for euryhaline fish as the European sea bass Dicentrarchus labrax. This species undertakes seasonal migrations towards lagoons and estuaries where a wide range of salinity variations occur along the year. We have previously reported intraspecific differences in freshwater tolerance, with an average 30% mortality rate. In this study, we bring new evidence of mechanisms underlying freshwater tolerance in sea bass at gill and kidney levels. In fresh water (FW), intraspecific differences in mRNA expression levels of several ion transporters and prolactin receptors were measured. We showed that the branchial Cl-/HCO3- anion transporter (slc26a6c) was over-expressed in freshwater intolerant fish, probably as a compensatory response to low blood chloride levels and potential metabolic alkalosis. Moreover, prolactin receptor a (prlra) and Na+/Cl- cotransporter (ncc1) but not ncc-2a expression seemed to be slightly increased and highly variable between individuals in freshwater intolerant fish. In the posterior kidney, freshwater intolerant fish exhibited differential expression levels of slc26 anion transporters and Na+/K+/2Cl(-) co-transporter 1b (nkcc1b). Lower expression levels of prolactin receptors (prlra, prlrb) were measured in posterior kidney which probably contributes to the failure in ion reuptake at the kidney level. Freshwater intolerance seems to be a consequence of renal failure of ion reabsorption, which is not sufficiently compensated at the branchial level.

Résumé: The Pacific oyster, Crassostrea gigas, was voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry, following a severe disease outbreak. Since then, the two species have been in contact in southern Europe and, therefore, have the potential to exchange genes. Recent evolutionary genomic works have provided empirical evidence that C. gigas and C. angulata exhibit partial reproductive isolation. Although hybridization occurs in nature, the rate of interspecific gene flow varies across the genome, resulting in highly heterogeneous genome divergence. Taking this biological property into account is important to characterize genetic ancestry and population structure in oysters. Here, we identified a subset of ancestry-informative makers from the most differentiated regions of the genome using existing genomic resources. We developed two different panels in order to (i) easily differentiate C. gigas and C. angulata, and (ii) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic populations. Our results confirm high genetic homogeneity among Pacific cupped oyster populations in France and reveal several cases of introgressions between Portuguese and Japanese oysters in France and Portugal.

Résumé: Studies on phytoplankton and in particular Harmful Algal Blooms (HABs) species in southern Mediterranean waters are scarce. We performed from April 2008 to June 2009 weekly investigations on microphytoplankton community structure and abundance in two contrasted marine ecosystems located in the western Moroccan Mediterranean coast, M'diq Bay and Oued Laou Estuary. Simultaneously, we measured the main physico-chemical parameters. Globally, the two studied areas showed comparable values of the assessed abiotic environmental factors. Temperature and salinity followed seasonal variation with values ranging from 13.5 degrees C to 21.4 degrees C and 31 to 36.8, respectively. Average nutrient values in surface water ranged from 0.7 to 45.76 mu M for dissolved inorganic nitrogen, 0.02-2.10 mu M for PO4 and 0.23-17.46 mu M for SiO4 in the study areas. A total of 92 taxa belonging to 8 taxonomic classes were found. The highest number of microphytoplankton abundance reached 1.2 x 10(6) cells L-1 with diatoms being the most abundant taxa. Factorial Discriminant Analysis (FDA) and Spearman correlation test showed a significant seasonal discrimination of dominant microphytoplankton species. These micro-organisms were associated with different environmental variables, in particular temperature and salinity. Numerous HABs species were encountered regularly along the year. Although Dinophysis species and Prorocentrum lima were present in both sites, no Lipophilic Shellfish Poisoning was detected for the analyzed bivalve mollusks. Domoic acid (DA), produced by toxic species of Pseudo-nitzschia was found with concentrations up to 18 mu g DA g(-1) in the smooth clam Callista chione. Data showed that the observed persistent and dramatic Paralytic Shellfish Poisoning (PSP) intoxication of mollusks resulted probably of Gymnodinium catenatum proliferations in both studied areas. Contrary to C. chione, the cockle Achanthocardia tuberculatum showed a permanent and extremely high toxicity level during the 15 months survey with up to 7545 mu g Equivalent Saxitoxin kg(-1) flesh (ten times higher than the sanitary threshold of 800 tg eqSTX Kg(-1) flesh). The present work highlights for the first time the dynamic of microphytoplankton including HABs species and their associated toxin accumulation in the commercially exploited shellfish in the southern western Mediterranean waters of Morocco. Furthermore, the acquired data will help us to improve the monitoring of HABs species and related toxins in these coastal marine systems.

