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Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0% of conserved actinopterygian genes, making the quality and completeness of this genome the highest among all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanocyte development) in A. clarkii compared with other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

Anemonefish are iconic examples of marine fishes living in mutualistic symbiosis with sea anemones. In a given sea anemone, the anemonefishes have a stereotyped social organization with a dominant female, a semi-dominant male, and several juveniles. A strict size-based hierarchy governs the social interactions within these colonies, with each individual differing from the previous or next fish in the order by +/- 20% size. This social organization is conserved across the Indo-Pacific in all 28 species of anemonefish found on any of ten giant sea anemone species. We report the existence of huge “megacolonies” of up to 100 fish living in large carpets of sea anemones. This alternative organization was observed for different fish and anemone species in different coral reef locations (French Polynesia, Japan, Taiwan, and Vietnam). In these colonies, the strict size-based hierarchy is no longer recognizable, and the level of aggressivity of the different members appears lower than in “normal” colonies. These megacolonies may correspond to a previously overlooked type of social organization that could be linked to host availability and offer a unique opportunity to understand anemonefish’s behavioral, social, and hormonal plasticity.

International audience; Fish development and acclimation to environmental conditions are strongly mediated by the hormonal endocrine system. In environments contaminated by anthropogenic stressors, hormonal pathway alterations can be detrimental for growth, survival, fitness, and at a larger scale for population maintenance. In the context of increasingly contaminated marine environments worldwide, numerous laboratory studies have confirmed the effect of one or a combination of pollutants on fish hormonal systems. However, this has not been confirmed in situ. In this review, we explore the body of knowledge related to the influence of anthropogenic stressors disrupting fish endocrine systems, recent advances (focusing on thyroid hormones and stress hormones such as cortisol), and potential research perspectives. Through this review, we highlight how harbours can be used as "in situ laboratories" given the variety of anthropogenic stressors (such as plastic, chemical, sound, light pollution, and invasive species) that can be simultaneously investigated in harbours over long periods of time.

Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfishAmphiprion clarkiipossesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome ofA. clarkiiis yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0 % of conserved actinopterygian genes, making the quality and completeness of this genome the highest amongst all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers oferbb3b(a gene involved in melanophore development) inA. clarkiicompared to other anemonefish, thus suggesting a possible link betweenerbb3band the natural melanism polymorphism observed inA. clarkii. The publication of this high-quality genome, along withA. clarkii’s many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

The spatio-temporal variability of fish distribution is important to better manage and protect the populations of endangered species. In this sense, the vertical movements of a vulnerable and protected species, Sciaena umbra, were assessed in a marine protected area (the Réserve Naturelle Marine de Cerbère-Banyuls, south of France) to study the variability of their bathymetric distribution at different time scales. Twenty adults were marked with acoustic transmitters and acoustically monitored over 2.5 years. This revealed that some individuals remained at shallow waters (, This study was funded by the National Rugby League/Provale as well as by the University of Perpignan Via Domitia Foundation through its support program for high level athletes.

Marine reserves constitute effective tools for preserving fish stocks and associated human benefits. However, not all reserves perform equally, and predicting the response of marine communities to management actions in the long run is challenging. Our decadal-scale survey of recreational fishing yields at France’s 45-year old Cerbère-Banyuls marine reserve indicated significant protection benefits, with 40-50% higher fishing yields per unit effort in the partial-protection zone of the reserve (where fishing is permitted but at a lower level) than in surrounding non-reserve areas. Over the period 2005-2014, catch per unit effort (CPUE) showed a similar pattern of decline inside and outside the reserve while weight per unit effort (WPUE) increased by 131% inside and decreased by 60% outside. Different CPUE and WPUE trajectories among fish families indicated changing catch assemblages, with yields increasing for the family most valued by fisheries, Sparidae (the ecological winners). However, reserve benefits were restricted to off-shore fishermen (the social winners), as on-shore yields were ∼4 times lower and declining, even inside the reserve. Our study illustrates how surveys of recreational fishing yields can help evaluate the effectiveness of marine protected areas for key social and ecological protagonists. We show that, more than four decades after its establishment, fishing efficiencies at the historical Cerbère-Banyuls marine reserve are still changing, but benefits in terms of catch abundance, weight, and composition remain predominantly restricted to off-shore fishermen. Further regulations appear necessary to guarantee that conservation strategies equitably benefit societal groups.

The concentration of human activities along the shoreline induces high levels of pressure, notably seascape urbanization caused by the proliferation of coastal and marine infrastructures such as ports, harbors, marinas and coastal defense structures. Because they are localized in sheltered and shallow coastal areas, these infrastructures inevitably lead to the loss of natural essential habitats once used as nursery ground by juvenile fish. Some studies have reported the presence of high juvenile densities on breakwaters and jetties suggesting those infrastructures could support the nursery function. However, ports seem unlikely to be used by juveniles due to their vertical and featureless docks. Here we explored the feasibility of using small artificial habitats to enhance the ecological value of ports. We set up a total of 108 artificial habitats in three different locations of the large commercial port of Marseille in the northwestern Mediterranean. We then surveyed juvenile fish on the artificial habitats and control docks on 7 different occasions between June and September 2014. Average species richness and densities were higher on the artificial habitats but displayed high spatial and taxa-specific variations. Hence, small artificial habitats are promising ecological engineering tools to enhance the nursery function inside ports and thus reduce the ecological footprint of those infrastructures.

