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Computational assessment of Amazon forest plots regrowth capacity under strong spatial variability for simulating logging scenarios
No full textIn this paper, we assess the regrowth capacity of tropical forest plots by developing an original computational procedure based on statistical model checking methods. We calibrate a new mathematical model of forest dynamics with respect to post-logging data, produced in the Amazon basin. Our mathematical model is determined by a mechanistic system of ordinary differential equations and integrates a new nonlinear aging term, which is necessary to reproduce the complex post-logging dynamics of the tropical forest plots. Our method is based on an efficient algorithmic procedure that explores the parameter space of the model and computes a score for each parameter value, depending on the distance between the trajectory of the model and the data. We distinguish a group of four reference plots, for which the logging was the most intense, from another group of five non-reference plots, which are fitted a posteriori. Our results provide a set trajectories of the new model, which successfully fit the non-monotone post-logging data on each forest plot, in spite of the high level of biological variability identified in the study site. Rather than a unique set of parameters, we return a small cell of parameters, extracted from the parameter space, which contains in its close vicinity several relevant sets of parameters that are equally able to reproduce the regrowth dynamics of distinct tropical forest plots. The size of the cells that should be extracted from the parameter space increases with the level of biological variability. Finally, we show how to use the calibrated mathematical model for simulating logging scenarios, so as to better understand the temporal dynamics of forest regrowth
Diversity of leaf functioning under water deficit in a large grapevine panel: high throughput phenotyping and genetic analyses
No full textInternational audienceWater resource is a major limiting factor impacted by climate change that threatens grapevine production and quality. Understanding the ecophysiological mechanisms involved in the response to water deficit is crucial to select new varieties more drought tolerant. A major bottleneck that hampers such advances is the lack of methods for measuring fine functioning traits on thousands of plants as required for genetic analyses. This study aimed at investigating how water deficit affects the trade-off between carbon gains and water losses in a large panel representative of the Vitis vinifera genetic diversity. 250 genotypes were grown under 3 watering scenarios (well-watered, moderate and severe water deficit) in a high-throughput phenotyping platform. To assess traits related to carbon and water functioning on the whole panel, we deployed an original approach where 120 leaves of 40 genotypes were phenotyped combining low-throughput devices to precisely measure ecophysiological traits, as well as innovative, portable high-throughput devices to measure near infrared reflectance, porometry and chlorophyll fluorescence. These data allowed us to build cutting-edge statistical models, such as multiblock models, which jointly use data from different devices, for predicting ecophysiological traits. Models for predicting photosynthesis and transpiration were accurate enough to be applied on the entire panel, only measured with high-throughput devices. Such predictions highlighted a wide range of genotypic variability and contrasting responses to water deficit. Multi-traits and Multi-Environment Genome Wide Association Studies further revealed genomic regions associated with these responses, and underlying candidate genes are being investigated
Steady-state semi-analytical solutions for assessing the two-dimensional groundwater hydraulic head depletion induced by river dam removal
No full textInternational audienceDams are pervasive features of the world’s river systems. The reservoir associated with the dam modifies the distribution of the hydraulic head in the aquifer and the natural groundwater flow. However, such modifications must be defined to forecast their environmental, economic and/or social impacts. Based on the method of fundamental solutions (MFS), steady-state semi-analytical solutions are proposed for evaluating the long-term spatial distribution of the rise or decline of the hydraulic head in an aquifer caused by a dam reservoir on a watercourse or its removal. MFS was chosen because of its ability to account for different boundary conditions along the banks of the watercourse. The dam reservoir can have a triangular or rectilinear geometry. The aquifer is assumed unconfined, homogeneous, inclined and finite. The solutions take into account both the reservoir-aquifer interaction and those between the stream and the aquifer up- and downstream of the reservoir. The reservoir-stream system fully penetrates the aquifer, and is separated from the aquifer by semi-pervious banks (Robin condition). Analysis of the semi-analytical solution included sensitivity tests, and assessment of the influence of several parameters: reservoir leakance parameter, width of the reservoir and width of the aquifer. The results show that the reservoir and river leakage parameters up- and downstream of the reservoir, as well as the geometry of the reservoir dam, are the main determining parameters of the extent of the induced groundwater mound. They show that low aquifer-river exchanges in the river upstream and downstream of the reservoir increases the spatial extension of the mound. The degree of error introduced by the method of linearization used to solve the governing partial differential equation is also discussed. A solution has been also developed with a pumping well, particularly to assess what the depletion of the water level at the well location might be if the dam is removed. The proposed solutions were applied at two field sites, giving satisfactory results.These semi-analytical solutions will be useful applications for assessing the long-term spatial impact on the aquifer of the emplacement, removal or leveling of a reservoir dam
Collaborative Benchmarking Rule-Reasoners with B-Runner
No full textNational audienceConducting experimental analysis on rule reasoners is a mainstream task for validating novel algorithms and systems. Nevertheless, providing robust, veriable, and reproducible experiments can still raise a sensible challenge. We propose to demonstrate B-Runner, an open library for collaborative benchmarking focusing on the deployment of articulate tests for knowledge and rule-based systems with low cost and high robustness. B-Runner reduces the benchmarking setup time while guaranteeing experiment repeatability. At the same time, it improves the scrutability of experimental protocols thereby enhancing their robustness as well as fairness of system comparisons. This demonstration proposes to show- case the use of the tool for systematically testing a number of systems as well as to introduce its architecture and its extensibility to novel tools and experimental protocols
