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Why new metadata? Avenues for improvement in the describing and storing of restoration monitoring data
No full textInternational audienceAssessing the effectiveness of restoration requires monitoring data. However, the collection of such data is subject to bias, making it difficult to distinguish between actual changes in the environment and variability in the conditions under which the data were collected. Metadata, which provide contextual information about data collection and compilation, are essential for analyzing data and accounting for potential collection biases. Given the lack of specific standards for describing and storing ecological restoration monitoring data, we questioned whether current data standards are sufficient for this purpose. A literature review was conducted to 1/provide a non-exhaustive list of metadata required to describe the restoration monitoring data collection process, with a focus on species data collection and 2/identify the main standards currently used to store ecological data at international, European and national (France) levels. We found that the most commonly used standards are DarwinCore, the Ecological Metadata Standard (EML), the Humboldt extension, the FGDC Biological Data Profile worldwide, the European INSPIRE standard in Europe, and the Système d'Information du Patrimoine Naturel (SINP) in France. Finally, we compared our list of metadata from the literature review and the list of metadata from the main standards. Our results indicate that (i) these standards are applicable to a wide range of biological and ecological data, (ii) they are not specifically designed for monitoring data, and (iii) they do not include enough fields for a complete description of these data. Our list of metadata could therefore complement the main metadata standards for describing and storing restoration monitoring data
The role of algae in structuring reef communities: innovative monitoring and ecological insights within a Mediterranean conservation priority area
No full textInternational audienceThe Mediterranean Sea is a “sea under siege”, facing numerous anthropogenic pressures leading to the spread of invasive species and the degradation of reefs, particularly the reduction of habitat-forming macroalgae to turf algae or sea urchin barrens. The coastal waters of Corsica, often considered as a “reference state” due to their lower human impact, have not been thoroughly studied with regard to infralittoral reef communities. This study aimed to characterize these communities and identify their biotic and abiotic drivers through an innovative monitoring protocol (VIT-Reef). From 2019 to 2021, we monitored infralittoral reef communities at 59 sites between 15 and 35 m depth within and adjacent to three MPAs, using innovative rapid assessment dive surveys for 74 benthic taxa. Our results highlighted vertical zonation in reef communities, in particular the depth extent of photophilic algae and the emergence of pre-coralligenous communities. Important ecological implications of taxa covariation were discussed, such as the negative relationship between canopy-forming macroalgae and the invasive algae, Caulerpa cylindracea . Notably, geographical contrasts were observed along northern, southern and western MPAs, primarily influenced by algal community changes. Cystoseira (sensu lato) forests were identified as the climax state on western reefs, while northern and southern reefs showed significant cover of Dictyota spp. and crustose corallines respectively, with concerning levels of Caulerpa cylindracea in deeper southern reefs. Our results underscored the structuring role of Cystoseira spp. forests and the effects of light, nutrients and Posidonia oceanica meadows extending into the reefs. This study highlighted the role of algae in structuring reef communities and will contribute to establish a baseline for conservation planning and predicting future changes in these high priority infralittoral communities
Contrasting Patterns of Connectivity Between Populations of Euphotic and Mesophotic Hydroids in Reunion Island Support the Deep Reef Refuge Hypothesis
No full textInternational audienceIn the context of coral reef decline, mesophotic coral ecosystems (MCEs, 30–150 m) offer hope for the recovery of degraded euphotic reefs. The Deep Reef Refuge Hypothesis (DRRH) postulates the potential of mesophotic reefs to reseed euphotic reefs. This hypothesis needs to be further tested by estimating connectivity along the depth gradient. Mesophotic data are lacking worldwide, particularly in the southwestern Indian Ocean (SWIO). Here, using a total of 2218 samples collected at depths ranging from 10 to 103 m, we estimated the connectivity of 7 hydroid species sampled at euphotic, upper, and lower mesophotic depths around Reunion Island using a multi‐species comparative framework. Population genetic analyses using 8–17 microsatellite markers per species (80 markers in total) as well as Bayesian inference were performed to estimate population structure and contemporary migration rates to highlight connectivity patterns and directionality of gene flow between depths. The results revealed three main genetic patterns depending on the species: a horizontal stepping stone pattern between areas around the island, a vertical stepping stone pattern between adjacent depths, and a quasi‐panmictic pattern. Each species showed some specificity within these patterns, but overall, at least 4 of the 7 species support the assumption of vertical connectivity from the Deep Reef Refuge Hypothesis, highlighting the importance of studying multiple species. The existence of vertical connectivity between euphotic and mesophotic depths in the southwestern Indian Ocean confirms the importance of mesophotic coral ecosystems for conservation efforts and our global understanding of coral reef ecosystem dynamics
