David Mouillot

David Mouillot
Université de Montpellier | UM1 · Unité mixte de recherche Ecologie des Systèmes Marins Côtiers (ECOSYM)

PhD

About

461
Publications
268,167
Reads
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29,767
Citations
Additional affiliations
January 2015 - present
James Cook University
Position
  • Professor (Associate)
January 2015 - present

Publications

Publications (461)
Article
Full-text available
The challenges of Reproducibility and Replicability (R & R) in computer science experiments have become a focus of attention in the last decade, as efforts to adhere to good research practices have increased. However, experiments using Deep Learning (DL) remain difficult to reproduce due to the complexity of the techniques used. Challenges such as...
Article
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 pr...
Article
Full-text available
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 an...
Poster
Full-text available
The challenges of Reproducibility and Replicability (R&R) have become a focus of attention in order to promote open and accessible research. Therefore, efforts have been made to develop good practices for R&R in the area of computer science. Nevertheless, Deep Learning (DL) based experiments remain difficult to reproduce by others due to the comple...
Poster
Full-text available
In computer science, there are more and more efforts to improve reproducibility. However, it is still difficult to reproduce the experiments of other scientists, and even more difficult when it comes to Deep Learning (DL). Making a DL research experiment reproducible requires a lot of work to document, verify, and make the system usable. These chal...
Article
Full-text available
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 a...
Article
Full-text available
Reef fishes are closely connected to many human populations, yet their contributions to society are mostly considered through their economic and ecological values. Cultural and intrinsic values of reef fishes to the public can be critical drivers of conservation investment and success, but remain challenging to quantify. Aesthetic value represents...
Article
Effective solutions to the ongoing “coral reef crisis” will remain limited until the underlying drivers of coral reef degradation are better understood. Here, we conduct a global-scale study of how four key metrics of ecosystem states and processes on coral reefs (top predator presence, reef fish biomass, trait diversity, and parrotfish scraping po...
Article
Full-text available
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 wel...
Article
Full-text available
Outside controlled experimental plots, the impact of community attributes on primary productivity has rarely been compared to that of individual species. Here, we identified plant species of high importance for productivity (key species) in >29,000 diverse grassland communities in the European Alps, and compared their effects with those of communit...
Article
Tropical inter-reefs represent a vast overlooked marine ecosystem that occurs between coral reefs and across the shelf. We deployed 60 baited remote underwater video stations (BRUVS) in New Caledonia to study inter-reef fish assemblages and habitats in three zones (bays, sandy lagoons, and sandy areas near the barrier reef) along an inshore-offshor...
Article
Full-text available
The ongoing decline of large marine vertebrates must be urgently mitigated, particularly under increasing levels of climate change and other anthropogenic pressures. However, characterizing the connectivity among populations remains one of the greatest challenges for the effective conservation of an increasing number of endangered species. Achievin...
Article
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 locat...
Article
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...
Article
Full-text available
Despite evidence of a positive effect of functional diversity on ecosystem productivity, the importance of functionally distinct species (i.e., species that display an original combination of traits) is poorly understood. To investigate how distinct species affect ecosystem productivity, we used a forest gap model to simulate realistic temperate fo...
Article
Full-text available
The contributions of species to ecosystem functions or services depend not only on their presence but also on their local abundance. Progress in predictive spatial modelling has largely focused on species occurrence rather than abundance. As such, limited guidance exists on the most reliable methods to explain and predict spatial variation in abund...
Article
Full-text available
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...
Article
Full-text available
1‐ Climate influences population genetic variation in marine species. Capturing these impacts remains challenging for marine fishes which disperse over large geographic scales spanning steep environmental gradients. It requires the extensive spatial sampling of individuals or populations, representative of seascape heterogeneity, combined with a se...
Article
Full-text available
Coral reefs are experiencing declines due to climate change and local human impacts. While at a local scale these impacts induce biodiversity loss and shifts in community structure, previous biogeographical analyses recorded consistent taxonomic structure of fish communities across global coral reefs. This suggests that regional communities represe...
Article
Full-text available
