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Reliable and efficient techniques are urgently needed to monitor elasmobranch populations that face increasing threats worldwide. Aerial video-surveys provide precise and verifiable observations for the rapid assessment of species distribution and abundance in coral reefs, but the manual processing of videos is a major bottleneck for timely conservation applications. In this study, we applied deep learning for the automated detection and mapping of vulnerable eagle rays from aerial videos. A light aircraft dedicated to touristic flights allowed us to collect 42 h of aerial video footage over a shallow coral lagoon in New Caledonia (Southwest Pacific). We extracted the videos at a rate of one image per second before annotating them, yielding 314 images with eagle rays. We then trained a convolutional neural network with 80% of the eagle ray images and evaluated its accuracy on the remaining 20% (independent data sets). Our deep learning model detected 92% of the annotated eagle rays in a diversity of habitats and acquisition conditions across the studied coral lagoon. Our study offers a potential breakthrough for the monitoring of ray populations in coral reef ecosystems by providing a fast and accurate alternative to the manual processing of aerial videos. Our deep learning approach can be extended to the detection of other elasmobranchs and applied to systematic aerial surveys to not only detect individuals but also estimate species density in coral reef habitats.

Analyses of genetic diversity can shed light on both the origins of biodiversity hotspots, as well as the conservation status of species that are impacted by human activities. With these objectives, we assembled a genomic dataset of 14,935 single nucleotide polymorphisms from 513 grey reef sharks (Carcharhinus amblyrhynchos) sampled across 17 locations in the tropical Indo-Pacific. We analysed geographic variation in genetic diversity, estimated ancient and contemporary effective population size (Ne) across sampling locations (using coalescent and linkage disequilibrium methods) and modelled the history of gene flow between the Coral Triangle and the Coral Sea. Genetic diversity decreased with distance away from the Coral Triangle and north-western Australia, implying that C. amblyrhynchos may have originated in this region. Increases in Ne were detected across almost all sampling locations 40,000-90,000 generations ago (approximately 0.6-1.5 mya, given an estimated generation time of 16.4 years), suggesting a range expansion around this time. More recent, secondary increases in Ne were inferred for the Misool and North Great Barrier Reef sampling locations, but joint modelling did not clarify whether these were due to population growth, migration, or both. Despite the greater genetic diversity and ancient Ne observed at sites around Australia and the Coral Triangle, remote reefs around north-western New Caledonia had the highest contemporary Ne, demonstrating the importance of using multiple population size assessment methods. This study provides insight into both the past and present demographics of C. amblyrhynchos and contributes to our understanding of evolution in marine biodiversity hotspots.

Dramatic declines in reef shark populations have been documented worldwide in response to human activities. Marine Protected Areas (MPAs) offer a useful mechanism to protect these species and their roles in coral reef ecosystems. The effectiveness of MPAs notably relies on compliance together with sufficient size to encompass animal home range. Here, we measured home range of 147 grey reef sharks, Carcharhinus amblyrhynchos, using acoustic telemetry in New Caledonia. The distribution of home range was then compared to local MPA sizes. We report a home range of 12 km2 of reef for the species with strong differences between adult males (21 km2), adult females (4.4 km2) and juveniles (6.2 km2 for males, 2.7 km2 for females). Whereas local historic MPA size seemed adequate to protect reef shark home range in general, these were clearly too small when considering adult males only, which is consistent with the reported failure of MPAs to protect sharks in New Caledonia. Fortunately, the recent implementation of several orders of magnitude larger MPAs in New Caledonia and abroad show that recent Indo-Pacific MPAs are now sufficiently large to protect the home ranges of this species, including males, across its geographical range. However, protection efforts are concentrated in a few regions and cannot provide adequate protection at a global scale.

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.

The worldwide decline of coral reefs necessitates targeting management solutions that can sustain reefs and the livelihoods of the people who depend on them. However, little is known about the context in which different reef management tools can help to achieve multiple social and ecological goals. Because of nonlinearities in the likelihood of achieving combined fisheries, ecological function, and biodiversity goals along a gradient of human pressure, relatively small changes in the context in which management is implemented could have substantial impacts on whether these goals are likely to be met. Critically, management can provide substantial conservation benefits to most reefs for fisheries and ecological function, but not biodiversity goals, given their degraded state and the levels of human pressure they face.

