Alice Valentini

Alice Valentini
SPYGEN · R&D

PhD

About

125
Publications
69,110
Reads
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7,396
Citations
Additional affiliations
March 2011 - present
SPYGEN
SPYGEN
Position
  • Research Officer
January 2010 - March 2011
Université Savoie Mont Blanc
Position
  • PostDoc Position
April 2008 - December 2009
University Joseph Fourier - Grenoble 1
Position
  • PostDoc Position

Publications

Publications (125)
Article
Full-text available
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...
Article
Full-text available
eDNA metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density / biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a qPCR approach to infer the absolute abundance of fish species. We...
Article
Full-text available
To mitigate the ongoing threats to coastal ecosystems, and the biodiversity erosion they are causing, Marine Protected Areas (MPAs) have emerged as powerful and widespread conservation tools. Strictly no‐take MPAs, also called marine reserves, undeniably promote fish biomass and density, but it remains unclear how biodiversity responds to protectio...
Article
Full-text available
Environmental DNA (eDNA) metabarcoding is revolutionizing the monitoring of aquatic biodiversity. The use of eDNA has the potential to enable non-invasive, cost-effective, time-efficient and high-sensitivity monitoring of fish assemblages. Although the capacity of eDNA metabarcoding to describe fish assemblages is recognised, research efforts are s...
Article
Full-text available
Abstract Human activities can degrade the quality of coral reefs and cause a decline in fish species richness and functional diversity and an erosion of the ecosystem services provided. Environmental DNA metabarcoding (eDNA) has been proposed as an alternative to Underwater Visual Census (UVC) to offer more rapid assessment of marine biodiversity t...
Article
Full-text available
Sturgeon populations are declining worldwide and are the target of extensive conservation efforts. Addressed in several pieces of legislation, sturgeons have received considerable attention as flagship or umbrella species. Despite the need for a better understanding of the distribution and population status, the use of traditional sampling methods...
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...
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
Assessing the impact of human activity on ecosystems often links local biodiversity to disturbances measured within the same locality. However, remote disturbances may also affect local biodiversity. Here, we used environmental DNA metabarcoding to evaluate the relationships between vertebrate biodiversity (fish and mammals) and disturbance intensi...
Article
Full-text available
The global biodiversity crisis from anthropogenic activities significantly weakens the functioning of marine ecosystems and jeopardizes their ecosystem services. Increasing monitoring of marine ecosystems is crucial to understand the breadth of the changes in biodiversity, ecosystem functioning and propose more effective conservation strategies. Su...
Article
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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...
Preprint
Sturgeon populations are declining worldwide and are the target of extensive conservation efforts. Addressed in several pieces of legislation, sturgeons have received considerable attention as flagship or umbrella species. Despite the need for a better understanding of the distribution and population status, the use of traditional sampling methods...
Article
Full-text available
Environmental DNA is mainly not only used at the interspecific level, to quantify species diversity in ecosystems, but can also be used to quantify intraspecific genetic variability, thus avoiding the need to sample individual tissue. However, errors in the amplification and sequencing of eDNA samples can blur this intraspecific signal and strongly...
Preprint
Full-text available
eDNA metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density / biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a qPCR approach to infer the absolute abundance of fish species. We...
Article
The contents of the digestive tracts of 21 loggerhead turtles (20 juveniles and 1 adult) collected along the French Mediterranean coast were extracted during necropsies. Hard and soft items were collected and identified by visual observation. A 15-mL sample of the liquid from the rinsed contents of each digestive tract was collected and dietary DNA...
Book
Full-text available
This publication is an output from EU COST Action DNAqua-Net (CA 15219 - Developing new genetic tools for bioassessment of aquatic ecosystems in Europe) and would not have been possible without the opportunities for international collaboration provided by the network, supported by COST (European Cooperation in Science and Technology). Therefore, ou...
Article
Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA. Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assembl...
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
Recent developments in environmental DNA (eDNA) metabarcoding suggest that eDNA-based representation of ecological communities can be a promising tool in both fundamental ecological research and environmental assessment. However, it is less known, how eDNA performs in characterising ecological communities and community-environment relationships at...
Article
Full-text available
Theidentification of key biodiversity areas (KBA) was initiated by the International Union for Conservation of Nature in 2004 to overcome taxonomic biases in the selection of important areas for conservation, including freshwater ecosystems. Since then, several KBAs have been identified mainly based on the presence of trigger species (i.e., species...
Article
Full-text available
The current biodiversity crisis calls for rapid and wide-ranging surveys to assess living organisms. However, some taxa are more elusive than others, making monitoring challenging. This is the case for soil invertebrates, but new molecular technologies such as eDNA metabarcoding could help to alleviate this problem. In this study, we evaluated the...
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
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 i...
Article
Full-text available
Freshwater ecosystems are the most vulnerable worldwide and freshwater bivalves rank amongst the most threatened animals in the world. Surveying and monitoring freshwater bivalves are difficult tasks: they are difficult to find, hard to identify (taxonomic expertise is needed), and working underwater is technically challenging. It is therefore cruc...
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
The current biodiversity crisis calls for rapid and wide-ranging surveys to assess living organisms. However, some taxa are more elusive than others, making monitoring challenging. This is the case for soil invertebrates, but new molecular technologies such as eDNA metabarcoding could help to alleviate this problem. In this study, we evaluated the...
Article
Full-text available
