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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., Global Ecology and Biogeography, ISSN:1466-822X, ISSN:1466-8238

Mesophotic 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., Environmental DNA, 5 (1), ISSN:2637-4943

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., Scientific Reports, 12 (1), ISSN:2045-2322

Supplementary Methods

Statistical sensitivity analyses

The documentation of biodiversity distribution through species range identification is crucial for macroecology, biogeography, conservation, and restoration. However, for plants, species range maps remain scarce and often inaccurate. We present a novel approach to map species ranges at a global scale, integrating polygon mapping and species distribution modelling (SDM). We develop a polygon mapping algorithm by considering distances and nestedness of occurrences. We further apply an SDM approach considering multiple modelling algorithms, complexity levels, and pseudo-absence selections to map the species at a high spatial resolution and intersect it with the generated polygons. We use this approach to construct range maps for all 1957 species of Fagales and Pinales with data compilated from multiple sources. We construct high-resolution global species richness maps of these important plant clades, and document diversity hotspots for both clades in southern and south-western China, Central America, and Borneo. We validate the approach with two representative genera, Quercus and Pinus, using previously published coarser range maps, and find good agreement. By efficiently producing high-resolution range maps, our mapping approach offers a new tool in the field of macroecology for studying global species distribution patterns and supporting ongoing conservation efforts., Entomologia Experimentalis et Applicata, 170 (6), ISSN:0013-8703, ISSN:1570-7458

WOS:000729415000001; International audience; 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.

Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The α and γ diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively with body size. Pelagic larval duration is found to be negatively related to genetic β diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.

Supplementary methods and discussion, Additional figures and simulations performed with allopatric model

Knowledge of species composition and their interactions, in the form of interaction networks, is required to understand processes shaping their distribution over time and space. As such, comparing ecological networks along environmental gradients represents a promising new research avenue to understand the organization of life. Variation in the position and intensity of links within networks along environmental gradients may be driven by turnover in species composition, by variation in species abundances and by abiotic influences on species interactions. While investigating changes in species composition has a long tradition, so far only a limited number of studies have examined changes in species interactions between networks, often with differing approaches. Here, we review studies investigating variation in network structures along environmental gradients, highlighting how methodological decisions about standardization can influence their conclusions. Due to their complexity, variation among ecological networks is frequently studied using properties that summarize the distribution or topology of interactions such as number of links, connectance, or modularity. These properties can either be compared directly or using a procedure of standardization. While measures of network structure can be directly related to changes along environmental gradients, standardization is frequently used to facilitate interpretation of variation in network properties by controlling for some co‐ variables, or via null models. Null models allow comparing the deviation of empirical networks from random expectations and are expected to provide a more mechanistic understanding of the factors shaping ecological networks when they are coupled with functional traits. As an illustration, we compare approaches to quantify the role of trait matching in driving the structure of plant–hummingbird mutualistic networks, i.e. a direct comparison, standardized by null models and hypothesis‐based metaweb. Overall, our analysis warns against a comparison of studies that rely on distinct forms of standardization, as they are likely to highlight different signals. Fostering a better understanding of the analytical tools available and the signal they detect will help produce deeper insights into how and why ecological networks vary along environmental gradients.

