Animal body-size variation influences multiple processes in marine ecosystems, but habitat heterogeneity has prevented a comprehensive assessment of size across pelagic (midwater) and benthic (seabed) systems along anthropic gradients. In this work, we derive fish size indicators from 17,411 stereo baited-video deployments to test for differences between pelagic and benthic responses to remoteness from human pressures and effectiveness of marine protected areas (MPAs). From records of 823,849 individual fish, we report divergent responses between systems, with pelagic size structure more profoundly eroded near human markets than benthic size structure, signifying greater vulnerability of pelagic systems to human pressure. Effective protection of benthic size structure can be achieved through MPAs placed near markets, thereby contributing to benthic habitat restoration and the recovery of associated fishes. By contrast, recovery of the world's largest and most endangered fishes in pelagic systems requires the creation of highly protected areas in remote locations, including on the High Seas, where protection efforts lag.

Abstract 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.

AimThe Mediterranean Sea is one of the most anthropized seas in the world but also a marine biodiversity hotspot with many fish species under threat. The main goal of the study is to test whether on the heavily fished and anthropized Mediterranean coast, the less impacted Corsica and Balearic Islands, can be considered as refugia for threatened and elasmobranch fishes independently of protection by marine reserves.LocationThe French Mediterranean coast and three north-western Mediterranean islands: Corsica and also Mallorca and Minorca from the Balearic archipelago.MethodsWe performed 187 fish surveys using environmental DNA metabarcoding on three islands and 109 along the continental coast. Of the 78 surveys on islands 22 correspond to no-take marine reserves and of the 109 continental surveys 26 were carried out within reserves. After eDNA filtration, extraction, amplification, and sequencing we estimated the number of fish species but also the number commercial, threatened and elasmobranch fish species on each sample. We then performed an ANOVA by permutation to test the effect of insularity and protection on these four biodiversity metrics. We also modelled these four biodiversity metrics as a function of protection and human pressure but also environmental, habitat and sampling conditions. We also built species accumulation curves to obtain asymptotes representing the potential regional pools for each species category on both island and continental coasts.ResultsWe obtained a total of 175,982,610 reads over the 187 eDNA samples that were assigned to 153 fish species including 17 elasmobranch species among which 7 were only detected on islands. We observed a higher total fish richness on continental than island surveys regardless of protection but a higher threatened and elasmobranch fish richness on the island than on continental surveys. We obtained a significant, negative and predominant human gravity impact on the diversity of elasmobranch species. The modelled asymptote reached 148 teleostean fish species on islands and 196 on the continental coastline with a very similar rate of diversity increase with sampling effort but the shape of the species accumulation curves differed markedly for elasmobranchs with a stronger increase in diversity with sampling effort on islands.Main ConclusionsOur findings highlight that Mediterranean islands can be refugia for sharks and rays but also threatened fishes in this overexploited region. Our results also suggest that reducing or banning trawling activities may play a key role for conserving vulnerable fishes, beyond the benefits of no-take marine reserves, which appear limited on these large home-range species.

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 alpha-and beta-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 alpha-and beta-diversity measured from our barcodes, and phylogenetic but also functional diversity. Results: We show that fish eDNA MOTU and sequence alpha-and beta-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 Human exploitation has profoundly depleted animal populations in the ocean, leading to declines in ecosystem productivity, resilience, and contributions to people 1,2 . However, it remains unclear how size structure of fish populations varies across marine habitat and levels of human exploitation while simultaneously underpinning food web architecture and ecosystem functioning 3 . Here, we process 6,701 pelagic and 10,710 benthic stereo-video deployments across all the oceans to extract body size of over 800,000 individual fish, spanning 6 orders of magnitude from zooplankton size-classes (<1 g), to large oceanic predators (>1,000 kg), in order to ultimately assess vulnerability to exploitation and responses to protection status. Size-spectra analysis reveals peaks in body size distributions which differ in their position between pelagic and benthic habitats. Typical body size of relatively small and large individuals is greater in strictly protected areas remote from human markets, than in unprotected areas close to markets. Pelagic size-spectra are more sensitive to market remoteness and respond more strongly to protection than their benthic counterparts which are more species-rich, and therefore more likely to provide trophic replacements 4 under exploitation, owing to body size redundancy 5 . This contrasted result suggests that fully protected areas can partly mitigate human impacts close to markets in benthic habitats while in pelagic habitats effective protection requires remoteness from humans. Thus, the restoration of fish body-size spectra, including some of the world’s largest and most endangered vertebrates 6 , can be promoted by implementing fully protected areas in pelagic habitats, particularly in remote locations.