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

Résumé: The La Perouse seamount (60 m depth) has so far been poorly studied despite it being a short distance (160 km) from Reunion Island. As part of the MADRidge project, a multidisciplinary cruise was conducted to evaluate the effect of this shallow seamount on the local hydrology and ecology. Current measurements, temperature and chlorophyll-a profiles, and mesozooplankton and micronekton samples were collected between the summit and 35 km away. Micronekton data were supplemented with stomach content of pelagic top predators as well as fisheries statistics from the domestic longline fleet operating from Reunion. Vertical current profiles revealed distinct patterns between the offshore and seamount-flanked stations, giving evidence of topographical induced flow instabilities, notably on its leeward side (west) relative to the east flank. Distinct patterns in temperature and chlorophyll-a vertical profiles suggest the formation of convergent and divergent circulation cells as a result of the irregular and crescent-like summit topography. Spatial differences in zooplankton abundance were detected with higher biovolumes on the leeward flank. The overall acoustic backscatter for micronekton over the summit was weaker than offshore, but highly concentrated in the upper layer. Albacore tuna and swordfish dominate the longline catch west of Reunion, seemingly in association with a deep (900 m) topographic feature. Yet the largest catch is not directly associated with La Perouse which would be too shallow for top predators to aggregate around in the long term. Enhanced levels of phytoplankton or zooplankton enrichment at La Perouse were not demonstrated in this study, nor was there notable diversity of micronekton species. This might explain the relatively limited importance of this seamount to the tuna fisheries in this region.

Résumé: The almaco jack, Seriola rivoliana, is a circumtropical pelagic fish of importance both in commercial fisheries and in aquaculture. To understand levels of genetic diversity within and among populations in the wild, population genetic structure and the relative magnitude of migration were assessed using mtDNA sequence data and single nucleotide polymorphisms (SNPs) from individuals sampled from locations in the Pacific and Atlantic Oceans. A total of 25 variable sites of cytochrome c oxidase subunit 1 and 3678 neutral SNPs were recovered. Three genetic groups were identified, with both marker types distributed in different oceanic regions: Pacific-1 in central Pacific, Pacific-2 in eastern Pacific and Atlantic in western Atlantic. Nonetheless, the analysis of SNP identified a fourth population in the Pacific coast of Baja California Sur, Mexico (Pacific-3), whereas that of mtDNA did not. This mito-nuclear discordance is likely explained by a recently diverged Pacific-3 population. In addition, two mtDNA haplogroups were found within the western Atlantic, likely indicating that the species came into the Atlantic from the Indian Ocean with historical gene flow from the eastern Pacific. Relative gene flow among ocean basins was low with rm < 0.2, whereas in the eastern Pacific it was asymmetric and higher from south to north (rm > 0.79). The results reflect the importance of assessing genetic structure and gene flow of natural populations for the purposes of sustainable management.

Résumé: The deep sea plays a critical role in global climate regulation through uptake and storage of heat and carbon dioxide. However, this regulating service causes warming, acidification and deoxygenation of deep waters, leading to decreased food availability at the seafloor. These changes and their projections are likely to affect productivity, biodiversity and distributions of deep-sea fauna, thereby compromising key ecosystem services. Understanding how climate change can lead to shifts in deep-sea species distributions is critically important in developing management measures. We used environmental niche modelling along with the best available species occurrence data and environmental parameters to model habitat suitability for key cold-water coral and commercially important deep-sea fish species under present-day (1951-2000) environmental conditions and to project changes under severe, high emissions future (2081-2100) climate projections (RCP8.5 scenario) for the North Atlantic Ocean. Our models projected a decrease of 28%-100% in suitable habitat for cold-water corals and a shift in suitable habitat for deep-sea fishes of 2.0 degrees-9.9 degrees towards higher latitudes. The largest reductions in suitable habitat were projected for the scleractinian coral Lophelia pertusa and the octocoral Paragorgia arborea, with declines of at least 79% and 99% respectively. We projected the expansion of suitable habitat by 2100 only for the fishes Helicolenus dactylopterus and Sebastes mentella (20%-30%), mostly through northern latitudinal range expansion. Our results projected limited climate refugia locations in the North Atlantic by 2100 for scleractinian corals (30%-42% of present-day suitable habitat), even smaller refugia locations for the octocorals Acanella arbuscula and Acanthogorgia armata (6%-14%), and almost no refugia for P. arborea. Our results emphasize the need to understand how anticipated climate change will affect the distribution of deep-sea species including commercially important fishes and foundation species, and highlight the importance of identifying and preserving climate refugia for a range of area-based planning and management tools.