International audience; Aim: The importance of quantifying the contribution of historical processes in shaping current biodiversity patterns is now recognized, but quantitative approaches that explicitly link speciation, extinction and dispersal processes to palaeo-environmental changes are currently lacking. Here, we propose a spatial diversification model of lineages through time (SPLIT) based on the reconstruction of palaeo-environments. We illustrate our approach using mangroves as a case study and evaluate whether habitat changes caused by plate tectonics explain the current biodiversity patterns of this group. Innovations: The SPLIT model allows one to simulate the evolutionary dynamics of species ranges by spatially linking speciation, extinction and dispersal processes to habitat changes over geological time periods. The SPLIT model provides a mechanistic expectation of speciation and extinction assuming that species are ecologically identical and not interacting. The likelihood of speciation and extinction is equivalent across species and depends on two dispersal parameters interacting with habitat dynamics (d a maximum dispersal distance and ds a distance threshold beyond which gene flow is absent). Beyond classical correlative approaches, this model tracks biodiversity dynamics under palaeo-environmental changes and provides multiple expectations (i.e., alpha-, beta-diversity, phylogenies) that can be compared to empirical patterns. Main conclusions: The SPLIT model allows a better understanding of the origin of biodiversity by explicitly accounting for habitat changes over geological times. The simulations applied to the mangrove case study reproduced the observed longitudinal gradient in species richness, the empirical pattern of beta-diversity and also provided inference on diversification rates. Future developments may include niche evolution and species interactions to evaluate the importance of non-neutral mechanisms. The method is fully implemented in the InsideDNA platform for bioinformatics analyses, and all modelling results can be accessed via interactive web links.

Knowledge of species composition and their interactions, in the form of interaction networks, is required to understand processes shaping their distribution over time and space. As such, comparing ecological networks along environmental gradients represents a promising new research avenue to understand the organization of life. Variation in the position and intensity of links within networks along environmental gradients may be driven by turnover in species composition, by variation in species abundances and by abiotic influences on species interactions. While investigating changes in species composition has a long tradition, so far only a limited number of studies have examined changes in species interactions between networks, often with differing approaches. Here, we review studies investigating variation in network structures along environmental gradients, highlighting how methodological decisions about standardization can influence their conclusions. Due to their complexity, variation among ecological networks is frequently studied using properties that summarize the distribution or topology of interactions such as number of links, connectance, or modularity. These properties can either be compared directly or using a procedure of standardization. While measures of network structure can be directly related to changes along environmental gradients, standardization is frequently used to facilitate interpretation of variation in network properties by controlling for some co‐variables, or via null models. Null models allow comparing the deviation of empirical networks from random expectations and are expected to provide a more mechanistic understanding of the factors shaping ecological networks when they are coupled with functional traits. As an illustration, we compare approaches to quantify the role of trait matching in driving the structure of plant–hummingbird mutualistic networks, i.e. a direct comparison, standardized by null models and hypothesis‐based metaweb. Overall, our analysis warns against a comparison of studies that rely on distinct forms of standardization, as they are likely to highlight different signals. Fostering a better understanding of the analytical tools available and the signal they detect will help produce deeper insights into how and why ecological networks vary along environmental gradients. Keywords: network; metaweb; motif; rarefaction analysis; null model; environmental gradient; network comparison; network properties

Although coral reefs support the largest concentrations of marine biodiversity worldwide, the extent to which the global system of marine-protected areas (MPAs) represents individual species and the breadth of evolutionary history across the Tree of Life has never been quantified. Here we show that only 5.7% of scleractinian coral species and 21.7% of labrid fish species reach the minimum protection target of 10% of their geographic ranges within MPAs. We also estimate that the current global MPA system secures only 1.7% of the Tree of Life for corals, and 17.6% for fishes. Regionally, the Atlantic and Eastern Pacific show the greatest deficit of protection for corals while for fishes this deficit is located primarily in the Western Indian Ocean and in the Central Pacific. Our results call for a global coordinated expansion of current conservation efforts to fully secure the Tree of Life on coral reefs., Nature Communications, 7, ISSN:2041-1723