AbstractMesophotic marine ecosystems are characterized by lower light penetration supporting specialized fish fauna. Due to their depths (−30–−150 m), accessibility is challenging, and the structure of mesophotic fish assemblages is generally less known than either shallow reefs or deep zones with soft bottoms which are generally trawled. Environmental DNA metabarcoding from seawater filtered in situ could improve our ability to monitor the diversity of mesophotic ecosystems. Here, we developed and tested a submersible standalone pumping device allowing targeted marine water filtering to explore the biodiversity of two mesophotic ecosystems, one temperate along the Provence coast in the North‐Western Mediterranean Sea and one tropical at the seamount La Pérouse in the Western Indian Ocean. We filtered water samples from depths ranging between 0 and 200 m in the Mediterranean Sea and between 60 and 140 m in the Indian Ocean and applied a metabarcoding protocol using the teleo primer pair targeting the 12S mitochondrial rDNA (Actinopterygii and Chondrichthyes). For both study regions, our eDNA surveys were able to recover highly diverse fish assemblages, and the compositional analysis of eDNA samples showed both a marked signal of fish compositional turnover and overlapping taxa between depth zones. Further, we observed that a substantial number of species were found in samples collected in depths beyond their reported depth range suggesting an underestimation of species' depth tolerances. eDNA metabarcoding should thus complement existing knowledge of species' geographic distributions across space and depth. Overall, our results demonstrate the potential of eDNA metabarcoding for future mesophotic surveys as it allows fast and broad biodiversity assessment.

Species inventories are the building blocks of our assessment of biodiversity patterns and human impact. Yet, historical inventories based on visual observations are often incomplete, impairing subsequent analyses of ecological mechanisms, extinction risk and management success. Environmental DNA (eDNA) metabarcoding is an emerging tool that can provide wider biodiversity assessments than classical visual-based surveys. However, eDNA-based inventories remain limited by sampling effort and reference database incompleteness. In this study, we propose a new framework coupling eDNA surveys and sampling-theory methods to estimate species richness in under-sampled and hyper-diverse regions where some species remain absent from the checklist or undetected by visual surveys. We applied this framework to the coastal fish diversity in the heart of the coral triangle, the richest marine biodiversity hotspot worldwide. Combining data from 279 underwater visual censuses, 92 eDNA samples and an extensive custom genetic reference database, we show that eDNA metabarcoding recorded 196 putative species not detected by underwater visual census including 37 species absent from the regional checklist. We provide an updated checklist of marine fishes in the 'Raja Ampat Bird's Head Peninsula' ecoregion with 2534 species including 1761 confirmed and 773 highly probable presences. The Chao lower-bound diversity estimator, based on the incidence of rare species, shows that the region potentially hosts an additional 123 fish species, including pelagic, cryptobenthic and vulnerable species. The extended and hidden biodiversity along with their asymptotic estimates highlight the ability of eDNA to expand regional inventories and species distributions to better guide conservation strategies.

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.