Résumé: Innovative fish diets made of terrestrial plants supplemented with sustainable protein sources free of fish-derived proteins could contribute to reducing the environmental impact of the farmed fish industry. However, such alternative diets may influence fish gut microbial community, health, and, ultimately, growth performance. Here, we developed five fish feed formulas composed of terrestrial plant-based nutrients, in which fish-derived proteins were substituted with sustainable protein sources, including insect larvae, cyanobacteria, yeast, or recycled processed poultry protein. We then analyzed the growth performance of European sea bass (Dicentrarchus labrax L.) and the evolution of gut microbiota of fish fed the five formulations. We showed that replacement of 15% protein of a vegetal formulation by insect or yeast proteins led to a significantly higher fish growth performance and feed intake when compared with the full vegetal formulation, with feed conversion ratio similar to a commercial diet. 16S rRNA gene sequencing monitoring of the sea bass gut microbial community showed a predominance of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. The partial replacement of protein source in fish diets was not associated with significant differences on gut microbial richness. Overall, our study highlights the adaptability of European sea bass gut microbiota composition to changes in fish diet and identifies promising alternative protein sources for sustainable aquafeeds with terrestrial vegetal complements.

Résumé: Nearly 30 years ago, emerged the concept of deterministic chaos. With it came sensitivity to initial conditions, nonlinearities, and strange attractors. This constituted a paradigm shift that profoundly altered how numerical modellers approached dynamic systems. It also provided an opportunity to resolve a situation of mutual misunderstanding between scientists and non-scientists about uncertainties and predictability in natural systems. Our proposition is that this issue can be addressed in an original way which involves modelling based on the principles of chance and necessity (CaN). We outline the conceptual and mathematical principles of CaN models and present an application of the model to the Barents Sea food-web. Because CaN models rely on concepts easily grasped by all actors, because they are explicit about knowns and unknowns and because the interpretation of their results is simple without being prescriptive, they can be used in a context of participatory management. We propose that, three decades after the emergence of chaos theories, CaN can be a practical step to reconcile scientists and non-scientists around the modelling of structurally and dynamically complex natural systems, and significantly contribute to ecosystem-based fisheries management.

Résumé: Structural changes in plankton primary producers have large implications for food web dynamics, energy fluxes and the vertical export of biogenic particulate carbon. Here we examine phytoplankton data spanning the period 1993-2008 from the Bay of Tunis, southwestern Mediterranean Sea, in relation to long term hydroclimate variability. We show a conspicuous shift in the structure of the phytoplankton community characterized by an increase of small-sized species and diversity loss, revealing a dominance of smaller blooming diatoms and cyanobacteria. Such changes were concurrent with marked modifications in hydroclimatic patterns experienced in the Bay of Tunis consisting of a shift towards enhanced winter precipitation together with rising temperatures. This novel study shows an overall rise in the proportion of small phytoplankton cells and a decreasing trend in phytoplankton diversity in the southern Mediterranean area. These findings warn of a potential decline of trophic efficiency and lesser food web stability resulting from mean size reduction and the diversity loss.

