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• Environmental DNA samples were taken seasonally in a Marine Protected Area. • Vulnerable species were mostly detected in the Fully Protected Area. • eDNA metabarcoding revealed seasonal changes in community composition. • Fish composition changes were detected along a depth gradient. • eDNA is useful for frequent monitoring in MPAs to guide management strategies. Marine fish communities suffer from anthropogenic pressures and climate change, which influence their spatio-temporal dynamics. Marine Protected Areas (MPAs) have been established worldwide to preserve these communities, while mesophotic ecosystems could provide natural refugia. Assessing the extent to which MPAs and deeper ecosystems can mitigate human and climate change impacts requires regular monitoring of temporal community dynamics. Environmental DNA (eDNA) surveys – being time- and cost-effective – can provide valuable insights on biodiversity change. Here, we initiated a long-term study based on eDNA monitoring in an MPA in the north-western Mediterranean Sea that includes areas with various protection levels. Specifically, from June 2021 to January 2023, we collected eDNA samples during the summer, fall, and winter seasons from shallow water (20 m depth), at 40 m depth, and from the mesophotic zone (80 m depth) in a Fully Protected Area (FPA) and in a nearby Lightly Protected Area (LPA) in the Riou archipelago (France). In this short period and relatively small area, we detected a total of 113 actinopterygian and chondrichthyan taxa. Species with high fishing vulnerability had higher detection rates in the FPA than in the LPA, suggesting a positive impact of FPAs on the conservation of these threatened species. A marked seasonal signal in species detections, including significantly lower detections of several species in winter, indicated a combined effect of species biological changes and migration behavior. The seasonality trend was stronger in the FPA than in the LPA, indicating that such areas may modify sub-yearly patterns in communities and ecosystem processes. Fish composition was associated with water depth, with marked species dissimilarities between shallow waters and the mesophotic zone, implying that multiple depths should be considered in MPA monitoring to fully capture the response of biodiversity to management. Our results point to the importance of temporal information combined with extensive sampling across depths and protection levels to fully understand the ecological dynamics and structure of coastal fish communities. [ABSTRACT FROM AUTHOR]

High-throughput DNA sequencing is becoming an increasingly important tool to monitor and better understand biodiversity responses to environmental changes in a standardized and reproducible way. Environmental DNA (eDNA) from organisms can be captured in ecosystem samples and sequenced using metabarcoding, but processing large volumes of eDNA data and annotating sequences to recognized taxa remains computationally expensive. Speed and accuracy are two major bottlenecks in this critical step. Here, we evaluated the ability of convolutional neural networks (CNNs) to process short eDNA sequences and associate them with taxonomic labels. Using a unique eDNA data set collected in highly diverse Tropical South America, we compared the speed and accuracy of CNNs with that of a well-known bioinformatic pipeline (OBITools) in processing a small region (60 bp) of the 12S ribosomal DNA targeting freshwater fishes. We found that the taxonomic labels from the CNNs were comparable to those from OBITools, with high correlation levels for the composition of the regional fish fauna. The CNNs enabled the processing of raw fastq files at a rate of approximately 1 million sequences per minute, which was about 150 times faster than with OBITools. Given the good performance of CNNs in the highly diverse ecosystem considered here, the development of more elaborate CNNs promises fast deployment for future biodiversity inventories using eDNA. [ABSTRACT FROM AUTHOR]

The global biodiversity crisis due to anthropogenic pressures jeopardizes marine ecosystem functioning and services. Community responses to these environmental changes can be assessed through functional diversity, a biodiversity component related to organism–environment interactions, and estimated through biological traits related to organism functions (locomotion, feeding mode, and reproduction). Fish play a key role in marine systems functioning and supply proteins for billions of humans worldwide, yet most of the knowledge is limited to several commercial species and little is known about the intraspecific variability of their functional traits. The data provided here consist of 867 records of individuals from 85 species of ray‐finned (Actinopterygii) and cartilaginous (Chondrichthyes) fish sampled in the Bay of Biscay (Atlantic, France) between autumn 2017 and 2019. We provided for each individual the taxonomic classification, 16 ecomorphological measures (5 directly made on fresh individuals and 11 realized using individual pictures) that were converted into nine ecomorphological traits classically documented in the literature (biomass, protrusion, oral gape shape, surface and position, eye size and position, body transversal shape and surface, pectoral fin position and caudal peduncle throttling) and eight life history traits obtained from FishBase (maximum length, average depth, depth range, trophic level, reproduction mode, fertilization mode, parental care, vertical position in the water column). These traits document several functions such as dispersion, feeding mode, habitat use, position in the food web, and reproduction. To improve the development of new traits, we provided a picture of each individual with an ROI file containing the different morpho‐anatomical measures made using "ImageJ" software and an R function to extract them. In addition, we provided the metadata from each sampling site (years, dates, stations, sampling hours, strata, gears, latitudes, longitudes, and depths) and environmental variables measured in situ (conductivity, salinity, water temperature, water density, and air temperature). This data set accounting for the intraspecific variability among 85 fish species is of interest to better understand the effects of environmental forcing in a global change context as in the Bay of Biscay, a highly fished transition zone harboring mixed assemblages of boreal, temperate, and subtropical fish species that are susceptible to display variability in functional trait to adapt to changing conditions. The data set is freely available without copyright restrictions; users should cite this paper in research products (publications, presentations, reports, etc.) derived from the data set. [ABSTRACT FROM AUTHOR]

