HAL-IRD
Not a member yet
83947 research outputs found
Sort by
Habitat quality assessment of temperate forest ecosystems: An airborne LiDAR-based approach to predict the Index of Biodiversity Potential (IBP) at large scale
No full textInternational audienceThe Index of Biodiversity Potential (IBP) assesses the forest stand’s capacity to host species based on 10 structural, compositional, and environmental factors. Widely used by French forest managers, its reliance on in-situ surveys limits large-scale applications. While LiDAR-derived metrics can finely describe forest structure, their relationship with the IBP remains unexplored.We aimed to study these relationships with the IBP management factors, some of which reflect forest structure such as the number of large trees and vertical strata. Using a dataset of 1536 IBP plots across France, we computed LiDAR-derived structural metrics along with other variables (e.g., topographic, spectral). We then analysed their statistical relationships with the IBP factors, and calibrated predictive models using both regression and classification machine learning algorithms. Finally, we mapped the IBP management score for the first time over a 890 km area within the forests of the Ariege Pyrenees Regional Natural Park (France).The results revealed strong correlations between the IBP management score, its factors, and remote sensing metrics. LiDAR-derived metrics describing canopy height and vertical complexity were particularly important for prediction, as well as biomass and topographic metrics. Our best model, with an RMSE of 5.24 ± 0.63, predicts IBP within 5 points—a threshold beyond which variations reflect actual changes in species richness within the forest stand.These findings emphasise the relevance of remote sensing data, in particular LiDAR, for describing structural field metrics. They demonstrate that remote sensing offers a viable approach for large-scale IBP assessment
Examining copper supply consistency in socioeconomic pathways: A mine-level dynamic approach
No full textInternational audiencePrimary copper production capacity is crucial given future demand and social, environmental, technical, economic, and political constraints, often overlooked in decarbonization pathway models. To address this, we propose a methodology to examine the consistency of the basic drivers of Shared Socioeconomic Pathways (SSPs) for primary copper requirements using the DyMEMDS stock-flow model. Our approach involves projecting primary copper production capacities to 2050 on a mine-by-mine basis, integrating mining industry dynamics based on commercial data. Results indicate significant concerns regarding the consistency of SSPs' basic drivers for copper requirements, revealing potential gaps exceeding 40 Mt in worst-case scenarios. Such discrepancies could impact technology deployments necessary for socioeconomic and decarbonisation assumptions. We recommend that the decarbonization modeling community align scenarios with mining industry constraints. Considering resource efficiency and circular economy strategies is essential for proposing more consistent scenarios to decision-makers, thereby mitigating risks of copper supply shortages hindering climate actio
Improving visibility for knowledge holders in ethnobiological and ethnopharmacological publications
No full textInternational audienceEthnopharmacological relevance: Ethnopharmacology and ethnobiology largely focus on the study of traditional knowledge related to medicinal and other uses of plants, animals or minerals. Despite decades of political advocacy, ethnopharmacological and ethnobiological information is still sometimes published without proper attribution of the cultural identities and affiliations of the communities that shared it.Aim of the study: Identify key guidelines to ensure the proper attribution of ethnobiological and ethnopharmacological knowledge recorded in scientific publications to the communities who provided it.Material and methods: This article is based on extensive group discussions that started at a workshop entitled “A worldwide database of local uses of biodiversity: Why? For whom? And how?” (18th Congress of the International Society of Ethnobiology in Marrakech, Morocco, May 15–19, 2024), and was attended by around 50 participants. The guidelines were developed through an iterative revision process.Results: We propose practical guidelines to improve the attribution and thus, visibility, of communities whose knowledge contributes to ethnobiological and ethnopharmacological publications. Recognising individual knowledge holders remains a critical topic on its own right.Conclusion: Transparent and consistent reporting of the provenance of place-based ancestral knowledge from communities is essential for advancing the objectives of the Nagoya Protocol, the Treaty on Intellectual Property, Genetic Resources and Associated Traditional Knowledge, and for strengthening academic inquir
Metal complexes – metal nanoparticles hybrid systems
No full textInternational audienceOne of the natural outcomes of the progress of coordination chemistry and nanochemistry is the development of hybrid nanomaterials that combine metal complexes and zerovalent metal nanoparticles. The linkage between these two components can rely on different interaction modes (covalent, ionic, π or host-guest interactions). The influence on the native properties of each component has been studied, and sometimes shows synergy. The advantages of such combined systems have been assessed in various fields, among which electronics, catalysis, biomedicine, and environmental applications, in which they have shown promising results. To shed light on this emerging field of coordination chemistry, and potentially contribute to its development, this review summarises the main strategies used to synthesize nanohybrids based on metal complex -metal nanoparticle association. The goal is to highlight the challenges associated with their synthesis and characterization, with emphasis on the combination of techniques used to elucidate their structure