Résumé: Spatial indicators are widely used to monitor species and are essential to management and conservation. In the present study, we tested the ability of 11 spatial indicators to quantify changes in species' geographic patterns: (1) spatial displacement of a patch of biomass ('shift'), (2) a spatial decrease in a patch, accompanied either by a loss of biomass ('shrink0') or (3) a relocation of the same biomass ('shrink1'), and (4) splitting of a patch into smaller patches ('split'). The geographic changes were simulated by manipulating the spatial distributions of the demersal species (observed during bottom trawl surveys). Hence, the spatial distributions of the latter being used as input data on which the manipulations were done. Additionally, other aspects of the indicators affecting the responses to the geographic changes were also tested, (1) homogeneous increase in biomass throughout the patch and (2) different sample sizes. The center of gravity (defined by latitude and longitude) was the only indicator that accurately detected the 'shift' in biomass. The index of aggregation identified a decrease in the area and biomass of the main biomass patch ('shrink0'), while the Gini index, equality area and spreading area were accurately identified a decrease in the area of the main biomass patch when total biomass did not decreased ('Shrink1'). Inertia and isotropy responded to all geographic changes, except for those in biomass or distribution area. None of the indicators successfully identified 'split' process. Likewise, one of the indicators were sensitive to a homogeneous increase in biomass or the type of spatial distribution. Overall, all indicators behaved similarly well when sample sizes exceeded 40 stations randomly located in the area. The framework developed provides an accessible and simple approach that can be used to evaluate the ability of spatial indicators to identify geographic processes using empirical data and can be extended to other indicators or geographic processes. We discuss perspectives of the development of spatial indicators especially within the application of EU's Marine Strategy Framework Directive.

Résumé: Triggerfish are widely distributed in tropical waters where they play an important ecological role. The black triggerfish Melichthys niger may be the dominant species around oceanic tropical islands, whereas pelagic triggerfish, such as the ocean triggerfish Canthidermis sufflamen, can assemble around fish aggregating devices (FADs) where they are a common bycatch of tuna fisheries. In this study we combined acoustic and optical recordings to provide the first in situ target strength (TS) measurement of black and ocean triggerfish. Data were collected in the Archipelago of Fernando de Noronha off north-east Brazil. The mean TS of a 27.8-cm-long black triggerfish at 70 and 200 kHz was -39.3 dB re 1 m(2) (CV = 14.0%) and -38.9 dB re 1 m(2) (CV = 14.4%) respectively. The mean TS values of ocean triggerfish (with a size range of 39-44 cm) at 70 and 200 kHz were -36.0 dB re 1 m(2) (CV = 15.7%) and -33.3 dB re 1 m(2) (CV = 14.0%) respectively. This work opens up the field for acoustic biomass estimates. In addition, we have shown that TS values for ocean triggerfish are within the same range as those of small tunas. Therefore, acoustic data transmitted from FADs equipped with echosounders can introduce a bias in tuna acoustic biomass estimation and lead to increased rates of bycatch.

Résumé: Energy flow and nutrient cycling dictate the functional role of organisms in ecosystems. Fishes are key vectors of carbon (C), nitrogen (N) and phosphorus (P) in aquatic systems, and the quantification of elemental fluxes is often achieved by coupling bioenergetics and stoichiometry. While nutrient limitation has been accounted for in several stoichiometric models, there is no current implementation that permits its incorporation into a bioenergetics approach to predict ingestion rates. This may lead to biased estimates of elemental fluxes. Here, we introduce a theoretical framework that combines stoichiometry and bioenergetics with explicit consideration of elemental limitations. We examine varying elemental limitations across different trophic groups and life stages through a case study of three trophically distinct reef fishes. Further, we empirically validate our model using an independent database of measured excretion rates. Our model adequately predicts elemental fluxes in the examined species and reveals species- and size-specific limitations of C, N and P. In line with theoretical predictions, we demonstrate that the herbivoreZebrasoma scopasis limited by N and P, and all three fish species are limited by P in early life stages. Further, we show that failing to account for nutrient limitation can result in a greater than twofold underestimation of ingestion rates, which leads to severely biased excretion rates. Our model improved predictions of ingestion, excretion and egestion rates across all life stages, especially for fishes with diets low in N and/or P. Due to its broad applicability, its reliance on many parameters that are well-defined and widely accessible, and its straightforward implementation via the accompanyingr-packagefishflux, our model provides a user-friendly path towards a better understanding of ecosystem-wide nutrient cycling in the aquatic biome. A freePlain Language Summarycan be found within the Supporting Information of this article.