Past environmental changes are expected to have profoundly impacted diversity dynamics through time. While some previous studies showed an association between past climate changes or tectonic events and important shifts in lineage diversification, it is only recently that past environmental changes have been explicitly integrated in diversification...
Article
Full-text available
Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eD...
Article
Full-text available
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...
Article
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 component...
Article
As climate change accelerates, species are shifting poleward and subtropical and tropical species are colonizing temperate environments. A popular approach for characterizing such responses is the community temperature index (CTI), which tracks the mean thermal affinity of a community. Studies in marine, freshwater, and terrestrial ecosystems have...
Article
Full-text available
Trait-based ecology aims to understand the processes that generate the overarching diversity of organismal traits and their influence on ecosystem functioning. Achieving this goal requires simplifying this complexity in synthetic axes defining a trait space and to cluster species based on their traits while identifying those with unique combination...
Article
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 targe...
Article
Full-text available
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. Her...
Preprint
Full-text available
While the impact of biodiversity, notably functional diversity, on ecosystem productivity has been extensively studied, little is known about the effect of individual species. Here, we identified species of high importance for productivity (key species) in over 28,000 diverse grassland communities in the European Alps, and compared their effects wi...
Article
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 bi...
Article
Full-text available
Deep learning has become a key tool for the automated monitoring of animal populations with video‐surveys. However, obtaining large amounts of images to train such models is a major challenge for rare and elusive species since field video‐surveys provide few sightings. We propose a methodological framework that takes advantage of videos accumulated...
Article
Full-text available
Marine protected areas (MPAs) are globally important environmental management tools that provide protection from the effects of human exploitation and activities, supporting the conservation of marine biological diversity, habitats, ecosystems and the processes they host, as well as resources in a broad sense. Consequently, they are also expected t...
Preprint
Full-text available
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 mar...
Article
How far do marine larvae disperse in the ocean? Decades of population genetic studies have revealed generally low levels of genetic structure at large spatial scales (hundreds of kilometres). Yet this result, typically based on discrete sampling designs, does not necessarily imply extensive dispersal. Here, we adopt a continuous sampling strategy a...
Preprint
Full-text available
The contributions of species to ecosystem functions or services depend not only on their presence in a given community, but also on their local abundance. Progress in predictive spatial modelling has largely focused on species occurrence, rather than abundance. As such, limited guidance exists on the most reliable methods to explain and predict spa...
Preprint
Full-text available
The intensification of anthropogenic pressures have increased consequences on biodiversity and ultimately on the functioning of ecosystems. To monitor and better understand biodiversity responses to environmental changes using standardized and reproducible methods, novel high-throughput DNA sequencing is becoming a major tool. Indeed, organisms she...
Article
Full-text available
Protected areas are the flagship management tools to secure biodiversity from anthropo-genic impacts. However, the extent to which adjacent areas with distinct protection levels host different species numbers and compositions remains uncertain. Here, using reef fishes, European alpine plants, and North American birds, we show that the composition o...
Article
• Bioinformatic analysis of eDNA metabarcoding data is crucial toward rigorously assessing biodiversity. Many programs are now available for each step of the required analyses, but their relative abilities at providing fast and accurate species lists have seldom been evaluated. • We used simulated mock communities and real fish eDNA metabarcoding d...
Article
Full-text available
Underwater cameras are widely used to monitor marine biodiversity, and the trend is increasing due to the availability of cheap action cameras. The main bottleneck of video methods now resides in the manual processing of images, a time-consuming task requiring trained experts. Recently, several solutions based on Deep Learning (DL) have been propos...
Article
Full-text available
A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03496-1.
Article
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 the...
Preprint
Full-text available
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...
Article
Full-text available
The ocean contains unique biodiversity, provides valuable food resources and is a major sink for anthropogenic carbon. Marine protected areas (MPAs) are an effective tool for restoring ocean biodiversity and ecosystem services1,2, but at present only 2.7% of the ocean is highly protected³. This low level of ocean protection is due largely to confli...
Presentation
Full-text available