Multi-millennial reconstruction of fire return intervals from a fynbos – Afrotemperate forest ecotone in the Cape Floristic Region, South Africa: Paleoecological implications for present-day management
No full textInternational audienceIn South Africa's highly biodiverse and fire-adapted Cape Floristic Region, fire is critical to maintaining ecosystem health and for the reproductive strategies of many endemic species. Ecological studies have identified fire return intervals (FRIs) of approximately 10 -15 years. However, the short timescale of these observations, derived from anthropogenically impacted systems, means that the extent to which these FRIs are maintained over millennia, and how vegetation dynamics co-vary with fire frequency is poorly resolved. Here, we analyze a highresolution macrocharcoal record from a lacustrine sedimentary archive to reconstruct fire return intervals over four millennia at a fynbos-afrotemperate forest ecotone along South Africa's southern Cape coast. We address variability in fire activity (i.e., more or less burning) and FRIs in relation to pollen-derived reconstructions of local vegetation change and regional shifts in moisture availability over the past 4200 years. We document a range of FRIs between 10.5 -166 years. We find that FRIs shift towards longer intervals, fire activity decreases, and afrotemperate forest vegetation becomes more abundant during periods of increased moisture availability. Our historical (1890 -2013 CE) FRI reconstruction is consistent with ~10 -15 years between burns, but one must only look back a few centuries to see FRIs far outside the range of variability observed today. This suggests that our present-day ecological lens is not representative of the full range of natural variability experienced at this site over the past four millennia. This work provides long-term ecological context to land managers working towards the conservation and protection of fynbos
Post‐Release Survival of the Pelagic Stingray (Pteroplatytrygon violacea, Bonaparte, 1832) in French Longline Fisheries in the Northwestern Mediterranean Sea
No full textInternational audienceBycatch remains a critical challenge in global fisheries, even when using selective gears such as longlines. In the French longline fishery targeting Atlantic bluefin tuna ( Thunnus thynnus ) in the Gulf of Lion, the common pelagic stingray ( Pteroplatytrygon violacea ) is the primary bycatch species. This study investigated the post‐release survival and behaviour of 38 stingrays (38–75 cm disc width) captured during the spring–summer seasons of 2022 and 2023, using electronic tagging (MRPats, sPats, and PSATLife). A clear seasonal trend was observed, with smaller individuals more frequently caught in summer, likely linked to warmer water conditions that also reduced tag retention time (1–70 days). Survival was estimated using the Kaplan–Meier method, accounting for uncertainty in post‐release status determination. The results indicated high survival rates ranging from 73% to 100% (median 87%), demonstrating the species' strong resilience to capture and handling. Tagging data also revealed extensive vertical and horizontal movements, with individuals reaching depths of nearly 700 m and traveling over 20 km per day. This brings new and valuable information on this poorly known species, albeit common in the Mediterranean, for the sustainable management of exploited resources in this area
Fine-Tuning Language Models for Structured Botanical Trait Extraction and Species Comparison
No full textInternational audienceAs artificial intelligence (AI) becomes central to biodiversity research, transforming morphological descriptions of species into structured data remains a challenge, particularly in botany, where species descriptions are rich in detail but lack formal structure. Despite the progress brought by transformer architectures (Vaswani et al. 2017) and their multilingual variants such as CamemBERT (Martin et al. 2020), most large language models (LLMs) are trained on general-domain English corpora, limiting their effectiveness for non-English biodiversity applications. We present a two-stage information extraction pipeline that fine-tunes LLaMA (Large Language Model Meta AI)- based LLMs (Touvron et al. 2023) to extract botanical traits from French floristic texts and enable species-level comparison at scale. Trained on a curated corpus of legacy botanical descriptions and expert-validated French question-answer pairs, the system demonstrates how domain-specific fine-tuning can bridge the gap between narrative botanical knowledge and structured trait data (Fig. 1). At the user-interface layer, we add a third stage that automatically converts the trait-value pairs generated by the question-answering module into a structured CSV table for downstream use. Our approach unifies question generation and trait extraction within a single information extraction workflow. First, predefined botanical traits (e.g., leaf shape, flower color) are reformulated as natural-language questions tailored to each species description. Then, using these questions as prompts, the model identifies and extracts the corresponding trait values: for example, extracting "lanceolate" as the standardized leaf shape from "lanceolate leaves." This converts unstructured text into consistent character-state pairs aligned with botanical ontologies. A proof-of-concept