Résumé: Aim: To determine which morphological characteristics make a fish species a good candidate for introduction and establishment, we tested whether (a) introduced species differ in morphology from non-introduced species (species only existing in native areas and not introduced to new areas) in each donor assemblage (biogeographic realm fauna); (b) within the introduced species, the morphology of established species (self-sustaining introduced species) differs from that of the non-established species; (c) within the established species, those exported out of their native realm have more extreme morphological traits than those translocated within their native realm. Major taxa studied: Freshwater fish. Location: Global. Time period: 1960s-2010s. Methods: We used a global database of freshwater fishes from the six realms. Ten morphological traits were measured on 9,150 species. Principal component analysis was conducted to combine the 10 traits into a multidimensional morphospace. We used permutational multivariate analysis of variance (PERMANOVA) and permutational analysis for the multivariate homogeneity of dispersions (PERMDISP2) to compare the distribution of species groups in the morphospace and Kolmogorov-Smirnov tests to compare their distributions on principal component (PC) axes. Results: The morphology of introduced species differed from that of non-introduced species in all the six biogeographic realms. Among introduced species, established species had more extreme morphological traits than non-established species in most realms. Among established species, exported species had more extreme morphological traits than translocated species. Main conclusions: Morphological differences between introduced and nonintroduced species rely on an anthropogenic trait selection for fisheries and angling, leading to the preference for the introduction of predators with large and laterally compressed bodies. Established introduced species represent a small subset of introduced species morphologies, with these species having more extreme morphological traits, probably making them more efficient in particular habitats than their non-established counterparts. This was particularly marked for fish morphologies adapted to lentic waters. Such a trend was apparent for exported species, which have more extreme traits than translocated species.

Résumé: Temperature-dependent sex determination (TSD) can be observed in multiple reptile and fish species. It is adaptive when varying environmental conditions advantage either males or females. A good knowledge of the thermosensitive period is key to understand how environmental changes may lead to changes in population sex ratio. Here, by manipulating temperature during development, we confirm that cold temperature (16°C) increases the proportion of fish that develop as females in European sea bass (Dicentrarchus labrax) until 56 days posthatching, but show that it has an opposite effect at later stages, with the proportion of males reaching 90% after 230 days at 16°C. This is the first observation of opposite effects of temperature at different time periods on the sex ratio of a vertebrate. Our results highlight the potential complexity of environmental effects on sex determination.

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 avoidance reaction by fish in front of an approaching vessel is a major source of bias in direct biomass assessment and ecological studies based on fisheries acoustics data. An experiment was carried out to compare echosounder data obtained using a small speedboat and a research fisheries vessel generating significant higher noise above conventional reduced-noise standard. The results show that there was no significant difference between the individual fish target strength distributions, and the numbers of schools recorded by both boats, these schools having similar areas and perimeters. However, the schools detected by the noisier vessel were significantly deeper, and unexpectedly had a significantly higher energy level. These findings suggest that noise-reduced vessels trigger a different vessel avoidance reaction. The noise-reduction standard is not sufficient to reduce avoidance behavior. It is also to take into consideration the ambient noise, which could impair perception of the platform by the fish, and the probability that the acoustic stimuli could be less important than visual perception under some local conditions. The paper introduces the concept of partial avoidance and presents a conceptual diagram of the strength of the avoidance reaction. Last, it is not recommended, because of noise reasons, that vessels routinely used for pelagic stock assessment surveys be changed. Indeed standardized time series, which could be disrupted when switching to a new vessel, are more important than the hypothetical gain from change to quieter vessels. Obviously, all long-term surveys must change vessels; best practice will be to estimate the vessel effect before any change to avoid disrupting the time series and/or perform vessel intercalibration surveys.

