Résumé
Abstract DNA metabarcoding is becoming the tool of choice for biodiversity assessment across taxa and environments. Yet, the artefacts present in metabarcoding datasets often preclude a proper interpretation of ecological patterns. Bioinformatic pipelines to remove experimental noise exist. However, these often only partially target produced artefacts, or are marker specific. In addition, assessments of data curation quality and chosen filtering thresholds are seldom available in existing pipelines, partly due to the lack of appropriate visualisation tools. Here, we present metabaR, an r package that provides a comprehensive suite of tools to effectively curate DNA metabarcoding data after basic bioinformatic analyses. In particular, metabaR uses experimental negative or positive controls to identify different types of artefactual sequences, that is, contaminants and tag-jumps. It also flags potentially dysfunctional PCRs based on PCR replicate similarities when those are available. Finally, metabaR provides tools to visualise DNA metabarcoding data characteristics in their experimental context as well as their distribution, and facilitates assessment of the appropriateness of data curation filtering thresholds. metabaR is applicable to any DNA metabarcoding experimental design but is most powerful when the design includes experimental controls and replicates. More generally, the simplicity and flexibility of the package makes it applicable any DNA marker, and data generated with any sequencing platform, and pre-analysed with any bioinformatic pipeline. Its outputs are easily usable for downstream analyses with any ecological r package. metabaR complements existing bioinformatics pipelines by providing scientists with a variety of functions to effectively clean DNA metabarcoding data and avoid serious misinterpretations. It thus offers a promising platform for automatised data quality assessments of DNA metabarcoding data for environmental research and biomonitoring.
Auteurs, date et publication :
Auteurs Lucie Zinger , Clément Lionnet , Anne-Sophie Benoiston , Julian Donald , Céline Mercier , Frédéric Boyer
Publication : Methods in Ecology and Evolution
Date : 2025
Volume : 12
Issue : 4
Pages : 586–592
Catégorie(s)
#CNRS #eDNAAuteurs, date et publication :
Auteurs Benoît Sotton , Alain Paris , Séverine Le Manach , Alain Blond , Gérard Lacroix , Alexis Millot , Charlotte Duval , Hélène Huet , Qin Qiao , Sophie Labrut , Giovanni Chiapetta , Joelle Vinh , Arnaud Catherine , Benjamin Marie
Publication : Scientific Reports
Date : 2025
Volume : 7
Issue : 1
Catégorie(s)
#ANR-Citation #CNRS #ENS #PLANAQUARésumé
Tropical plants are expected to have a higher variety of defensive traits, such as a more diverse array of secondary metabolic compounds in response to greater pressures of antagonistic interactions, than their temperate counterparts. We test this hypothesis using advanced metabolomics linked to a novel stoichiometric compound classification to analyze the complete foliar metabolomes of four tropical and four temperate tree species, which were selected so that each subset contained the same amount of phylogenetic diversity and evenness. We then built Bayesian phylogenetic multilevel models to test for tropical–temperate differences in metabolite diversity for the entire metabolome and for four major families of secondary compounds. We found strong evidence supporting that the leaves of tropical tree species have a higher phenolic diversity. The functionally closer group of polyphenolics also showed moderate evidence of higher diversity in tropical species, but there were no differences either for the entire metabolome or for the other major families of compounds analyzed. This supports the interpretation that this tropical–temperate contrast must be related to the functional role of phenolics and polyphenolics.