In a context of marine biodiversity erosion, the need to better understand the effects of overfishing stands out. New genetic techniques such as environmental DNA (eDNA) metabarcoding have emerged and allow the detection of a wider range of species compared to conventional methods, but still fall short of providing reliable abundance estimations and subsequent ecological indicators. In this paper, we propose a combination of metabarcoding and quantitative polymerase chain reaction to obtain the quantity of eDNA molecules per species. This method was used inside and outside six no-take Mediterranean marine reserves to measure the effect of the protection on fish species and build a new indicator. Even if the total quantity of fish eDNA molecules was not different between the inside and outside of the reserves, we detected that cryptobenthic fish eDNA was significantly associated to the outside of reserves. Based on this observation, we propose a novel ecological indicator, the Demerso-pelagic to Benthic fish eDNA Ratio (DeBRa), taking advantage of the eDNA capacity to detect cryptobenthic reef fishes which are often missed by classical surveys. The DeBRa was significantly higher inside reserves, reflecting a higher relative quantity of eDNA molecules belonging to pelagic and demersal fishes under protection against fishing, therefore it appears to be a reliable eDNA-based indicator of human pressure. Furthermore, the DeBRa was not sensitive to habitat or environmental variations and does not require a complete reference database of eDNA sequences since it can rely on sequences assigned at the genus or family scale if possible and necessary.

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. One of the major limitations currently impairing the large-scale application of DNA-based inventories, such as eDNA or bulk-sample analysis is the lack of species sequences available in public genetic databases. These gaps are still largely unknown spatially and taxonomically for most regions of the world, which can hinder targeted future sequencing efforts. We propose GAPeDNA, a user-friendly web-interface (Fig. 1) that provides a global overview of genetic database completeness for a given taxon across space and conservation status. As an initial 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 DNA-based inventories at larger scale. It is flexible and can be expanded to other taxa and primers upon data availability. Using our global fish case study, we show that gaps increase toward the tropics where species diversity and the number of threatened species were 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. As an open-acces, updatable and flexible tool, GAPeDNA can be used to evaluate the completeness of sequence reference libraries of various markers and for any taxonomic group.

The link between biodiversity and ecosystem functioning has been the topic of considerable research, but it remains unclear how biodiversity decline is compromising ecosystem functionality, particularly in the pelagic realm. Here, we explore how pelagic fish species diversity relates to functional diversity by sampling two locations, which, on the basis of biogeography, environmental conditions and human pressures, were expected to host pronounced differences in species composition and abundances and therefore functionality. Strings of five drifting mid-water Baited Remote Underwater Video Systems were used to survey pelagic vertebrate diversity and abundance in two isolated oceanic island systems, the Malpelo Fauna and Flora Sanctuary—a large, 25-year-old marine protected area—and an unprotected area in Cape Verde. Functional diversity, which offers insight into a community’s resilience against disturbance, was analysed using six key functional traits of marine fishes. Abundance was recorded as MaxN, the maximum number of individuals of a given species in a single frame during the 2-h deployment time. Cape Verde showed high overall abundance (Total MaxN 873) and low biomass (3559 kg), with a predominance of smaller fishes. Malpelo showed high biomass (7839 kg) but lower abundance (Total MaxN 465), with a predominance of large species. Species and functional diversity were marginally different between locations. Multivariate analysis of species relative abundances showed significant divergence between locations, although community functional traits overlapped strongly, suggesting that both communities share a similar structure and vulnerability. The existence of a common functional ‘backbone’ in diverging species communities across the oceans, under different productivity regimes, and under different protection levels, suggests that although pelagic communities may differ considerably in terms of species composition, this does not translate into a differing functional structure and resilience potential. Whether this vulnerability is a common feature of pelagic communities and how this contrasts with benthic systems warrants further research.

AbstractEnvironmental 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.

Abstract Monitoring large marine mammals is challenging due to their low abundances in general, an ability to move over large distances and wide geographical range sizes. The distribution of the pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales is informed by relatively rare sightings, which does not permit accurate estimates of their distribution ranges. Hence, their conservation status has long remained Data Deficient (DD) in the Red list of the International Union for Conservation of Nature (IUCN), which prevent appropriate conservation measures. Environmental DNA (eDNA) metabarcoding uses DNA traces left by organisms in their environments to detect the presence of targeted taxon, and is here proved to be useful to increase our knowledge on the distribution of rare but emblematic megafauna. Retrieving eDNA from filtered surface water provides the first detection of the Dwarf sperm whale (Kogia sima) around the remote Malpelo island (Colombia). Environmental DNA collected during oceanic missions can generate better knowledge on rare but emblematic animals even in regions that are generally well sampled for other taxa.

Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long‐term remote video to assess species’ phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.

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.