Correction: Ecosystem-based assessment of a widespread Mediterranean marine habitat: The Coastal Detrital Bottoms, with a special focus on epibenthic assemblages
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Rapport de mission : Grand recensement de la biodiversité par ADN environnemental, Conservation et Surveillance de la biodiversité terrestre - Guyane - Juin 2025
No full textPatriNat est engagée dans l’accompagnement des acteurs des territoires d’Outre-mer pour une meilleure prise en compte de la biodiversité, notamment avec le renforcement des programmes socles sur la connaissance, le déploiement de projets et des expertises locales. Ce déplacement collectif et institutionnel visait tout d’abord à établir un état des lieux des projets actuels de connaissance utilisant l’ADN environnemental et de travailler collectivement et localement sur la mise en place d’une feuille de route et d’une vision partagée pour le développement des techniques moléculaires sur le territoire guyanais. Un autre but de cette mission était de recueillir les besoins des acteurs locaux et de travailler conjointement au développement de programmes en matière de surveillance de la biodiversité terrestre et de priorisation des enjeux de conservation des espèces. Durant cette mission au mois de juin 2025, l'équipe de PatriNat a dédié un temps spécifique d’échanges avec les représentants de ses tutelles OFB, IRD et CNRS en Guyane. Une série de rencontres institutionnelles et techniques a aussi eu lieu, principalement à Cayenne, pour recevoir l’avis des parties prenantes sur le suivi et la conservation de la biodiversité. Du côté de la société civile, plusieurs associations et naturalistes se sont rendus disponibles, et grâce au soutien de la CTG et à l’appui de la DGTM, plusieurs moments forts d’échanges collectifs ont pu avoir lieu sur des sujets scientifiques de haut niveau. Il faut noter la co-organisation avec la CTG d’une journée dédiée aux sujets ADNe en Guyane, qui s’est tenue le 11 juin à la Maison des Cultures et des Mémoires et dans les locaux de l’IRD. Par ailleurs, plusieurs ateliers de travail se sont déroulés dans les locaux de la DGTM et de l’OFB, notamment sur les programmes de surveillance de la biodiversité et les espèces à fort enjeux de conservation. La participation au CSRPN du 12 juin a permis des échanges riches avec les experts réunis sur la consolidation des connaissances essentielles pour faire face aux enjeux de conservation du territoire. De plus, quelques visites de terrain et de sites clés pour l’expertise scientifique locale ont également pu avoir lieu, comme le marais de Kaw, le campus de Kourou et l’Herbier de Cayenne. Ce rapport de mission présente le programme de ce déplacement, les principaux sujets abordés avec les acteurs locaux et les éléments essentiels de programmation qui en découlent
IBASAM: a spatially explicit demo-genetic individual-based model for anadromous salmonids (meta)populations
No full textData availability: The model executable file, Java source codes, R scripts to create initialization files, launch the model, analyze simulation results (including Shiny app), as well as a comprehensive user guide, are all available at https://doi.org/10.5281/zenodo.14825431.The model was coded on the Capsis-4 modelling platform (http://capsis.cirad.fr) maintained by François de Coligny and Nicolas Beudez. We thank Miguel de Navascués for discussions on the ABC approach. We acknowledge CSC (IT Center for Sciences, Finland) for access to computational resources.The dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0).International audienceTo improve our understanding and management of species' response to environmental and anthropogenic changes, there is a critical need for integrative modeling approaches that encompass demographic, ecological and evolutionary processes in a unified framework. This is especially crucial for anadromous salmonid fishes that hold significant socio-economic value. Mechanistic models, particularly Demo-Genetic Agent-Based Models (DG-ABMs), are promising tools to address this challenge. Building on previous work, we present IBASAM, an Individual Based Anadromous SAlmonids Model. It incorporates significant advancements, including new processes such as dispersal and in-river movement, enhanced flexibility for simulating diverse spatial configurations-from river dendritic networks to metapopulations and multiple marine areas-and the integration of variation in life history phenology and the genetic architecture of traits. Additionally, a user-friendly interface has been developed to facilitate broader application. This improved versatility enables IBASAM application to a number of populations and species of anadromous salmonids, making it well-suited for a wide range of ecological and evolutionary studies. The model is particularly suited for investigating (meta)population eco-evolutionary dynamics, persistence, and adaptation to environmental changes, as well as exploring management options including fisheries regulation and river connectivity restoration. We summarize the model's structure and illustrate some of its novelties, parameterization, and emerging patterns with the case study of a naturally reproducing Atlantic salmon population simulated over 100 years, with constant fishing rates and no climatic trend. Our simulations successfully reproduced 30 variables observed over 30 years in the Scorff population. IBASAM opens up new opportunities for research on the response of salmonid meta-populations to environmental changes, the exploration of management practices, with further developments possible