The FishMed database provides traits, phylogeny, current and projected species distribution of Mediterranean fishes, and associated sea surface temperature (SST) from the regional oceanic model NEMOMED8. Data for the current geographical distributions of 635 Mediterranean fish species were compiled from a published expert knowledge atlas of fishes of the northern Atlantic and the Mediterranean (FNAM) edited between 1984 and 1986 and from an updated exotic fish species list. Two future sets of projected species distributions were obtained for the middle and end of the 21st century by using an ensemble forecasting approach for 288 coastal Mediterranean fish species based on SST according to the IPPC/SRES A2 scenario implemented with the Mediterranean climatic model NEMOMED8. The functional part of the database encompasses 12 biological and ecological traits (maximal and common lengths, vertical distribution, habitat, migration type, mode of reproduction, sex shift, semelparity, diet type (larvae and adults), social behavior, species origin, and depth) for the 635 fish species. To build the phylogeny we inferred the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank including 62% of Mediterranean teleost species plus nine outgroups. Maximum likelihood Bayesian phylogenetic and dating analyses were calibrated using 20 fossil species. An additional 124 fish species were grafted onto the chronogram according to their taxonomic affinity to obtain a phylogenetic tree including 498 species. Finally we also present the associated SST data for the observed period (1961–1980) and for the middle (2040–2059) and the end of the 21st century (2080–2099) obtained from NEMOMED8 according to the IPCC A2 scenario. The FishMed database might be of interest in the context of global anthropogenic changes as coastal Mediterranean ecosystems are currently recognized as one of the most impacted ecosystems on earth.

International audience

International audience

International audience

16 pages, 6 figures, 6 tables Aim A large body of knowledge exists on individual anthropogenic threats that have an impact on marine biodiversity in the Mediterranean Sea, although we know little about how these threats accumulate and interact to affect marine species and ecosystems. In this context, we aimed to identify the main areas where the interaction between marine biodiversity and threats is more pronounced and to assess their spatial overlap with current marine protected areas in the Mediterranean. Location Mediterranean Sea. Methods We first identified areas of high biodiversity of marine mammals, marine turtles, seabirds, fishes and commercial or well-documented invertebrates. We mapped potential areas of high threat where multiple threats are occurring simultaneously. Finally we quantified the areas of conservation concern for biodiversity by looking at the spatial overlap between high biodiversity and high cumulative threats, and we assessed the overlap with protected areas. Results Our results show that areas with high marine biodiversity in the Mediterranean Sea are mainly located along the central and north shores, with lower values in the south-eastern regions. Areas of potential high cumulative threats are widespread in both the western and eastern basins, with fewer areas located in the south-eastern region. The interaction between areas of high biodiversity and threats for invertebrates, fishes and large animals in general (including large fishes, marine mammals, marine turtles and seabirds) is concentrated in the coastal areas of Spain, Gulf of Lions, north-eastern Ligurian Sea, Adriatic Sea, Aegean Sea, south-eastern Turkey and regions surrounding the Nile Delta and north-west African coasts. Areas of concern are larger for marine mammal and seabird species. Main conclusions These areas may represent good candidates for further research, management and protection activities, since there is only a maximum 2% overlap between existing marine protected areas (which cover 5% of the Mediterranean Sea) and our predicted areas of conservation concern for biodiversity MC was funded by a European Community Marie-Curie postdoctoral Fellowship through the International Outgoing Fellowships (Call: FP7-PEOPLE-2007-4-1-IOF) to ECOFUN.DM was supported by a Marie Curie International Outgoing Fellowship (FISHECO) with agreement number IOF-GA-2009-236316. This work was partly funded by Fondation Total, Fondation pour la Recherche sur la Biodiversité (project BIODIVMED) and Centre National de la Recherche Scientifique throught program BiodivMEx. This work was supported by the Sea Around Us project, a scientific collaboration between the University of British Columbia and the Pew Environment Group

1. 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. 2. 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. 3. 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. 3. 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. 4. Retrieving eDNA from filtered surface water provides the first detection of the Dwarf sperm whale (Kogia sima) around the remote Malpelo island (Colombia). 5. 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., Ecology and Evolution, 11 (7), ISSN:2045-7758