[Display omitted] • The spatiotemporal dynamics of demersal fish communities were investigated in the Bay of Biscay (BoB) and Celtic Sea (CS). • Two decades of changes in temperature, trophic resources, habitat and fishing pressure on community were assessed. • Diversity patterns showed greater variability in space than in time and species richness and abundance weakly changed. • Communities are becoming more spatially similar (homogeneous) in the CS and differentiated in the BoB. • Such patterns are best explained by the dynamics of trophic resources mediated by small pelagic species. Climate change and resource exploitation represent strong selection pressure affecting the spatio-temporal dynamics of marine assemblages that ensure food provision for humans. However, such dynamics remain poorly documented, and their drivers unclear. Here, we investigate changes in fish assemblages of two key European fishing areas, the Bay of Biscay (BoB) and the Celtic Sea (CS), during the last two decades. We quantify the relative contribution of change in energy (i.e. temperature and trophic resources), habitat (depth, substrate, oxygen) and fishing pressure to explaining observed spatial and temporal variations in fish diversity. We used long-term scientific surveys to evaluate the spatio-temporal changes in species richness (SR), abundance and composition of demersal fish (Actinopterygii) assemblages at different spatial scales combined with a range of regression models and variance partitioning. Diversity patterns showed greater variability in space than in time: SR weakly changed over time, while compositional dissimilarity showed local patterns of taxonomic homogenization in the CS and differentiation in the southern BoB, where local assemblages were becoming more similar and dissimilar over time, respectively. Energy funnelled through small pelagic species as a potential trophic link affecting the dynamics of demersal assemblages was the most important driver, while habitat and fishing pressure had limited importance. Our study revealed contrasted dynamics of demersal fish assemblages at a regional scale that were best explained by the dynamics of small pelagic species. Direct effects of environmental forcing and fishing pressure were limited in both regions which have a long history of fishing and still remain relatively buffered from global warming effects. This research paved the way to combine methods inspired by biogeography with scientific monitoring surveys to detect spatio-temporal dynamics of fish assemblages and their drivers in marine ecosystems under multiple pressures. [ABSTRACT FROM AUTHOR]

Marine protected areas (MPAs) are major tools to protect biodiversity and sustain fisheries. For species with a sedentary adult phase and a dispersive larval phase, the effectiveness of MPA networks for population persistence depends on connectivity through larval dispersal. However, connectivity patterns between MPAs remain largely unknown at large spatial scales. Here, we used a biophysical model to evaluate connectivity between MPAs in the Mediterranean Sea, a region of extremely rich biodiversity that is currently protected by a system of approximately a hundred MPAs. The model was parameterized according to the dispersal capacity of the dusky grouper Epinephelus marginatus, an archetypal conservation-dependent species, with high economic importance and emblematic in the Mediterranean. Using various connectivity metrics and graph theory, we showed that Mediterranean MPAs are far from constituting a true, well-connected network. On average, each MPA was directly connected to four others and MPAs were clustered into several groups. Two MPAs (one in the Balearic Islands and one in Sardinia) emerged as crucial nodes for ensuring multi-generational connectivity. The high heterogeneity of MPA distribution, with low density in the South-Eastern Mediterranean, coupled with a mean dispersal distance of 120 km, leaves about 20% of the continental shelf without any larval supply. This low connectivity, here demonstrated for a major Mediterranean species, poses new challenges for the creation of a future Mediterranean network of well-connected MPAs providing recruitment to the whole continental shelf. This issue is even more critical given that the expected reduction of pelagic larval duration following sea temperature rise will likely decrease connectivity even more. [ABSTRACT FROM AUTHOR]