showing the input species descriptions processed by the pipeline is shown in Fig. 2. The LLaMA model was fine-tuned via Low-Rank Adaptation (LoRA) (Hu et al. 2021) on ~17,000 manually verified French question-answer pairs derived from floristic descriptions across multiple French-language flora, including: Flore de Nouvelle-Calédonie and Flore du Cameroun . Building on FloraNER (Named Entity Recognition) (Nainia et al. 2024a) and earlier CamemBERT-based pipelines (Nainia et al. 2024b), the current system, F-LoRA-QA (Nainia et al. 2025b), substantially improves structured trait generation from domain-specific descriptions. In evaluation, F-LoRA-QA outperformed an untuned LLaMA baseline with ~4× higher BLEU score (Bilingual Evaluation Understudy), a 16% gain in semantic similarity, and exact-match accuracy rising from 2% to 24%. Expert botanists further validated trait accuracy, completeness, fluency, and terminology, supporting critiques of over-reliance on automatic metrics for domain question answering (Nainia et al. 2025a). A key application is the enrichment of descriptor-based systems like Xper³ (Kerner et al. 2025), which rely on structured trait matrices to describe and differentiate taxa. Fig. 3 and Fig. 4 illustrate trait discovery, value extraction, and a comparison matrix with evidence links, supporting descriptor systems and interoperable biodiversity databases
Un œil numérique sur les cimes: Comment le non-invasif redéfinit la carte archéologique en montagne
No full textApport du Lidar HD de l'IGN et de la photogrammétrie par drone ✓ 23 années de prospection pédestres ✓ 882 structures inventoriées Apport du Lidar HD de l'IG
Aquaculture potential evolution during early domestication trials in a model species (Danio rerio) with different breeding strategies
No full textInternational audienceDomestication is a cornerstone for diversifying aquaculture, and the feasibility of domesticating a wild fishpopulation can be assessed through its aquaculture potential (i.e., a measure based on key phenotypic traitsrelated to growth and reproduction in captivity while meeting stakeholders’ expectations). As domesticationmodifies these traits, aquaculture potential is expected to evolve over generations, influenced by breedingstrategies. However, little is known about how different management approaches may shape this evolutionduring early domestication. In this study, we tracked changes in aquaculture potential over four captive gen-erations of wild-caught zebrafish (Danio rerio), subjected to three breeding strategies: no selection (NS), single-function selective breeding program (S-SBP; growth-related traits), and multi-function selective breeding pro-gram (M-SBP: growth, reproduction, welfare). S-SBP and M-SBP employed within-family selection based on aphenotypic index. We developed a standardized Aquaculture Potential Score (APS) integrating growth (standardlength, height/length ratio, specific growth rate), reproductive (fecundity, sperm motility), and welfare traits(stress-induced cortisol, Fulton’s condition factor). Trait evolution was assessed using linear model predictionsand genetic trends based on estimated breeding values and heritability derived from pedigrees. Selectivebreeding (S-SBP and M-SBP) rapidly improved growth and morphometric traits, whereas NS lines showedminimal change. Reproductive and welfare traits, however, remained largely static due to both low heritability(h2 < 0.20) and environmental modulation. Consequently, APS remained stable across generations, with growthgains offset by stagnation in other domains. These findings underscore that (i) early selection may effectivelyimprove high-heritability traits; (ii) composite metrics like APS may obscure divergent trait responses
Sequential Phage Pretreatment and TiO2–Thyme Essential Oil Photocatalysis: A Synergistic Approach to Pseudomonas aeruginosa Biofilm Inhibition and Control
No full textInternational audienceThis work introduces an original sequential bio-inspired strategy combining lytic phage pretreatment with TiO2–thyme essential oil (TEO) photocatalysis, achieving near-complete inhibition of both biofilm initiation and maturation. By simultaneously targeting planktonic cells, mature biofilms, and extracellular DNA (eDNA), this approach addresses key mechanisms involved in biofilm persistence. Pseudomonas aeruginosa ATCC 4114 was selected as the biological model due to its relevance in water distribution systems and its strong biofilm-forming ability. Experimental results showed that phage pretreatment alone inhibited biofilm formation by planktonic cells by up to 99.6% (inactivation rate constant k = 0.034 min−1) and weakened bacterial attachment in mature biofilms by 89.06% (k = 0.011 min−1). To further enhance photocatalytic efficacy, titanium dioxide (TiO2) was combined with TEO at 0.05% (v/v) as a bio-inspired photosensitizer. UV–Vis spectroscopy confirmed TiO2-TEO interactions that extended light absorption into the visible region (400–700 nm), thereby enhancing photocatalytic efficiency. This combination was designed to suppress residual biofilm development and disrupt extracellular DNA (eDNA), a critical component of biofilm structure and stability. The integrated approach involving phage pretreatment followed by TiO2–TEO (0.05%) photocatalysis achieved 99.99% inhibition of both biofilm initiation and maturation phases, with significantly increased kinetic parameters (A = 2.62 for planktonic cells and A = 3.65 for sessile cells; k = 0.076 min−1 and 0.063 min−1, respectively; p < 0.01). This study provides novel insights into water disinfection strategies using photocatalytic treatment, emphasizing the importance of monitoring post-treatment bacterial virulence factor expression