Quantifying the diversity of species 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, the reliability of biodiversity detection from eDNA samples can be low in marine environments because eDNA density is low and certainly patchy in this vast, heterogenous and dynamic environment. So, the number of sampling replicates and filtered volume necessary to obtain accurate estimates of biodiversity in rich tropical marine environments using eDNA metabarcoding is still unknown. Here, we used a paired sampling design of 30L per replicate on 68 reef transects from 8 sites in three tropical regions and identified fish Molecular Taxonomic Units (MOTUs) using a 12S marker. We quantified local biodiversity variation as MOTU richness, compositional turnover and compositional nestedness between replicated pairs of seawater samples. We report 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, localised diversity accumulation curves showed that even 6 replicates (180L) in the same location underestimated local diversity (for an area <1km). However, sampling of regional diversity using ∼25 replicates in variable locations (often covering 10s of km) achieved saturation of biodiversity accumulation curves. Our results demonstrate high variability of diversity estimates perhaps arising from heterogeneous and local distribution of eDNA distribution in seawater or highly skewed frequencies of eDNA traces. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes of local assemblages. Future biomonitoring efforts could be strongly undermined by a high level of false-negative detections under low replication protocols. We reveal the need to increase replicates or increase sampled water volume to better inform management of marine biodiversity using eDNA.

Coral reefs host the highest fish diversity on Earth despite covering less than 0.1% of the ocean’s seafloor. At the same time they are also extremely threatened. Data syntheses over decades of surveys estimate the total number of coral reef fishes to vary from 2,400 to 8,000 species distributed among roughly 100 families. But this diversity remains largely unknown. Here, we investigated how environmental DNA (eDNA) could describe the distribution of fish diversity in coral reefs. We generated 504,457,267 raw 12S ribosomal DNA (rDNA) sequence reads from 251 samples (2,693 PCR replicates) collected at 25 sites in 145 stations covering five regions across the Indian, Pacific and Atlantic Oceans. Bioinformatic analysis clustered these sequences into 2,160 molecular operational taxonomic units (MOTUs) corresponding to distinct species (Marques 2020) We compared our results, with visual census surveys from Reef Life Survey, on 2,813 transects in tropical regions. Our outcomes demonstrate the capacity of eDNA metabarcoding from water samples to reconstruct well-known biogeographic patterns of fish diversity on coral reefs, such as species richness gradients towards the coral triangle, and family proportion stability across sites (Bellwood and Hughes 2001). Additionally, eDNA survey data documented a higher fish species (16%) and family (50%) diversity than estimates obtained with underwater visual surveys carried out on 20 times more sites. MOTU richness per family retrieved with eDNA closely matched fish species richness within families recorded in visual census data. However, eDNA revealed higher richness of reef-associated species and species from adjacent habitats, of cryptobenthic or nocturnal species, but also of pelagic and wide-ranging species. eDNA survey data showed that fish diversity is characterized by spatially heterogeneous species assemblages among regions, with more dissimilarity among adjacent coral reefs than detected with visual survey data. Unlike visual surveys, eDNA metabarcoding revealed the same prevalence of rarity as expected under the neutral theory of biodiversity, suggesting the predominance of random processes and ecological equivalence within trophic groups at large scale to explain fish biodiversity patterns on coral reefs. Our study demonstrates how sequencing eDNA from water provides a rapid and effective approach to characterize and assess coral reef diversity across large spatial scales, thereby also uncovering hidden biodiversity patterns.

Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA (eDNA) metabarcoding, with three primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the estuary of the Don Diego River in Colombia. With eDNA, we detected not only aquatic organisms, including fishes, amphibians, and reptiles, but also a large diversity of terrestrial, arboreal, and flying vertebrates, including mammals and birds, living in the estuary surroundings. Further, the eDNA signal remained relatively localized along the watercourse. A transect from the deep outer section of the estuary, across the river mouth toward the inner section of the river, showed marked taxonomic turnover from typical marine to freshwater fishes, while eDNA of terrestrial and arboreal species was mainly found in the inner section of the estuary. Our results indicate that eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem. Abstract in Spanish is available with online material.

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 (R² = 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.