The global network of protected areas has rapidly expanded in the past decade and is expected to cover at least 30% of land and sea by 2030 to halt biodiversity erosion. Yet, the distribution of protected areas is highly heterogeneous on Earth and the social-environmental preconditions enabling or hindering protected area establishment remain poorly understood. Here, using fourteen socioeconomic and environmental factors, we characterize the multidimensional niche of terrestrial and marine protected areas, which we use to accurately establish, at the global scale, whether a particular location has preconditions favourable for paestablishment. We reveal that protected areas, particularly the most restrictive ones, over-aggregate where human development and the number of non-governmental organizations are high. Based on the spatial distribution of vertebrates and the likelihood to convert non-protected areas into strictly protected areas, we identify 'potential' versus 'unrealistic' conservation gains on land and sea, which we define as areas of high vertebrate diversity that are, respectively, favourable and unfavourable to protected area establishment. Where protected areas are unrealistic, alternative strategies such as other effective area-based conservation measures or privately protected areas, could deliver conservation outcomes., (© 2024. The Author(s).)

Islands have been used as model systems to study ecological and evolutionary processes, and they provide an ideal set-up for validating new biodiversity monitoring methods. The application of environmental DNA metabarcoding for monitoring marine biodiversity requires an understanding of the spatial scale of the eDNA signal, which is best tested in island systems. Here, we investigated the variation in Actinopterygii and Elasmobranchii species composition recovered from eDNA metabarcoding along a gradient of distance-to-reef in four of the five French Scattered Islands in the Western Indian Ocean. We collected surface water samples at an increasing distance from reefs (0 m, 250 m, 500 m, 750 m). We used a metabarcoding protocol based on the 'teleo' primers to target marine reef fishes and classified taxa according to their habitat types (benthic or pelagic). We investigated the effect of distance-to-reef on β diversity variation using generalised linear mixed models and estimated species-specific distance-to-reef effects using a model-based approach for community data. Environmental DNA metabarcoding analyses recovered distinct fish species compositions across the four inventoried islands and variations along the distance-to-reef gradient. The analysis of β - diversity variation showed significant taxa turnover between the eDNA samples on and away from the reefs. In agreement with a spatially localised signal from eDNA, benthic species were distributed closer to the reef than pelagic ones. Our findings demonstrate that the combination of eDNA inventories and spatial modelling can provide insights into species habitat preferences related to distance-to-reef gradients at a small scale. As such, eDNA can not only recover large compositional differences among islands but also help understand habitat selection and distribution of marine species at a finer spatial scale., Competing Interests: The authors declare there are no conflicts of interests., (© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Understanding the ecological rules structuring the organization of species interactions is a prerequisite to predicting how ecosystems respond to environmental changes. While the ecological determinants of single networks have been documented, it remains unclear whether network ecological rules are conserved along spatial and environmental gradients. To address this gap, we reconstructed 48 plant-herbivore interaction networks along six elevation gradients in the Central European Alps in Switzerland, using DNA metabarcoding on orthoptera faeces. We developed hypotheses on the ecological mechanisms expected to structure interaction networks, based on plant phylogeny, plant abundance, leaf toughness, leaf nitrogen content and plant metabolomics. We show that plant phylogenetic relationships and species abundance have the greatest explanatory power regarding the structure of the ecological networks. Moreover, we found that leaf nitrogen content is a key determinant of interactions in warmer environments, while phenolic compounds and tannins are more important in colder environments, suggesting that determinants of species interactions can shift along environmental gradients. With this work, we propose an approach to study the mechanisms that structure the way species interact with each other between bioregions and ecosystems., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Elasmobranchs (sharks, rays and skates) are among the most threatened marine vertebrates, yet their global functional diversity remains largely unknown. Here, we use a trait dataset of >1000 species to assess elasmobranch functional diversity and compare it against other previously studied biodiversity facets (taxonomic and phylogenetic), to identify species- and spatial- conservation priorities. We show that threatened species encompass the full extent of functional space and disproportionately include functionally distinct species. Applying the conservation metric FUSE (Functionally Unique, Specialised, and Endangered) reveals that most top-ranking species differ from the top Evolutionarily Distinct and Globally Endangered (EDGE) list. Spatial analyses further show that elasmobranch functional richness is concentrated along continental shelves and around oceanic islands, with 18 distinguishable hotspots. These hotspots only marginally overlap with those of other biodiversity facets, reflecting a distinct spatial fingerprint of functional diversity. Elasmobranch biodiversity facets converge with fishing pressure along the coast of China, which emerges as a critical frontier in conservation. Meanwhile, several components of elasmobranch functional diversity fall in high seas and/or outside the global network of marine protected areas. Overall, our results highlight acute vulnerability of the world's elasmobranchs' functional diversity and reveal global priorities for elasmobranch functional biodiversity previously overlooked., (© 2023. The Author(s).)