Aim To investigate biotic and abiotic correlates of reef-fish species richness across multiple spatial scales. Location Tropical reefs around the globe, including 485 sites in 109 sub-provinces spread across 14 biogeographic provinces. Time period Present. Major taxa studied 2,523 species of reef fish. Methods We compiled a database encompassing 13,050 visual transects. We used hierarchical linear Bayesian models to investigate whether fish body size, reef area, isolation, temperature, and anthropogenic impacts correlate with reef-fish species richness at each spatial scale (i.e., sites, sub-provinces, provinces). Richness was estimated using coverage-based rarefaction. We also tested whether species packing (i.e., transect-level species richness/m(2)) is correlated with province-level richness. Results Body size had the strongest effect on species richness across all three spatial scales. Reef area and temperature were both positively correlated with richness at all spatial scales. At the site scale only, richness decreased with reef isolation. Species richness was not correlated with proxies of human impacts. Species packing was correlated with species richness at the province level following a sub-linear power function. Province-level differences in species richness were also mirrored by patterns of body size distribution at the site scale. Species-rich provinces exhibited heterogeneous assemblages of small-bodied species with small range sizes, whereas species-poor provinces encompassed homogeneous assemblages composed by larger species with greater dispersal capacity. Main conclusions Our findings suggest that body size distribution, reef area and temperature are major predictors of species richness and accumulation across scales, consistent with recent theories linking home range to species-area relationships as well as metabolic effects on speciation rates. Based on our results, we hypothesize that in less diverse areas, species are larger and likely more dis

Baselines and benchmarks (B&Bs) are needed to evaluate the ecological status and fisheries potential of coral reefs. B&Bs may depend on habitat features and energetic limitations that constrain biomass within the natural variability of the environment and fish behaviors. To evaluate if broad B&Bs exist, we compiled data on the biomass of fishes in ~1000 reefs with no recent history of fishing in 19 ecoregions. These reefs spanned the full longitude and latitude of Indian and Pacific Ocean reefs and included older high-compliance fisheries closures (>15 yr closure) and remote reef areas (>9 h travel time from fisheries markets). There was no significant change in biomass over the 15 to 48 yr closure period but closures had only ~40% of the biomass (740 kg ha −1 , lower confidence interval [LCI] = 660 kg ha −1 , upper confidence interval [UCI] = 810 kg ha −1 , n = 157) of remote tropical reefs (1870 [1730, 2000] kg ha −1 , n = 503). Remote subtropical reefs had lower biomass (950 [860, 1040] kg ha −1 , n = 329) than tropical reefs. Closures and remote reef fish biomass responded differently to environmental variables of coral cover, net primary productivity, and light, indicating that remote reefs are more limited by productivity and habitat than closures. Closures in fished seascapes are unlikely to achieve the biomass and community composition of remote reefs, which suggests fisheries benchmarks will differ substantially from wilderness baselines. A fishery benchmark (B 0 ) of ~1000 kg ha −1 adjusted for geography is suggested for fisheries purposes. For ecological purposes, a wilderness baseline of ~1900 kg ha −1 is appropriate for including large and mobile species not well protected by closures.

© 2019 The Authors In the present era of rapid global change, innovative monitoring methods can greatly enhance our ability to detect ecological disturbances and prioritise conservation areas in a timely and cost-effective manner. While Passive Acoustic Monitoring (PAM) has recently emerged as a promising tool for monitoring ecological states in marine environments, the specifics of how to apply this method remains poorly defined. In this study we examined how different combinations of sampling settings (frequency bandwidth, time of sampling (day/night), and sample duration) influenced the ability of two acoustic indices, the Sound Pressure Level (SPL) and the Acoustic Complexity Index (ACI), to discriminate different ecological states (ecostates) of coral reefs. We applied an iterative approach to select the most efficient and consistent combinations of sampling settings to use for these two acoustic indices, depending on the stability of their discriminating power across different time scales (successive days, moon phases, and seasons), and the minimum sampling effort required for reliable ecostate assessment. The ability of SPL and ACI to discriminate ecostate-specific soundscapes was more stable and required less sampling effort at nighttime. For indices calculated in the higher frequency band (>2 kHz), very short recording times (≤20 min divided into 5 s samples) were sufficient to discriminate ecostates, whereas longer recording times (≥200 min divided into 5 min samples) were necessary when using indices calculated in the lower frequency bands (<1 kHz). An optimised sampling scheme, i.e. the group of the five best combinations of settings to discern among coral reef ecostates, was determined at Reunion Island, Indian Ocean, then tested at New Caledonia, Pacific Ocean. Here, the classifications obtained through visual surveys and with the optimised acoustic sampling scheme were congruent. The concordance of our results with visual fish counts confirms the pote

© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. The grey reef shark, Carcharhinus amblyrhynchos, is one of the most abundant coral reef sharks throughout the Indo-Pacific. However, this species has been critically impacted across its range, with well-documented population declines of > 90% attributed to human activities. A key knowledge gap in the successful implementation of grey reef shark conservation plans is the understanding of large-scale movement patterns, along with the associated biological and ecological drivers. To address this shortfall, we acoustically monitored 147 adult and juvenile grey reef sharks of all sexes for more than 2 yr across the New Caledonian archipelago, West Pacific. Here, we document multiple adult males undertaking return journeys of up to nearly 700 km in consecutive years. This constitutes the first evidence of repeated long-range migrations for this species. Although only a limited number of adult males were definitively tracked undertaking migrations, similar timing in changes in the detection patterns of a further 13 animals, mostly adult males, suggests this behavior may be more common than previously thought. The paucity of evidence for juvenile migrations and timing of adult movements suggest that mating is the motivation behind these migrations. Our results have important implications for management, given the potential of mature individuals to recurrently travel outside managed or protected areas. Future management of this species clearly needs to consider the importance of large-scale migratory behaviors when developing management plans.

Determining whether many functionally complementary species or only a subset of key species are necessary to maintain ecosystem functioning and services is a critical question in community ecology and biodiversity conservation. Identifying such key species remains challenging, especially in the tropics where many species co-occur and can potentially support the same or different processes. Here, we developed a new community-wide scan (CWS) approach, analogous to the genome-wide scan, to identify fish species that significantly contribute, beyond the socio-environmental and species richness effects, to the biomass and coral cover on Indo-Pacific reefs. We found that only a limited set of species (51 out of approx. 400, approx. 13%), belonging to various functional groups and evolutionary lineages, are strongly and positively associated with fish biomass and live coral cover. Many of these species have not previously been identified as functionally important, and thus may be involved in unknown, yet important, biological mechanisms that help sustain healthy and productive coral reefs. CWS has the potential to reveal species that are key to ecosystem functioning and services and to guide management strategies as well as new experiments to decipher underlying causal ecological processes. © 2018 The Author(s).

Coral reefs provide ecosystem goods and services for millions of people in the tropics, but reef conditions are declining worldwide. Effective solutions to the crisis facing coral reefs depend in part on understanding the context under which different types of conservation benefits can be maximized. Our global analysis of nearly 1,800 tropical reefs reveals how the intensity of human impacts in the surrounding seascape, measured as a function of human population size and accessibility to reefs (“gravity”), diminishes the effectiveness of marine reserves at sustaining reef fish biomass and the presence of top predators, even where compliance with reserve rules is high. Critically, fish biomass in high-compliance marine reserves located where human impacts were intensive tended to be less than a quarter that of reserves where human impacts were low. Similarly, the probability of encountering top predators on reefs with high human impacts was close to zero, even in high-compliance marine reserves. However, we find that the relative difference between openly fished sites and reserves (what we refer to as conservation gains) are highest for fish biomass (excluding predators) where human impacts are moderate and for top predators where human impacts are low. Our results illustrate critical ecological trade-offs in meeting key conservation objectives: reserves placed where there are moderate-to-high human impacts can provide substantial conservation gains for fish biomass, yet they are unlikely to support key ecosystem functions like higher-order predation, which is more prevalent in reserve locations with low human impacts.

© 2018 National Academy of Sciences. All Rights Reserved. Coral reefs provide ecosystem goods and services for millions of people in the tropics, but reef conditions are declining worldwide. Effective solutions to the crisis facing coral reefs depend in part on understanding the context under which different types of conservation benefits can be maximized. Our global analysis of nearly 1,800 tropical reefs reveals how the intensity of human impacts in the surrounding seascape, measured as a function of human population size and accessibility to reefs (“gravity”), diminishes the effectiveness of marine reserves at sustaining reef fish biomass and the presence of top predators, even where compliance with reserve rules is high. Critically, fish biomass in high-compliance marine reserves located where human impacts were intensive tended to be less than a quarter that of reserves where human impacts were low. Similarly, the probability of encountering top predators on reefs with high human impacts was close to zero, even in high-compliance marine reserves. However, we find that the relative difference between openly fished sites and reserves (what we refer to as conservation gains) are highest for fish biomass (excluding predators) where human impacts are moderate and for top predators where human impacts are low. Our results illustrate critical ecological trade-offs in meeting key conservation objectives: reserves placed where there are moderate-to-high human impacts can provide substantial conservation gains for fish biomass, yet they are unlikely to support key ecosystem functions like higher-order predation, which is more prevalent in reserve locations with low human impacts.