Auteurs, date et publication :
Auteurs Guille Peguero , Albert Gargallo-Garriga , Joan Maspons , Karel Klem , Otmar Urban , Jordi Sardans , Josep Peñuelas
Publication : Plants
Date : 2021
Volume : 10
Issue : 3
Pages : 554
Catégorie(s)
#CNRS #FORET NouraguesAuteurs, date et publication :
Auteurs Florence D. Hulot , Maurice Rossi , Bruno Verdier , Jean-Pascal Urban , Lydie Blottière , Fantina Madricardo , Beatriz Decencière
Publication : Limnology and Oceanography: Methods
Date : 2025
Volume : 15
Issue : 2
Pages : 154-165
Catégorie(s)
#ANR-Citation #CNRS #ENS #PLANAQUARésumé
Dynamic avalanche modeling requires as input the volumes and areas of the snow released, and consequently the fracture heights. Determining these parameters requires high-resolution spatial snow surface data from before and after an avalanche. In snow and avalanche research, terrestrial laser scanners are used increasingly to efficiently and accurately map snow surfaces and depths over an area of several km2. In practice however, several problems may occur, which must be recognized and accounted for during post-processing and interpretation. Thus, we combine terrestrial laser scanning with photogrammetry, total station measurements and field snow observations to document and accurately survey an artificially triggered avalanche at the Col du Lautaret test site (2058 m) in the French Alps. The ability of TLS to determine avalanche modeling input parameters efficiently and accurately is shown, and we demonstrate how, merging TLS with the other methods facilitates and improves data post-processing and interpretation. Finally, we present for this avalanche the data required for the parameterization and validation of dynamic avalanche models.
Auteurs, date et publication :
Auteurs Alexander Prokop , Peter Schön , Florian Singer , Gaëtan Pulfer , Mohamed Naaim , Emmanuel Thibert , Alvaro Soruco
Publication : Cold Regions Science and Technology
Date : 2025
Volume : 110
Pages : 223-230
Catégorie(s)
#CNRS #Lautaret #UGARésumé
Mediterranean forests are found in the Mediterranean basin, California, the South African Cape Province, South and southwestern Australia and parts of Central Chile. They represent 1.8 % of the world forest areas of which the vast majority is found in the Mediterranean basin, where historical and paleogeographic episodes, long-term human influence and geographical and climatic contrasts have created ecosystemic diversity and heterogeneity. Even if evergreen is dominant, deciduous trees are also represented, with different forest types including dense stands with a closed canopy (forests sensu stricto) and pre-forestal or pre-steppic structures with lower trees density and height. The Mediterranean basin is also a hot spot of forest species and genetic diversity, with 290 woody species versus only 135 for non-Mediterranean Europe. However, the characteristics of the Mediterranean area (long-standing anthropogenic pressure, significant current human activity and broad biodiversity) make it one of the world's regions most threatened by current changes. Four examples of Mediterranean forest types, present in south and north of the Mediterranean basin and more or less threatened, are developed in order to show that linking “hard sciences” and humanities and social sciences is necessary to understand these complex ecosystems. We show also that these forests, in spite of specific climatic constraints, can also be healthy and productive and play a major ecological and social role. Furthermore, even if the current human activity and global change constitute a risk for these exceptional ecosystems, Mediterranean forests represent a great asset and opportunities for the future of the Mediterranean basin.
Auteurs, date et publication :
Auteurs Thierry Gauquelin , Geneviève Michon , Richard Joffre , Robin Duponnois , Didier Genin , Bruno Fady , Magda Bou Dagher-Kharrat , Arezki Derridj , Said Slimani , Wadi Badri , Mohamed Alifriqui , Laurent Auclair , Romain Simenel , Mohamed Aderghal , Ezékiel Baudoin , Antoine Galiana , Yves Prin , Hervé Sanguin , Catherine Fernandez , Virginie Baldy
Publication : Regional Environmental Change
Date : 2025
Volume : 18
Pages : 623-636
Catégorie(s)
#CNRS #FORET O3HPRésumé
Methods We addressed this issue by studying the effect of PSM extracted from four Mediterranean woody plants on germination speed and final percentages of a subordinate herbaceous plant, Linum perenne.
Results By using hydro- and thermal time threshold models, we show how PSM interact with temperature and moisture levels to limit germination at dry and upper thermal limits, with the magnitude of effects depending on the source plant. PSM effects on germination, also observed on natural soils, persisted after their removal from the seed environment.