International audience; Man-made infrastructures have become ubiquitous components of coastal landscapes, leading to habitat modification that affects the abundance and diversity of marine organisms. Marine coastal fish have a complex life cycle requiring different essentialhabitats. One of these habitats is known as a nursery, a place where juveniles can settle in large numbers, survive and grow to contribute to the adult population. Nurseries are mainly found in shallow, sheltered zones and are thus particularly impacted by urbanization, notably by harbors. The vertical featureless structure of docks is very unlikely to be used by juveniles, which need complex habitats to find food and shelter from predators. Recent attempts to rehabilitate the nursery function in such environments by using artificial habitats have proven efficient in increasing juvenile densities. However, nothing is known about the survival of juveniles in these habitats, preventing any conclusions on the effectiveness of this means of restoration from being drawn. Here, we set up tank experiments to test the relationship between habitat preferences and the survival rate of two species of seabream when facing stalk-attacking combers. Habitat choice was consistent with survival results, indicating that artificial habitats might not represent unintended ecological traps for juveniles. However, the artificial habitats’ effect on survival was variable between species. Therefore, our results suggest that habitat diversity might be of prime importance to sustain juveniles of different species and stress the need for the development of diverse artificial habitats to counteract the effects of seascape homogenization.

International audience; Metallic and organic pollutants constitute a serious threat for coral reef ecosystems, potentially affecting a great number of species interacting within complex trophodynamic processes. Pesticides, PCBs and trace elements were measured on coral reef communities of three Pacific islands (Moorea, Wallis and New Caledonia) in relation with d15N values, a proxy of trophic level. Several potential sources of organic matter, benthic invertebrates and fish belonging to various trophic strategies were sampled at each island. Wallis and New Caledonia displayed, respectively, the highest concentrations of pesticides and trace elements. In the three islands, most trace element concentrations (Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and V) decreased when d15N was rising (i.e. bioreduction), whereas Hg and Se biomagnified with increasing d15N values. Only few trace elements in some islands did not show any significant trend in relation with d15N (i.e., Ag in New Caledonia, Zn in Wallis and As plus Zn in Moorea). PCBs concentrations showed a significant bioreduction in New Caledonia and in Moorea, but a significant biomagnification in Wallis. Aldrin and heptachlor were the only pesticides to show a similar significant bioreduction in the three islands. Other pesticides, such as chlordecone, diazinon, endosulfan I and II, heptachlor-epoxide A and B, lindane and pp’-DDE displayed contrasted patterns (e.g. chlordecone significantly biomagnified in New Caledonia, significantly bioreduced in Wallis and did not displayed any significant trend in Moorea). Finally, for unclear reasons, Moorea displayed only negative significant correlations between d15N and all pesticides (except pp’-DDT). Our results highlight that trophic level, here assessed through d15N values, is a good predictor of metallic trace elements biomagnification or bioreduction in coral reef organisms. However, at large spatial scale, trophic level relevance to predict pesticides and PCBs biomagnification or bioreduction should be considered with caution and studied in close relation with local characteristics.

Despite the increasing use of acoustic cameras in fish ecology and fisheries studies, the quantification of biases associated with this method have received little attention. In this note, we used data collected from an ARIS acoustic camera, positioned in a channel linking a lagoon to the sea, to quantify differences in European eel (Anguilla anguilla) counts and size estimates made by two experienced operators. Count estimates made from 58 videos were highly consistent between the two operators (R2 = 0.99), although statistically different. Compared to the known sizes for the 82 eels, sizes estimated manually from video were underestimated. The resulting mean error percentages were significantly different between the two operators (−3.9% ± 8.5 (SD) and −6.6% ± 8.9). This error percentage was significantly influenced by the known size of the eels but not by the detection range. Our results highlighted the importance of taking into account the biases in counts and size estimates in fish ecology and fisheries studies based on acoustic cameras. These biases have to be quantified and, if possible, corrected using similar protocols as described in this study, when multiple operators analyse acoustic videos or when comparing the results from different studies.

Along the littoral, a growing number of anthropogenic structures have caused substantial habitat destruction. Despite their detrimental impact, these constructions could play a role in the functioning of coastal ecosystems. The objective of this work was to assess the distribution of juvenile coastal fish along a seascape composed of various natural and artificial habitats in order to determine the potential role of coastal infrastructures as juvenile habitat. We surveyed juvenile populations on various infrastructures and natural sites along a 100 km shoreline of the French Mediterranean coast. Juvenile densities varied according to the level of artificialization of the sites. Densities were the highest on coastal defense structures, intermediate in natural sites and lowest in harbors. Focusing inside harbors revealed highly variable densities depending on the type of habitat, with densities on ripraps or jetties that were equivalent to those of natural sites. Our results underline the importance of anthropogenic structures as potential juvenile habitats, which is too often not considered in management plans.

Coastal nursery habitats are essential for the renewal of adult fish populations. We quantified the availability of a coastal nursery habitat (shallow heterogeneous rocky bottoms) and the spatial variability of its juvenile fish populations along 250 km of the Catalan coastline (France and Spain). Nurseries were present in 27% of the coastline, but only 2% of them benefited from strict protection status. For nine taxa characteristic of this habitat, total juvenile densities varied significantly between nursery sites along the coastline, with the highest densities being found on the northern sites. Recruitment level (i.e. a proxy of nursery value) was not explained by protection level, but it was moderately and positively correlated with an anthropization index. Patterns of spatial variations were taxa-specific. Exceptional observations of four juveniles of the protected grouper Epinephelus marginatus were recorded. Our data on habitat availability and recruitment levels provides important informations which help to focus MPA management efforts.