Biodiversity monitoring delivers vital information to those making conservation decisions. Comprehensively measuring terrestrial biodiversity usually requires costly methods that can rarely be deployed at large spatial scales over multiple time periods, limiting conservation efficiency. Here we investigated the capacity of environmental DNA (eDNA)...
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...
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
• 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
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...
Presentation
Full-text available
Abstract for DNAQUA International Conference : international Conference on the Use of DNA for Water Biomonitoring - 2021
Article
Full-text available
Les inventaires d’espèces dulçaquicoles par analyse de l’ADN environnemental (ADNe) se sont développés depuis une dizaine d’années. Nous présentons ici l’application de cette méthode à l’inventaire des Bivalves d’eau douce de France. De 2015 à 2018, nous avons réalisé plusieurs tests de terrain en France, en choisissant différentes conditions envir...
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
Innovative techniques, such as environmental DNA (eDNA) metabarcoding, are now promoting broader biodiversity monitoring at unprecedented scales, due to the reduction in time, presumably lower cost, and methodological efficiency. Our goal was to assess the efficiency of established inventory techniques (live‐trapping grids, pitfall traps, camera tr...
Article
Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient method to assess aquatic species presence. While the method could in theory be used to investigate non‐aquatic fauna, its development for inventorying semi‐aquatic and terrestrial fauna is still at its early stages. Here we aimed at investigating the potential of aquati...
Article
Full-text available
Most of the present EU Water Framework Directive (WFD) compliant fish‐based assessment methods of European rivers are multi‐metric indices computed from traditional electrofishing (TEF) samples, but this method has known shortcomings, especially in large rivers. The probability of detecting rare species remains limited, which can alter the sensitiv...
Article
Macroinvertebrate assemblages are the most common bioindicators used for stream biomonitoring, yet the standard approach exhibits several time‐consuming steps, including the sorting and identification of organisms based on morphological criteria. In this study, we examined if DNA metabarcoding could be used as an efficient molecular‐based alternati...
Article
Full-text available
Environmental DNA (eDNA) metabarcoding has recently gain much attention to assess aquatic environment biodiversity. A great variety of protocols have been developed to collect, extract, and analyze eDNA, some of which are continuously evolving and optimized with technological improvements. Such technological shifts might deprecate the biological da...
Preprint
Full-text available
Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA. Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assembl...
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
Metabarcoding of bulk or environmental DNA has great potential for biomonitoring freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensiv...
Article
Declines and extinctions are increasing globally and challenge conservationists to keep pace with biodiversity monitoring. Organisms leave DNA traces in the environment, e.g. in soil, water, and air. These DNA traces are referred to as environmental DNA (eDNA). The analysis of eDNA is a highly sensitive method with the potential to rapidly assess l...
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
Full-text available
Sinds 2013 vindt in Nederland onderzoek plaats naar de toepassing van eDNA-metabarcoding voor de Kaderrichtlijn Water-vismonitoring. De resultaten zijn veelbelovend: deze hightech-methode detecteert meer soorten waarbij zelfs de eDNA-verhoudingen tussen aanwezige soorten onderling te meten zijn. eDNA: game changer voor KRW-vismonitoring? Als onderd...
Data
Commented maps of all the freshwater bivalve species in France with distinction between traditional data and eDNA data
Article
Full-text available
Rapid, early, and reliable detection of invasive pathogenic microorganisms is essential in order to either predict or delineate an outbreak, and monitor appropriate mitigation measures. The chytrid fungus Batrachochytrium salamandrivorans is expanding in Europe, and infection with this fungus may cause massive mortality in urodelans (salamanders an...
Article
Full-text available
The ecological requirements of brown bears are poorly known in the Himalaya region, which complicates conservation efforts. We documented the diet of the Himalayan brown bear (Ursus arctos isabellinus) by combining classical scat analysis and a newly developed molecular genetic technique (the trnL approach), in Deosai National Park, Pakistan. Brown...
Article
As fish communities are a major concern in rivers ecosystems, we investigated if their environmental (e)DNA signals vary according to the sampling period or hydromorphological conditions. Three rivers were studied over a year using eDNA metabarcoding approach. The majority of the species (c. 80%) were detected all year round in two rivers having si...
Method
Full-text available
Depuis une dizaine d’années des outils d’inventaire de la biodiversité, utilisant l’ADN environnemental (ADNe), se développent. L'ADNe peut être extrait d’échantillons environnementaux de sol, d’eau ou d’air, sans avoir besoin d’isoler au préalable des individus cibles. L’ADNe est amplifié en utilisant des amorces spécifiques à un groupe taxonomiqu...
Research
Full-text available
Depuis une dizaine d’années des outils d’inventaire de la biodiversité, utilisant l’ADN environnemental (ADNe), se développent. L'ADNe peut être extrait d’échantillons environnementaux de sol, d’eau ou d’air, sans avoir besoin d’isoler au préalable des individus cibles. L’ADNe est amplifié en utilisant des amorces spécifiques à un groupe taxonomiqu...
Article
Large herbivores that survived the Pleistocene/Holocene transition are hypothesized to have been forced to take refuge, as a result of environmental changes and human pressure, into forest habitats. Today, there is an open question of the degree to which extant large herbivores are well adapted to the forests that allowed for the herbivores’ persis...
Article
Full-text available
The early detection and identification of pathogenic microorganisms is essential in order to deploy appropriate mitigation measures. Viruses in the Iridoviridae family, such as those in the Ranavirus genus, can infect amphibian species without resulting in mortality or clinical signs, and they can also infect other hosts than amphibian species. Dia...
Article
Full-text available
Environmental DNA (eDNA) metabarcoding is a promising tool to estimate aquatic biodiversity. It is based on the capture of DNA from a water sample. The sampled water volume, a crucial aspect for efficient species detection, has been empirically variable (ranging from few centiliters to tens of liters). This results in a high variability of sampling...