Résumé: Periodically harvested closures are a widespread, centuries-old form of fisheries management that protects fish between pulse harvests and can generate high harvest efficiency by reducing fish wariness of fishing gear. However, the ability for periodic closures to also support high fisheries yields and healthy marine ecosystems is uncertain, despite increased promotion of periodic closures for managing fisheries and conserving ecosystems in the Indo-Pacific. We developed a bioeconomic fisheries model that considers changes in fish wariness, based on empirical field research, and quantified the extent to which periodic closures can simultaneously maximize harvest efficiency, fisheries yield and conservation of fish stocks. We found that periodic closures with a harvest schedule represented by closure for one to a few years between a single pulse harvest event can generate equivalent fisheries yield and stock abundance levels and greater harvest efficiency than achievable under conventional fisheries management with or without a permanent closure. Optimality of periodic closures at maximizing the triple objective of high harvest efficiency, high fisheries yield, and high stock abundance was robust to fish life history traits and to all but extreme levels of overfishing. With moderate overfishing, there emerged a trade-off between periodic closures that maximized harvest efficiency and no-take permanent closures that maximized yield; however, the gain in harvest efficiency outweighed the loss in yield for periodic closures when compared with permanent closures. Only with extreme overfishing, where fishing under nonspatial management would reduce the stock to <= 18% of its unfished level, was the harvest efficiency benefit too small for periodic closures to best meet the triple objective compared with permanent closures. Synthesis and applications. We show that periodically harvested closures can, in most cases, simultaneously maximize harvest efficiency, fisheries yield, and fish stock conservation beyond that achievable by no-take permanent closures or nonspatial management. Our results also provide design guidance, indicating that short closure periods between pulse harvest events are most appropriate for well-managed fisheries or areas with large periodic closures, whereas longer closure periods are more appropriate for small periodic closure areas and overfished systems.

Résumé: Air-breathing and amphibious fishes are essential study organisms to shed insight into the required physiological shifts that supported the full transition from aquatic water-breathing fishes to terrestrial air-breathing tetrapods. While the origin of air-breathing in the evolutionary history of the tetrapods has received considerable focus, much less is known about the evolutionary physiology of air-breathing among fishes. This review summarizes recent advances within the field with specific emphasis on the cardiorespiratory regulation associated with air-breathing and terrestrial excursions, and how respiratory physiology of these living transitional forms are affected by development and personality. Finally, we provide a detailed and re-evaluated model of the evolution of air-breathing among fishes that serves as a framework for addressing new questions on the cardiorespiratory changes associated with it. This review highlights the importance of combining detailed studies on piscine air-breathing model species with comparative multi-species studies, to add an additional dimension to our understanding of the evolutionary physiology of air-breathing in vertebrates.

Résumé: Habitat dynamics interacting with species dispersal abilities could generate gradients in species diversity and prevalence of species traits when the latter are associated with species dispersal potential. Using a process-based model of diversification constrained by a dispersal parameter, we simulated the interplay between reef habitat dynamics during the past 140 million years and dispersal, shaping lineage diversification history and assemblage composition globally. The emerging patterns from the simulations were compared to current prevalence of species traits related to dispersal for 6315 tropical reef fish species. We found a significant spatial congruence between the prevalence of simulated low dispersal values and areas with a large proportion of species characterized by small adult body size, narrow home range mobility behaviour, pelagic larval duration shorter than 21 days and diurnal activity. Species characterized by such traits were found predominantly in the Indo-Australian Archipelago and the Caribbean Sea. Furthermore, the frequency distribution of the dispersal parameter was found to match empirical distributions for body size, PLD and home range mobility behaviour. Also, the dispersal parameter in the simulations was associated to diversification rates and resulted in trait frequency matching empirical distributions. Overall, our findings suggest that past habitat dynamics, in conjunction with dispersal processes, influenced diversification in tropical reef fishes, which may explain the present-day geography of species traits.

Résumé: The large-scale distribution pattern of megafauna communities along the Mediterranean middle slope was explored. The study was conducted between 500 and 800 m depth where deep-water fishery occurs. Although community studies carried out deeper than 500 m are partly available for some geographic areas, few large-scale comparative studies have been carried out. Within the framework of the MEDITS survey programme, we compared the megafauna community structure in ten geographical sub-areas (GSAs) along the Mediterranean coasts. Additionally, the spatial distribution of fishing was analysed using vessel monitoring by satellite information. Overall, the community showed a significant difference between sub-areas, with a decreasing eastward pattern in abundance and biomass. Longitude was the main factor explaining variation among sub-areas (by generalized additive models). However, we found a region which did not follow the general pattern. GSA 6 (northern Spain) showed significantly lower abundance and a different composition structure to the adjacent areas. The decrease in community descriptors (i.e. abundance and biomass) in this area is probably a symptom of population changes induced by intense fishery exploitation. Overall, a combination of environmental variables and human-induced impacts appears to influence the bentho-pelagic communities along the slope areas of the Mediterranean.