Habitat dynamics interacting with species dispersal abilities could generate gradients in species diversity and prevalence of species traits when the latter are associated with species dispersal potential. Using a process‐based model of diversification constrained by a dispersal parameter, we simulated the interplay between reef habitat dynamics during the past 140 million years and dispersal, shaping lineage diversification history and assemblage composition globally. The emerging patterns from the simulations were compared to current prevalence of species traits related to dispersal for 6315 tropical reef fish species. We found a significant spatial congruence between the prevalence of simulated low dispersal values and areas with a large proportion of species characterized by small adult body size, narrow home range mobility behaviour, pelagic larval duration shorter than 21 days and diurnal activity. Species characterized by such traits were found predominantly in the Indo‐Australian Archipelago and the Caribbean Sea. Furthermore, the frequency distribution of the dispersal parameter was found to match empirical distributions for body size, PLD and home range mobility behaviour. Also, the dispersal parameter in the simulations was associated to diversification rates and resulted in trait frequency matching empirical distributions. Overall, our findings suggest that past habitat dynamics, in conjunction with dispersal processes, influenced diversification in tropical reef fishes, which may explain the present‐day geography of species traits., Ecography, 42 (12), ISSN:0906-7590, ISSN:1600-0587

Marine reserves are viewed as flagship tools to protect exploited species and to contribute to the effective management of coastal fisheries. Yet, the extent to which marine reserves are globally interconnected and able to effectively seed areas, where fisheries are most critical for food and livelihood security is largely unknown. Using a hydrodynamic model of larval dispersal, we predict that most marine reserves are not interconnected by currents and that their potential benefits to fishing areas are presently limited, since countries with high dependency on coastal fisheries receive very little larval supply from marine reserves. This global mismatch could be reversed, however, by placing new marine reserves in areas sufficiently remote to minimize social and economic costs but sufficiently connected through sea currents to seed the most exploited fisheries and endangered ecosystems., Nature Communications, 8, ISSN:2041-1723

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 21st 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.

The documentation of biodiversity distribution through species range identification is crucial for macroecology, biogeography, conservation, and restoration. However, for plants, species range maps remain scarce and often inaccurate. We present a novel approach to map species ranges at a global scale, integrating polygon mapping and species distribution modelling (SDM). We develop a polygon mapping algorithm by considering distances and nestedness of occurrences. We further apply an SDM approach considering multiple modelling algorithms, complexity levels, and pseudo-absence selections to map the species at a high spatial resolution and intersect it with the generated polygons. We use this approach to construct range maps for all 1957 species of Fagales and Pinales with data compilated from multiple sources. We construct high-resolution global species richness maps of these important plant clades, and document diversity hotspots for both clades in southern and south-western China, Central America, and Borneo. We validate the approach with two representative genera, Quercus and Pinus, using previously published coarser range maps, and find good agreement. By efficiently producing high-resolution range maps, our mapping approach offers a new tool in the field of macroecology for studying global species distribution patterns and supporting ongoing conservation efforts., New Phytologist, 235 (2), ISSN:0028-646X, ISSN:1469-8137

Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring of organisms is becoming easier and promises a revolution in our approaches to detect changes in biodiversity over space and time. A cornerstone of eDNA approach is the development of primer pairs that allow amplifying the DNA of specific taxonomic groups, which is then used to link the DNA sequence to taxonomic identification. Here, we propose a framework for comparing primer pairs regarding (a) their capacity to bind and amplify a broad coverage of species within the target clade using in silico PCR, (b) their capacity to not only discriminate between species but also genera or families, and (c) their in situ specificity and efficiency across a variety of environments. As a case study, we focus on two mitochondrial 12S primer pairs, MiFish-U and teleo, which were designed to amplify fishes. We found that the performance of in silico PCRs were high for both primer pairs, but teleo amplified more genera across Actinopterygii, Chondrichthyes, and Petromyzontomorphi than MiFish-U. In contrast, the discriminatory power for species, genera, and families were higher for MiFish-U than teleo, likely associated with the greater length of the amplified DNA fragments. The evaluation of their in situ efficiency showed a higher recovered species richness of teleo compared to MiFish-U in tropical and temperate freshwater environments, but that generally both teleo and MiFish-U primers pairs perform well to monitor fish species. Since more species were detected when used together, those primer pairs are best used in combination to increase the ability of species detection., Environmental DNA, 3 (6), ISSN:2637-4943

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns., Royal Society Open Science, 5 (3), ISSN:2054-5703