Abstract for DNAQUA International Conference : international Conference on the Use of DNA for Water Biomonitoring - 2021
Article
Coral reefs are highly diverse marine ecosystems offering invaluable services to hundreds of million people worldwide. These ecosystems are currently threatened by global and local stressors, particularly affecting structurally complex coral species in depauperate zones such as the Caribbean. Marine protected areas (MPAs) can counteract climatic an...
Article
Full-text available
Species’ traits, rather than taxonomic identities, determine community assembly and ecosystem functioning, yet biogeographic patterns have been far less studied for traits. While both environmental conditions and evolutionary history shape trait biogeography, their relative contributions are largely unknown for most organisms. Here, we explore the...
Article
Full-text available
• 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 distribu...
Article
Full-text available
The response-and-effect framework is a trait-based approach that seeks to break down the mechanistic links between ecosystem disturbances, species' traits, and ecosystem processes. We apply this framework to a review of the literature on coral reef fish traits, in order to illustrate the research landscape and structure a path forward for the field...
Preprint
Full-text available
Intraspecific genetic diversity should be dependent on species ecology, but the influence of ecological traits on interspecific differences in genetic variation is yet to be explored. Generating sequenced data for 20 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from...
Article
Full-text available
Functionally distinct species (i.e. species with unique trait combinations in the community) can support important ecological roles and contribute disproportionately to ecosystem functioning. Yet, how functionally distinct species have responded to recent climate change and human exploitation has been widely overlooked. Here, using ecological trait...
Article
Full-text available
Contrary to most terrestrial organisms, which release their carbon into the atmosphere after death, carcasses of large marine fish sink and sequester carbon in the deep ocean. Yet, fisheries have extracted a massive amount of this “blue carbon,” contributing to additional atmospheric CO 2 emissions. Here, we used historical catches and fuel consump...
Preprint
Full-text available
Limiting climate warming below 2°C requires both reducing anthropic greenhouse gas emissions and sequestering more atmospheric carbon. Natural Climate Solutions (NCS) rely on the ability of ecosystems to capture and store carbon. Despite the important role of marine megafauna on the ocean carbon cycle, its potential as a NCS has not yet been explor...
Article
Full-text available
Identifying species that are both geographically restricted and functionally distinct, i.e. supporting rare traits and functions, is of prime importance given their risk of extinction and their potential contribution to ecosystem functioning. We use global species distributions and functional traits for birds and mammals to identify the ecologicall...
Preprint
Full-text available
Coral reefs are experiencing declines due to climate change and local human impacts. While at local scale biodiversity loss induces shifts in community structure, previous biogeographical analyses recorded consistent taxonomic structure of fish communities across global coral reefs. This suggest that regional communities represent a random subset o...
Article
Full-text available
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 re...
Article
Full-text available
Rapid degradation of the world's coral reefs jeopardizes their ecological functioning and ultimately imperils the well-being of the millions of people with reef-dependent livelihoods. Ecosystem accessibility is the main driver of their conditions, with the most accessible ecosystems being most at risk of resource depletion. People's socioeconomic c...
Article
Full-text available
Many islands are biodiversity hotspots but also extinction epicenters. In addition to strong cultural connections to nature, islanders derive a significant part of their economy and broader wellbeing from this biodiversity. Islands are thus considered as the socio-ecosystems most vulnerable to species and habitat loss. Yet, the extent and key corre...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
Human activities impact all ecosystems on Earth, which urges scientists to better understand biodiversity changes across temporal and spatial scales. Environmental DNA (eDNA) metabarcoding is a promising non‐invasive method to assess species composition in a wide range of ecosystems. Yet, this method requires the completeness of a reference databas...
Article
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 a...
Article
Full-text available
Processing data from surveys using photos or videos remains a major bottleneck in ecology. Deep Learning Algorithms (DLAs) have been increasingly used to automatically identify organisms on images. However, despite recent advances, it remains difficult to control the error rate of such methods. Here, we proposed a new framework to control the error...
Article
Full-text available
Current approaches that compare spatial genetic structure of a given species and the dispersal of its mobile phase can detect a mismatch between both patterns mainly due to processes acting at different temporal scales. Genetic structure result from gene flow and other evolutionary and demographic processes over many generations, while dispersal pr...
Article
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 ach...