Résumé: Moving toward ecosystem-based fisheries management (EBFM) necessitates a suite of ecological indicators that are responsive to fishing pressure, capable of tracking changes in the state of marine ecosystems, and related to management objectives. In this study, we employed the gradient forest method to assess the performance of 14 key ecological indicators in terms of specificity, sensitivity and the detection of thresholds for EBFM across ten marine ecosystems using four modelling frameworks (Ecopath with Ecosim, OSMOSE, Atlantis, and a multi-species size-spectrum model). Across seven of the ten ecosystems, high specificity to fishing pressure was found for most of the 14 indicators. The indicators biomass to fisheries catch ratio (B/C), mean lifespan and trophic level of fish community were found to have wide utility for evaluating fishing impacts. The biomass indicators, which have been identified as Essential Ocean Variables by the Global Ocean Observing System (GOOS), had lower performance for evaluating fishing impacts, yet they were most sensitive to changes in primary productivity. The indicator B/C was most sensitive to low levels of fishing pressure with a generally consistent threshold response around 0.4*FMSY (fishing mortality rate at maximum sustainable yield) across nine of the ten ecosystems. Over 50% of the 14 indicators had threshold responses at, or below ∼0.6* FMSY for most ecosystems, indicating that these ecosystems would have already crossed a threshold for most indicators when fished at FMSY. This research provides useful insights on the performance of indicators, which contribute to facilitating the worldwide move toward EBFM.

Résumé: Multidisciplinary ocean observing activities provide critical ocean information to satisfy ever-changing socioeconomic needs and require coordinated implementation. The upper oxycline (transition between high and low oxygen waters) is fundamentally important for the ecosystem structure and can be a useful proxy for multiple observing objectives connected to eastern boundary systems (EBSs) that neighbor oxygen minimum zones (OMZs). The variability of the oxycline and its impact on the ecosystem (VOICE) initiative demonstrates how societal benefits drive the need for integration and optimization of biological, biogeochemical, and physical components of regional ocean observing related to EBS. In liaison with the Global Ocean Oxygen Network, VOICE creates a roadmap toward observation-model syntheses for a comprehensive understanding of selected oxycline-dependent objectives. Local to global effects, such as habitat compression or deoxygenation trends, prompt for comprehensive observing of the oxycline on various space and time scales, and for an increased awareness of its impact on ecosystem services. Building on the Framework for Ocean Observing (FOO), we present a first readiness level assessment for ocean observing of the oxycline in EBS. This was to determine current ocean observing design and future needs in EBS regions (e.g., the California Current System, the Equatorial Eastern Pacific off Ecuador, the Peru-Chile Current system, the Northern Benguela off Namibia, etc.) building on the FOO strategy. We choose regional champions to assess the ocean observing design elements proposed in the FOO, namely, requirement processes, coordination of observational elements, and data management and information products and the related best practices. The readiness level for the FOO elements was derived for each EBS through a similar and very general ad hoc questionnaire. Despite some weaknesses in the questionnaire design and its completion, an assessment was achievable. We found that fisheries and ecosystem management are a societal requirement for all regions, but maturity levels of observational elements and data management and information products differ substantially. Identification of relevant stakeholders, developing strategies for readiness level improvements, and building and sustaining infrastructure capacity to implement these strategies are fundamental milestones for the VOICE initiative over the next 2-5 years and beyond.

Résumé: To facilitate the wider implementation of ecosystem modeling platforms and, thereby, to help advance ecosystem-based fisheries management (EBFM) worldwide, tools delivering a large quantity of inputs to ecosystem models are needed. We developed a web application providing OSMOSE ecosystem models with values for trophic, growth and reproduction parameters derived from data from two global information systems (FishBase and SeaLifeBase). Our web application guides the user through simple queries to extract information from FishBase and SeaLifeBase data archives, and it delivers all the configuration files necessary for running an OSMOSE model. Here, we present our web application and demonstrate it for the West Florida Shelf ecosystem. Our software architecture can serve as a basis for designing other advanced web applications using FishBase and SeaLifeBase data in support of EBFM.