Figure S1: Observed species richness for the fourteen studied plant families ; Figure S2: Predicted α-diversity according to the best matching simulation; Figure S3: Phylogeny shape characteristics; Figure S4: Cell-level projection of the meta-community model

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 21st 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., Scientific Reports, 10 (1), ISSN:2045-2322

Grasslands deliver the resources for food production and are among the most biologically diverse ecosystems. These characteristics are often in conflict as increasing yield through fertilization can lead to biodiversity loss. Thus, the challenge in grassland management is to sustain both yield and diversity. Biodiversity–ecosystem functioning experiments typically reveal a positive relationship between manipulated species diversity and productivity. In contrast, observations of the effect of increasing productivity via fertilization suggest a negative association with biodiversity. Using a mathematical model simulating species co-existence along a resource gradient, we show that trade-offs and species pool structure (size and trait distribution) determines the shape of the productivity-diversity relationship. At a constant resource level, over-yielding drives a positive relationship between biodiversity and productivity. In contrast, along a resource gradient, the shape of the productivity-diversity relationship is determined by the distribution of species along trade-off axes and often resulted in a bell-shaped relationship. In accordance to this theoretical result, we then explain the general trend of plant biodiversity loss with fertilisation in the European flora, by showing empirical evidence that trait distribution of plant species pools throughout Europe is biased toward species preferring poorer soils., Scientific Reports, 7, ISSN:2045-2322

Coral reefs and their associated fauna are largely impacted by ongoing climate change. Unravelling species responses to past climatic variations might provide clues on the consequence of ongoing changes. Here, we tested the relationship between changes in sea surface temperature and sea levels during the Quaternary and present-day distributions of coral reef fish species. We investigated whether species-specific responses are associated with life-history traits. We collected a database of coral reef fish distribution together with life-history traits for the Indo-Pacific Ocean. We ran species distribution models (SDMs) on 3,725 tropical reef fish species using contemporary environmental factors together with a variable describing isolation from stable coral reef areas during the Quaternary. We quantified the variance explained independently by isolation from stable areas in the SDMs and related it to a set of species traits including body size and mobility. The variance purely explained by isolation from stable coral reef areas on the distribution of extant coral reef fish species largely varied across species. We observed a triangular relationship between the contribution of isolation from stable areas in the SDMs and body size. Species, whose distribution is more associated with historical changes, occurred predominantly in the Indo-Australian archipelago, where the mean size of fish assemblages is the lowest. Our results suggest that the legacy of habitat changes of the Quaternary is still detectable in the extant distribution of many fish species, especially those with small body size and the most sedentary. Because they were the least able to colonize distant habitats in the past, fish species with smaller body size might have the most pronounced lags in tracking ongoing climate change., Ecology and Evolution, 7 (6), ISSN:2045-7758

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., Environmental DNA, 3 (1), ISSN:2637-4943

Figure S1: Observed species richness for the fourteen studied plant families ; Figure S2: Predicted α-diversity according to the best matching simulation; Figure S3: Phylogeny shape characteristics; Figure S4: Cell-level projection of the meta-community model

Genetic diversity is estimated to be declining faster than species diversity under escalating threats, but its spatial distribution remains poorly documented at the global scale. Theory predicts that similar processes should foster congruent spatial patterns of genetic and species diversity, but empirical studies are scarce. Using a mined database of 50,588 georeferenced mitochondrial DNA barcode sequences (COI) for 3,815 marine and 1,611 freshwater fish species respectively, we examined the correlation between genetic diversity and species diversity and their global distributions in relation to climate and geography. Genetic diversity showed a clear spatial organisation, but a weak association with species diversity for both marine and freshwater species. We found a predominantly positive relationship between genetic diversity and sea surface temperature for marine species. Genetic diversity of freshwater species varied primarily across the regional basins and was negatively correlated with average river slope. The detection of genetic diversity patterns suggests that conservation measures should consider mismatching spatial signals across multiple facets of biodiversity., Nature Communications, 11 (1), ISSN:2041-1723