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Small-scale fisheries provide nutrients to hundreds of millions of people worldwide, with yields dependent on the condition of marine habitats such as coral reefs. Small-scale fisheries are a particularly important food source in societies with nutrient deficiencies and where unhealthy food alternatives are widely available. Using data from coral reef surveys around two islands in French Polynesia (Moorea and Raiatea), we show how the availability of nutrients to fisheries changed in relation to the condition of coral habitat. Fish biomass and nutrient availability were highest when coral cover was low around both islands, driven predominantly by abundant herbivorous reef fish. We also investigated the importance of fish in people's diets, to determine if fish consumption was aligned with available fisheries resources on local reefs and if nutrient intakes from fish could be explained by people's socioeconomic background. People ate a higher diversity of reef fish in Raiatea, however nutrient intakes from fish were higher in Moorea. Most people ate more fish than meat on both islands, however fish consumption declined over generations. People from fishing households had higher nutrient intakes from reef and pelagic fish, and people from farming households had higher intakes from reef fish. Preference for eating reef fish over pelagic fish was also associated with higher total nutrient intakes. Promoting traditional diets rich in fish could be key to meeting people's nutritional needs in French Polynesia while reducing diet-related health issues linked to the overconsumption of fat. French and Tahitian versions of the Abstract are available in Supplementary Material. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Coral reef fisheries supply nutritious catch to tropical coastal communities, where the quality of reef seafood is determined by both the rate of biomass production and nutritional value of reef fishes. Yet our understanding of reef fisheries typically uses targets of total reef fish biomass rather than individual growth (i.e. biomass production) and nutrient content (i.e. nutritional value of reef fish), limiting the ability of management to sustain the productivity of nutritious catches. Here, we use modelled growth coefficients and nutrient concentrations to develop a new metric of nutrient productivity of coral reef fishes. We then evaluate this metric with underwater visual surveys of reef fish assemblages from four tropical countries to examine nutrient productivity of reef fish food webs. Species' growth coefficients were associated with nutrients that vary with body size (calcium, iron, selenium and zinc), but not total nutrient density. When integrated with fish abundance data, we find that herbivorous species typically dominate standing biomass, biomass turnover and nutrient production on coral reefs. Such bottom-heavy trophic distributions of nutrients were consistent across gradients of fishing pressure and benthic composition. We conclude that management restrictions that promote sustainability of herbivores and other low trophic-level species can sustain biomass and nutrient production from reef fisheries that is critical to the food security of over 500 million people in the tropics. [ABSTRACT FROM AUTHOR]

Aim: Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio‐economic factors. Location: Tropical, temperate and polar coastal areas. Time period: Present day. Major taxa studied: Marine fishes. Methods: We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio‐economic factors on α‐ and β‐diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α‐ and β‐diversity measured from our barcodes, and phylogenetic but also functional diversity. Results: We show that fish eDNA MOTU and sequence α‐ and β‐diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions: Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions. [ABSTRACT FROM AUTHOR]

Wild‐caught fish are a bioavailable source of nutritious food that, if managed strategically, could enhance diet quality for billions of people. However, optimising nutrient production from the sea has not been a priority, hindering development of nutrition‐sensitive policies. With fisheries management increasingly effective at rebuilding stocks and regulating sustainable fishing, we can now begin to integrate nutritional outcomes within existing management frameworks. Here, we develop a conceptual foundation for managing fisheries for multispecies Maximum Nutrient Yield (mMNY). We empirically test our approach using size‐based models of North Sea and Baltic Sea fisheries and show that mMNY is predicted by the relative contribution of nutritious species to total catch and their vulnerability to fishing, leading to trade‐offs between catch and specific nutrients. Simulated nutrient yield curves suggest that vitamin D, which is deficient in Northern European diets, was underfished at fishing levels that returned maximum catch weights. Analysis of global catch data shows there is scope for nutrient yields from most of the world's marine fisheries to be enhanced through nutrient‐sensitive fisheries management. With nutrient composition data now widely available, we expect our mMNY framework to motivate development of nutrient‐based reference points in specific contexts, such as data‐limited fisheries. Managing for mMNY alongside policies that promote access to fish could help close nutrient gaps for coastal populations, maximising the contribution of wild‐caught fish to global food and nutrition security. [ABSTRACT FROM AUTHOR]

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems. [ABSTRACT FROM AUTHOR]

Functional diversity (FD), the diversity of organism attributes that relates to their interactions with the abiotic and biotic environment, has been increasingly used for the last two decades in ecology, biogeography and conservation. Yet, FD has many facets and their estimations are not standardized nor embedded in a single tool. mFD (multifaceted functional diversity) is an R package that uses matrices of species assemblages and species trait values as building blocks to compute most FD indices. mFD is firstly based on two functions allowing the user to summarize trait and assemblage data. Then it calculates trait‐based distances between species pairs, informs the user whether species have to be clustered into functional entities and finally computes multidimensional functional space. To let the user choose the most appropriate functional space for computing multidimensional functional diversity indices, two mFD functions allow assessing and illustrating the quality of each functional space. Next, mFD provides 6 core functions to calculate 16 existing FD indices based on trait‐based distances, functional entities or species position in a functional space. The mFD package also provides graphical functions based on the ggplot library to illustrate FD values through customizable and high‐resolution plots of species distribution among functional entities or in a multidimensional space. All functions include internal validation processes to check for errors in data formatting which return detailed error messages. To facilitate the use of mFD framework, we built an associated website hosting five tutorials illustrating the use of all the functions step by step. [ABSTRACT FROM AUTHOR]