The bathymetric and geographical distribution of marine species represent a key information in biodiversity conservation. Yet, deep-sea ecosystems are among the least explored on Earth and are increasingly impacted by human activities. Environmental DNA (eDNA) metabarcoding has emerged as a promising method to study fish biodiversity but applications to the deep-sea are still scarce. A major limitation in the application of eDNA metabarcoding is the incompleteness of species sequences available in public genetic databases which reduces the extent of detected species. This incompleteness by depth is still unknown. Here, we built the global bathymetric and geographical distribution of 10,826 actinopterygian and 960 chondrichthyan fish species. We assessed their genetic coverage by depth and by ocean for three main metabarcoding markers used in the literature: teleo and MiFish-U/E. We also estimated the number of primer mismatches per species amplified by in silico polymerase chain reaction which influence the probability of species detection. Actinopterygians show a stronger decrease in species richness with depth than Chondrichthyans. These richness gradients are accompanied by a continuous species turnover between depths. Fish species coverage with the MiFish-U/E markers is higher than with teleo while threatened species are more sequenced than the others. "Deep-endemic" species, those not ascending to the shallow depth layer, are less sequenced than not threatened species. The number of primer mismatches is not higher for deep-sea species than for shallower ones. eDNA metabarcoding is promising for species detection in the deep-sea to better account for the 3-dimensional structure of the ocean in marine biodiversity monitoring and conservation. However, we argue that sequencing efforts on "deep-endemic" species are needed., Competing Interests: All authors declare that there is no conflict of interest regarding the publication of this article., (© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Setting appropriate conservation strategies in a multi-threat world is a challenging goal, especially because of natural complexity and budget limitations that prevent effective management of all ecosystems. Safeguarding the most threatened ecosystems requires accurate and integrative quantification of their vulnerability and their functioning, particularly the potential loss of species trait diversity which imperils their functioning. However, the magnitude of threats and associated biological responses both have high uncertainties. Additionally, a major difficulty is the recurrent lack of reference conditions for a fair and operational measurement of vulnerability. Here, we present a functional vulnerability framework that incorporates uncertainty and reference conditions into a generalizable tool. Through in silico simulations of disturbances, our framework allows us to quantify the vulnerability of communities to a wide range of threats. We demonstrate the relevance and operationality of our framework, and its global, scalable and quantitative comparability, through three case studies on marine fishes and mammals. We show that functional vulnerability has marked geographic and temporal patterns. We underline contrasting contributions of species richness and functional redundancy to the level of vulnerability among case studies, indicating that our integrative assessment can also identify the drivers of vulnerability in a world where uncertainty is omnipresent., (© 2022. The Author(s).)

Although extinctions due to climate change are still uncommon, they might surpass those caused by habitat loss or overexploitation over the next few decades. Among marine megafauna, mammals fulfill key and irreplaceable ecological roles in the ocean, and the collapse of their populations may therefore have irreversible consequences for ecosystem functioning and services. Using a trait-based approach, we assessed the vulnerability of all marine mammals to global warming under high and low greenhouse gas emission scenarios for the middle and the end of the 21 st century. We showed that the North Pacific Ocean, the Greenland Sea and the Barents Sea host the species that are most vulnerable to global warming. Future conservation plans should therefore focus on these regions, where there are long histories of overexploitation and there are high levels of current threats to marine mammals. Among the most vulnerable marine mammals were several threatened species, such as the North Pacific right whale (Eubalaena japonica) and the dugong (Dugong dugon), that displayed unique combinations of functional traits. Beyond species loss, we showed that the potential extinctions of the marine mammals that were most vulnerable to global warming might induce a disproportionate loss of functional diversity, which may have profound impacts on the future functioning of marine ecosystems worldwide.

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

The productivity of marine ecosystems and the services they provide to humans are largely dependent on complex interactions between prey and predators. These are embedded in a diverse network of trophic interactions, resulting in a cascade of events following perturbations such as species extinction. The sheer scale of oceans, however, precludes the characterization of marine feeding networks through de novo sampling. This effort ought instead to rely on a combination of extensive data and inference. Here we investigate how the distribution of trophic interactions at the global scale shapes the marine fish food web structure. We hypothesize that the heterogeneous distribution of species ranges in biogeographic regions should concentrate interactions in the warmest areas and within species groups. We find that the inferred global metaweb of marine fish-that is, all possible potential feeding links between co-occurring species-is highly connected geographically with a low degree of spatial modularity. Metrics of network structure correlate with sea surface temperature and tend to peak towards the tropics. In contrast to open-water communities, coastal food webs have greater interaction redundancy, which may confer robustness to species extinction. Our results suggest that marine ecosystems are connected yet display some resistance to perturbations because of high robustness at most locations.