Conclusions We conclude that the impact of climate change on reproduction of herbaceous plants can be modulated by effects of PSM from woody plants,
Auteurs, date et publication :
Auteurs Hazem Hashoum , Arne Saatkamp , Thierry Gauquelin , Julien Ruffault , Catherine Fernandez , Anne Bousquet-Mélou
Publication : Plant and Soil
Date : 2025
Volume : 446
Issue : 1-2
Pages : 291-305
Catégorie(s)
#CNRS #FORET Nouragues #FORET O3HPAuteurs, date et publication :
Auteurs S. Barot , J.-C. Lata , G. Lacroix
Publication : Ecological Engineering
Date : 2025
Volume : 45
Pages : 13-23
Catégorie(s)
#CNRS #Ecotron IleDeFrance #ENS #PLANAQUARésumé
Organisms can gain information about predation risks from their parents, their own personal experience, and their conspecifics and adjust their behavior to alleviate these risks. These different sources of information can, however, provide conflicting information due to spatial and temporal variation of the environment. This raises the question of how these cues are integrated to produce adaptive antipredator behavior. We investigated how common lizards (Zootoca vivipara) adjust the use of conspecific cues about predation risk depending on whether the information is maternally or personally acquired. We experimentally manipulated the presence of predator scent in gestating mothers and their offspring in a full-crossed design. We then tested the consequences for social information use by monitoring offspring social response to conspecifics previously exposed to predator cues or not. Lizards were more attracted to the scent of conspecifics having experienced predation cues when they had themselves no personal information about predation risk. In contrast, they were more repulsed by conspecific scent when they had personally obtained information about predation risk. However, the addition of maternal information about predation risk canceled out this interactive effect between personal and social information: lizards were slightly more attracted to conspecific scent when these two sources of information about predation risk were in agreement. A chemical analysis of lizard scent revealed that exposure to predator cues modified the chemical composition of lizard scents, a change that might underlie lizards’ use of social information. Our results highlight the importance of considering multiple sources of information while studying antipredator defenses.
Auteurs, date et publication :
Auteurs Laurane Winandy , Lucie Di Gesu , Marion Lemoine , Staffan Jacob , José Martin , Christine Ducamp , Michèle Huet , Delphine Legrand , Julien Cote
Publication : Behavioral Ecology
Date : 2021
Issue : araa151
Catégorie(s)
#ANR-Citation #CNRS #Metatron terrestreRésumé
Predation is a strong selective pressure generating morphological, physiological and behavioural responses in organisms. As predation risk is often higher during juvenile stages, antipredator defences expressed early in life are paramount to survival. Maternal effects are an efficient pathway to produce such defences. We investigated whether maternal exposure to predator cues during gestation affected juvenile morphology, behaviour and dispersal in common lizards (Zootoca vivipara). We exposed 21 gravid females to saurophagous snake cues for one month while 21 females remained unexposed (i.e. control). We measured body size, preferred temperature and activity level for each neonate, and released them into semi-natural enclosures connected to corridors in order to measure dispersal. Offspring from exposed mothers grew longer tails, selected lower temperatures and dispersed thrice more than offspring from unexposed mothers. Because both tail autotomy and altered thermoregulatory behaviour are common antipredator tactics in lizards, these results suggest that mothers adjusted offspring phenotype to risky natal environments (tail length) or increased risk avoidance (dispersal). Although maternal effects can be passive consequences of maternal stress, our results strongly militate for them to be an adaptive antipredator response that may increase offspring survival prospects.
Auteurs, date et publication :
Auteurs Elvire Bestion , Aimeric Teyssier , Fabien Aubret , Jean Clobert , Julien Cote
Publication : Proceedings of the Royal Society B: Biological Sciences
Date : 2025
Volume : 281
Issue : 1792