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Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non‐overlapping assemblages rather than subsets of one another. As a result, non‐saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false‐negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA. [ABSTRACT FROM AUTHOR]

Rapid degradation of the world's coral reefs jeopardizes their ecological functioning and ultimately imperils the wellbeing of the millions of people with reef-dependent livelihoods. Ecosystem accessibility is the main driver of their conditions, with the most accessible ecosystems being most at risk of resource depletion. People's socioeconomic conditions can change as they get further from urban centers and can profoundly influence people's relationship with the environment. However, the mechanisms through which increasing accessibility from human societies affects natural resources are still unclear. A plausible mechanism through which markets influence the environment is through the socioeconomic changes that tend to accompany accessibility. We used social and ecological data from 10 coastal communities and 31 reefs in northwest Madagascar to (i) unravel the respective influences of the local fish market and coastal communities on reef fish biomass and (ii) investigate how communities' socioeconomic and resource use characteristics change with increasing proximity to markets. We used generalized additive models to reveal that reef fish biomass is strongly related to the accessibility of both markets and local communities. We also highlight that the ways coastal communities use marine resources changes predictably with market proximity. More precisely, market proximity affects fishing gear (technique effect), wealth, and selling strategies (scale effect) of coastal communities. Our findings emphasize the need to better quantify links between markets and fishing communities through household-level surveys to implement market-based actions that could help to regulate the effect of markets on both fish stocks and fishing communities. [ABSTRACT FROM AUTHOR]

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 (∼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. [ABSTRACT FROM AUTHOR]

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 <100 kg/ha to >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. [ABSTRACT FROM AUTHOR]

Since the 1950s, industrial fisheries have expanded globally, as fishing vessels are required to travel further afield for fishing opportunities. Technological advancements and fishery subsidies have granted ever-increasing access to populations of sharks, tunas, billfishes, and other predators. Wilderness refuges, defined here as areas beyond the detectable range of human influence, are therefore increasingly rare. In order to achieve marine resources sustainability, large no-take marine protected areas (MPAs) with pelagic components are being implemented. However, such conservation efforts require knowledge of the critical habitats for predators, both across shallow reefs and the deeper ocean. Here, we fill this gap in knowledge across the Indo-Pacific by using 1,041 midwater baited videos to survey sharks and other pelagic predators such as rainbow runner (Elagatis bipinnulata), mahi-mahi (Coryphaena hippurus), and black marlin (Istiompax indica). We modeled three key predator community attributes: vertebrate species richness, mean maximum body size, and shark abundance as a function of geomorphology, environmental conditions, and human pressures. All attributes were primarily driven by geomorphology (35%−62% variance explained) and environmental conditions (14%−49%). While human pressures had no influence on species richness, both body size and shark abundance responded strongly to distance to human markets (12%−20%). Refuges were identified at more than 1,250 km from human markets for body size and for shark abundance. These refuges were identified as remote and shallow seabed features, such as seamounts, submerged banks, and reefs. Worryingly, hotpots of large individuals and of shark abundance are presently under-represented within no-take MPAs that aim to effectively protect marine predators, such as the British Indian Ocean Territory. Population recovery of predators is unlikely to occur without strategic placement and effective enforcement of large no-take MPAs in both coastal and remote locations. [ABSTRACT FROM AUTHOR]

Sobral et al. (Ecology Letters, 19, 2016, 1091) reported that the loss of bird functional and phylogenetic diversity due to species extinctions was not compensated by exotic species introductions. Here, we demonstrate that the reported changes in biodiversity were underestimated because of methodological pitfalls. [ABSTRACT FROM AUTHOR]

The depletion of natural resources has become a major issue in many parts of the world, with the most accessible resources being most at risk. In the terrestrial realm, resource depletion has classically been related to accessibility through road networks. In contrast, in the marine realm, the impact on living resources is often framed into the Malthusian theory of human density around ecosystems. Here, we develop a new framework to estimate the accessibility of global coral reefs using potential travel time from the nearest human settlement or market. We show that 58% of coral reefs are located < 30 min from the nearest human settlement. We use a case study from New Caledonia to demonstrate that travel time from the market is a strong predictor of fish biomass on coral reefs. We also highlight a relative deficit of protection on coral reef areas near people, with disproportional protection on reefs far from people. This suggests that conservation efforts are targeting low-conflict reefs or places that may already be receiving de facto protection due to their isolation. Our global assessment of accessibility in the marine realm is a critical step to better understand the interplay between humans and resources. [ABSTRACT FROM AUTHOR]

Worryingly, B hotspots b of large individuals and of shark abundance are presently under-represented within no-take MPAs that aim to effectively protect marine predators, such as the British Indian Ocean Territory. 1 Letessier TB, Mouillot D, Bouchet PJ, Vigliola L, Fernandes MC, Thompson C, et al. (2019) Remote reefs and seamounts are the last refuges for marine predators across the Indo-Pacific. [Extracted from the article]