Résumé: Reef sharks are vulnerable predators experiencing severe population declines mainly due to overexploitation. However, beyond direct exploitation, human activities can produce indirect or sublethal effects such as behavioral alterations. Such alterations are well known for terrestrial fauna but poorly documented for marine species. Using an extensive sampling of 367 stereo baited underwater videos systems, we show modifications in grey reef shark (Carcharhinus amblyrhynchos) occurrence and feeding behavior along a marked gradient of isolation from humans across the New Caledonian archipelago (South-Western Pacific). The probability of occurrence decreased by 68.9% between wilderness areas (more than 25 hours travel time from the capital city) and impacted areas while the few individuals occurring in impacted areas exhibited cautious behavior. We also show that only large no-entry reserves (above 150 km(2)) can protect the behavior of grey reef sharks found in the wilderness. Influencing the fitness, human linked behavioral alterations should be taken into account for management strategies to ensure the persistence of populations.

Résumé: Aim To define the major biogeographical regions and transition zones for freshwater fish species. Taxon Strictly freshwater species of actinopterygian fish (i.e. excluding marine and amphidromous fish families). Methods We based our bioregionalization on a global database of freshwater fish species occurrences in drainage basins, which, after filtering, includes 11,295 species in 2,581 basins. On the basis of this dataset, we generated a bipartite (basin-species) network upon which we applied a hierarchical clustering algorithm (the Map Equation) to detect regions. We tested the robustness of regions with a sensitivity analysis. We identified transition zones between major regions with the participation coefficient, indicating the degree to which a basin has species from multiple regions. Results Our bioregionalization scheme showed two major supercontinental regions (Old World and New World, 50% species of the world and 99.96% endemics each). Nested within these two supercontinental regions lie six major regions (Nearctic, Neotropical, Palearctic, Ethiopian, Sino-Oriental and Australian) with extremely high degrees of endemism (above 96% except for the Palearctic). Transition zones between regions were of limited extent compared to other groups of organisms. We identified numerous subregions with high diversity and endemism in tropical areas (e.g. Neotropical), and a few large subregions with low diversity and endemism at high latitudes (e.g. Palearctic). Main conclusions Our results suggest that regions of freshwater fish species were shaped by events of vicariance and geodispersal which were similar to other groups, but with freshwater-specific processes of isolation that led to extremely high degrees of endemism (far exceeding endemism rates of other continental vertebrates), specific boundary locations and limited extents of transition zones. The identified bioregions and transition zones of freshwater fish species reflect the strong isolation of freshwater fish faunas for the past 10-20 million years. The extremely high endemism and diversity of freshwater fish fauna raises many questions about the biogeographical consequences of current introductions and extinctions.

Résumé: The understanding of macroalgae functions and processes requires a good understanding of the spatial distribution of the functional diversity of macroalgae. In coral reef environments, this information remains fragmentary. Here, based on 314 species sorted according to a set of 10 functional traits, the functional niches of macroalgae at three remote coral reefs of the iles Eparses in the Indian Ocean (Europa, Glorioso, and Juan de Nova) are described. For the comparison of intra- and inter-reef functional structures, we characterized both taxonomic and functional beta diversities, and their turnover and nestedness-resultant components. Within the three reefs, we observed strong taxonomic and functional dissimilarities across sampling sites, mainly determined by turnover. Null models highlighted several processes, which structured macroalgal assemblages across sites: a combined effect of environmental variables (geomorphology and wave exposure), limiting similarity and stochastic effects. At the inter-reef scale, the three reefs only shared a small number of species, but the functional beta diversity between Glorioso and Juan de Nova was weak. This suggested that although assemblages were different, fairly similar environmental conditions may have homogenized macroalgae functions through both ecological and evolutionary scale processes. Our results support the idea that macroalgal assemblages can provide similar functional trait portfolios, despite distinct species composition. We stress the need to focus on macroalgae life-history traits for a better understanding of the processes structuring their communities.