© 2018 The Author(s). Determining whether many functionally complementary species or only a subset of key species are necessary to maintain ecosystem functioning and services is a critical question in community ecology and biodiversity conservation. Identifying such key species remains challenging, especially in the tropics where many species co-occur and can potentially support the same or different processes. Here, we developed a new community-wide scan (CWS) approach, analogous to the genome-wide scan, to identify fish species that significantly contribute, beyond the socio-environmental and species richness effects, to the biomass and coral cover on Indo-Pacific reefs. We found that only a limited set of species (51 out of approx. 400, approx. 13%), belonging to various functional groups and evolutionary lineages, are strongly and positively associated with fish biomass and live coral cover. Many of these species have not previously been identified as functionally important, and thus may be involved in unknown, yet important, biological mechanisms that help sustain healthy and productive coral reefs. CWS has the potential to reveal species that are key to ecosystem functioning and services and to guide management strategies as well as new experiments to decipher underlying causal ecological processes.

© 2018 The Authors. In the era of "Anthropocene defaunation," large species are often no longer detected in habitats where they formerly occurred. However, it is unclear whether this apparent missing, or "dark," diversity of megafauna results from local species extirpations or from failure to detect elusive remaining individuals. We find that despite two orders of magnitude less sampling effort, environmental DNA (eDNA) detects 44% more shark species than traditional underwater visual censuses and baited videos across the New Caledonian archipelago (south-western Pacific). Furthermore, eDNA analysis reveals the presence of previously unobserved shark species in humanimpacted areas. Overall, our results highlight a greater prevalence of sharks than described by traditional survey methods in both impacted and wilderness areas. This indicates an urgent need for large-scale eDNA assessments to improve monitoring of threatened and elusive megafauna. Finally, our findings emphasize the need for conservation efforts specifically geared toward the protection of elusive, residual populations.

Coral reefs are among the most species-rich and threatened ecosystems on Earth, yet the extent to which human stressors determine species occurrences, compared with biogeography or environmental conditions, remains largely unknown. With ever-increasing human-mediated disturbances on these ecosystems, an important question is not only how many species can inhabit local communities, but also which biological traits determine species that can persist (or not) above particular disturbance thresholds. Here we show that human pressure and seasonal climate variability are disproportionately and negatively associated with the occurrence of large-bodied and geographically small-ranging fishes within local coral reef communities. These species are 67% less likely to occur where human impact and temperature seasonality exceed critical thresholds, such as in the marine biodiversity hotspot: the Coral Triangle. Our results identify the most sensitive species and critical thresholds of human and climatic stressors, providing opportunity for targeted conservation intervention to prevent local extinctions.

© 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Ongoing declines in the structure and function of the world's coral reefs require novel approaches to sustain these ecosystems and the millions of people who depend on them. A presently unexplored approach that draws on theory and practice in human health and rural development is to systematically identify and learn from the 'outliers' - places where ecosystems are substantially better ('bright spots') or worse ('dark spots') than expected, given the environmental conditions and socioeconomic drivers they are exposed to. Here we compile data from more than 2,500 reefs worldwide and develop a Bayesian hierarchical model to generate expectations of how standing stocks of reef fish biomass are related to 18 socioeconomic drivers and environmental conditions. We identify 15 bright spots and 35 dark spots among our global survey of coral reefs, defined as sites that have biomass levels more than two standard deviations from expectations. Importantly, bright spots are not simply comprised of remote areas with low fishing pressure; they include localities where human populations and use of ecosystem resources is high, potentially providing insights into how communities have successfully confronted strong drivers of change. Conversely, dark spots are not necessarily the sites with the lowest absolute biomass and even include some remote, uninhabited locations often considered near pristine. We surveyed local experts about social, institutional, and environmental conditions at these sites to reveal that bright spots are characterized by strong sociocultural institutions such as customary taboos and marine tenure, high levels of local engagement in management, high dependence on marine resources, and beneficial environmental conditions such as deep-water refuges. Alternatively, dark spots are characterized by intensive capture and storage technology and a recent history of environmental shocks.