Mesure du mercure et méthylmercure chez G. fossarum encagé sur le bassin Rhin-Meuse : variation spatiale des concentrations et contributions
No full textNational audienceLe devenir du mercure (Hg) dans les hydrosystèmes dépend de sa forme chimique, qui conditionne sa distribution entre l’eau, le sédiment et le biote, ainsi que sa toxicité. La méthylation du mercure a principalement lieu dans les sédiments en conditions suboxiques et conduit à la formation du méthylmercure CH3Hg+ (MeHg). En plus d’être une forme particulièrement toxique, MeHg présente la particularité de franchir facilement les barrières biologiques pour se bioaccumuler et se bioamplifier le long de la chaîne trophique. Le méthylmercure représente ainsi plus de 80% de la concentration en mercure total (HgT) dans la chair des poissons prédateurs. En conséquence, la biosurveillance de la qualité chimique des rivières est focalisée sur les poissons de haut niveau trophique. L’encagement de gammares (Gammarus fossarum) est déployé depuis 2018 comme outil en biosurveillance. Il pourrait constituer une alternative à la pêche de poissons, d’autant que les gammares possèdent une forte capacité à bioaccumuler HgT, avec des différences significatives de bioaccumulation selon les organes (Gestin et al., 2021). L’hypothèse ici est que la concentration en HgT total ne soit pas un bon proxy de la bioaccumulation du MeHg. La proportion MeHg/HgT semble très variable selon les espèces de macroinvertébrés (Gentès et al., 2021) et reste peu documentée. Chez le gammare, de premiers résultats semblent confirmer la variabilité de la proportion MeHg/HgT (Gasnault, 2023). Dans le but de mieux connaitre le devenir du mercure et du MeHg chez le gammare, une expérimentation de plus large envergure a été menée en janvier 2025. Après tri et calibration, des gammares mâles de taille homogène ont été encagés durant 7 jours sur 28 sites répartis sur 14 cours d’eau du bassin versant Rhin-Meuse, sélectionnés pour couvrir un large gradient de contamination en HgT. Suite à cette exposition, l’analyse du HgT a été réalisée à l’aide d’un analyseur direct de mercure (DMA-180) et l’analyse du MeHg a été menée par dilution isotopique par chromatographie en phase gazeuse couplée à un spectromètre de masse à plasma inductif (GC-ICPMS). Les résultats des concentrations en HgT et MeHg ainsi que leurs proportions respectives seront présentés. Nous évaluerons l’existence d’un lien entre la concentration en HgT et la proportion de MeHg accumulé chez les gammares. Enfin, en nous appuyant sur les données du réseau Naïades, nous examinerons dans quelle mesure la concentration en MeHg dans les gammares encagés peut être proposée comme indicateur de la contamination en Hg des poissons
Trends of ungulate species in Europe: not all stories are equal
No full textArticle archivé dans EcoEvoRxivInternational audienceWild ungulates have deep impacts on socio-ecological systems, and analyzing large-scale population trends in a multispecies set can identify their environmental and socio-economic drivers. We collected annual hunting bags (n = 11,046, period 1975-2018) of 7 wild ungulates of high management interest across 25 European countries. We identified different temporal trends in hunting bags and for roe deer, red deer, wild boar, fallow deer, and mouflon, we also evaluated the social and environmental drivers of their abundances. Number of harvested red deer, fallow deer, and wild boar increased steadily across Europe, with minor differences among countries, despite variations in land use and climate. On the contrary, roe deer harvest has decreased in six European countries since the late 1990s, probably due to reduced ecotone areas and locally also due to predation, intraspecific competition, and/or climate severity. Northern chamois harvests in Austria and Switzerland have decreased markedly, probably due to increasing temperatures, which decrease the survival of kids at high altitudes. Wild boar harvests have decreased in Poland, Estonia, Latvia, and Lithuania since the African Swine Fever outbreak in 2013-2014. Minor differences emerged between countries adopting different management regimes for wild ungulates. While many studies pointed out landscape changes as the cornerstone for the increase in wild ungulates across Europe, our research emphasizes important species-specific differences. There is a need to predict how landscape and climate change and the growing presence of large carnivores, will affect populations of species already showing signs of decline, like European roe deer and northern chamois
Les ongulés sauvages en France. Synthèse des données du Réseau Ongulés Sauvages OFB-FNC-FDC: Rapport 2025 - version 1
No full textCe rapport offre une vue d’ensemble actualisée des populations d’ongulés sauvages en France, en s’appuyant sur la longue série de données collectées par le réseau Ongulés sauvages OFB-FNC-FDC entre 1985 et 2025. L'ensemble de ces données permettent de mieux comprendre la dynamique, la gestion et la conservation des ongulés en France