Environmental DNA reveals unsuspected shark diversity and calls for monitoring and protection of residual populations.

Environmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal DNA traces. Examining the capacity of eDNA to provide accurate biodiversity measures in species‐rich ecosystems such as coral reefs is a prerequisite for their application in long‐term monitoring. Here, we surveyed two Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected a large quantity of surface water (30 L per filter) above the reefs and applied a metabarcoding protocol using three different primer sets targeting the 12S mitochondrial DNA, which are specific to the vertebrates Actinopterygii and Elasmobranchii. By assigning eDNA sequences to species using a public reference database, we detected the presence of 107 and 85 fish species, 106 and 92 genera, and 73 and 57 families in Providencia and Gayraca Bay, respectively. Of the species identified using eDNA, 32.7% (Providencia) and 18.8% (Gayraca) were also found in the UVCs. We further found congruence in genus and species richness and abundance between eDNA and UVC approaches in Providencia but not in Gayraca Bay. Mismatches between eDNA and UVC had a phylogenetic and ecological signal, with eDNA detecting a broader phylogenetic diversity and more effectively detecting smaller species, pelagic species and those in deeper habitats. Altogether, eDNA can be used for fast and broad biodiversity surveys and is applicable to species‐rich ecosystems in the tropics, but improved coverage of the reference database is required before this new method could serve as an effective complement to traditional census methods.

Aim Environmental DNA metabarcoding has recently emerged as a non‐invasive tool for aquatic biodiversity inventories, frequently surpassing traditional methods for detecting a wide range of taxa in most habitats. The major limitation currently impairing the large‐scale application of eDNA‐based inventories is the lack of species sequences available in public genetic databases. Unfortunately, these gaps are still unknown spatially and taxonomically, hindering targeted future sequencing efforts. Innovation We propose GAPeDNA, a user‐friendly web interface that provides a global overview of genetic database completeness for a given taxon across space and conservation status. As an application, we synthetized data from regional checklists for marine and freshwater fishes along with their IUCN conservation status to provide global maps of species coverage using the European Nucleotide Archive public reference database for 19 metabarcoding primers. This tool automatizes the scanning of gaps in these databases to guide future sequencing efforts and support the deployment of eDNA inventories at larger scale. This tool is flexible and can be expanded to other taxa and primers upon data availability. Main conclusions Using our global fish case study, we show that gaps increase towards the tropics where species diversity and the number of threatened species are the highest. It highlights priority areas for fish sequencing like the Congo, the Mekong and the Mississippi freshwater basins which host more than 60 non‐sequenced threatened fish species. For marine fishes, the Caribbean and East Africa host up to 42 non‐sequenced threatened species. By presenting the global genetic database completeness for several primers on any taxa and building an open‐access, updatable and flexible tool, GAPeDNA appears as a valuable contribution to support any kind of eDNA metabarcoding study.

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.

Reef sharks are declining world‐wide under ever‐increasing fishing pressure, with potential consequences on ecosystem functioning. Marine protected areas (MPAs) are currently one of the management tools used to counteract the pervasive impacts of fishing. However, MPAs in which reef sharks are abundant tend to be located in remote and underexploited areas, preventing a fair assessment of management effectiveness beyond remoteness from human activities. Here, we determine the conditions under which MPAs can effectively protect sharks along a wide gradient of reef accessibility, from the vicinity of a regional capital towards remote areas, using 385 records from baited remote underwater video systems and 2,790 underwater visual censuses performed in areas open to fishing and inside 15 MPAs across New Caledonia (South‐Western Pacific). We show that even one of the world's oldest (43 years), largest (172 km2) and most restrictive (no‐entry) MPA (Merlet reserve) on coral reefs has between 17.3% and 45.3% fewer shark species and between 37.2% and 79.8% fewer shark abundance than remote areas in a context where sharks are not historically exploited. On coral reefs situated at less than 1 hr of travel time from humans, shark populations are so low in abundance (less than 0.05 individuals per 1,000 m2) that their functional roles are severely limited. Synthesis and applications. Remote areas are the last sanctuaries for reef sharks, providing a new baseline from which to evaluate human impacts on the species. However, there is no equivalent close to human activities even in large, old and strongly restrictive marine protected areas. As such sharks deserve strong protection efforts. The large, no‐entry marine protected areas, close to humans, offer limited benefits for reef shark populations, but provide more realistic conservation targets for managers of human‐dominated reefs. The exclusion of human activities on a sufficiently large area is key to protect reef shark populations. However, this strategy remains difficult to apply in many countries critically depending on reef resources for food security or livelihood.

Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict ( R ² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.

Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.

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