AdvenAlg, a software to help with the identification and a knowledge of the main crop weeds in Mediterranean Algeria
No full textInternational audienceAccess to AdvenAlg is via the URL address: www.wikwio.org/alg/ which currently allows the identification of 125 important species of algerian weeds in field crops. They are divided according to their noxiousness into 15 agronomically major species, 20 secondary species, and 90 minor species. This modern computer-assisted identification (CAI) method allows simple and precise identification of plant species based on illustrated characters (and not described by botanical jargon as is the case with classic dichotomous keys), therefore in a graphic manner, by creating a composite portrait of the plant. Emphasis is placed on vegetative characters to enable recognition of incomplete samples. A composite portrait of the plant is created using a process allowing the free choice of characters, error management, the absence of technical terminology and self-correction. At any time, it is possible to access macro photographs and descriptive texts and print them. The AdvenAlg database, available in French or English, will be gradually updated with other species of crop weeds from the same phytogeographic region. All AdvenAlg species sheets can also be consulted on the Wiktrop collaborative portal dedicated to the sharing and dissemination of knowledge on weeds in tropical and Mediterranean crops: http://portal.wiktrop.org
Screening of Triploid Banana Population Under Natural and Controlled Black Sigatoka Disease for Genomic Selection
No full textInternational audienceBlack sigatoka disease (BSD) is the most important foliar threat in banana production, and breeding efforts against it should take advantage of genomic selection (GS), which has become one of the most explored tools to increase genetic gain, save time, and reduce selection costs. To evaluate the potential of GS in banana for BSD, 210 triploid accessions were obtained from the African Banana and Plantain Research Center to constitute a training population. The variability in the population was assessed at the phenotypic level using BSD- and agronomic-related traits and at the molecular level using single-nucleotide polymorphisms (SNPs). The analysis of variance showed a significant difference between accessions for almost all traits measured, although at the genomic group level, there was no significant difference for BSD-related traits. The index of non-spotted leaves among accessions ranged from 0.11 to 0.8. The accessions screening in controlled conditions confirmed the susceptibility of all genomic groups to BSD. The principal components analysis with phenotypic data revealed no clear diversity partition of the population. However, the structure analysis and the hierarchical clustering analysis with SNPs grouped the population into four clusters and two subpopulations, respectively. The field and laboratory screening of the banana GS training population confirmed that all genomic groups are susceptible to BSD but did not reveal any genetic structure, whereas SNP markers exhibited clear genetic structure and provided useful information in the perspective of applying GS
Replication-independent change in the frequencies of distinct genome segments of a multipartite virus during its transit within aphid vectors
No full textInternational audienceMultipartite viruses exhibit a fragmented genome composed of several nucleic acid segments individually packaged in distinct viral particles. The genome of all species of the genus Nanovirus holds eight segments, which accumulate at a very specific and reproducible relative frequency in the host plant tissues. In a given host species, the steady state pattern of the segments’ relative frequencies is designated the genome formula and is thought to have an adaptive function through the modulation of gene expression. Nanoviruses are aphid-transmitted circulative non-propagative viruses, meaning that the virus particles are internalized into the midgut cells, transferred to the hemolymph, and then to the saliva, with no replication during this transit. Unexpectedly, a previous study on the faba bean necrotic stunt virus revealed that the genome formula changes after ingestion by aphids. We investigate here the possible mechanism inducing this change by first comparing the relative segment frequencies in different compartments of the aphid. We show that changes occur both in the midgut lumen and in the secreted saliva but not in the gut, salivary gland, or hemolymph. We further establish that the viral particles differentially resist physicochemical variations, in particular pH, ionic strength, and/or type of salt, depending on the encapsidated segment. We thus propose that the replication-independent genome formula changes within aphids are not adaptive, contrary to changes occurring in plants, and most likely reflect a fortuitous differential degradation of virus particles containing distinct segments when passing into extra-cellular media such as gastric fluid or saliva. IMPORTANCE The genome of multipartite viruses is composed of several segments individually packaged into distinct viral particles. Each segment accumulates at a specific frequency that depends on the host plant species and regulates gene expression. Intriguingly, the relative frequencies of the genome segments also change when the octopartite faba bean necrotic stunt virus (FBNSV) is ingested by aphid vectors, despite the present view that this virus travels through the aphid gut and salivary glands without replicating. By monitoring the genomic composition of FBNSV populations during the transit in aphids, we demonstrate here that the changes take place extracellularly in the gut lumen and in the saliva. We further show that physicochemical factors induce differential degradation of viral particles depending on the encapsidated segment. We propose that the replication-independent changes within the insect vector are not adaptive and result from the differential stability of virus particles containing distinct segments according to environmental parameters
Avis de l'Anses relatif au projet « Jourdain » de réutilisation des eaux usées traitées pour l'alimentation d'une retenue d'eau destinée à la production d’eau destinée à la consommation humaine (Vendée)
No full textCitation suggérée : Anses. (2024). Avis relatif aux relatif aux projets de décret et d'arrêté relatifs à l'utilisation d'eaux non potables pour certains usages domestiques. (saisine 2023-SA-0037). MaisonsAlfort : Anses, 66 p.L’augmentation de la fréquence et de la durée des vagues de chaleur et des sécheresses, en lien avec les changements climatiques1 et la croissance démographique et ses conséquences en termes d’urbanisation, d’industrialisation et de besoins d’irrigation pour la production agricole, affecte le cycle de l’eau et la disponibilité des ressources en eau douce sur terre. Cette raréfaction des ressources en eau est considérée comme un risque majeur par le groupe d’experts intergouvernemental sur l’évolution du climat (GIEC). En France, la fréquence plus élevée des épisodes de sécheresse et des vagues de chaleur impose des mesures de restriction d’eau, avec un risque croissant de multiplication des conflits d’usage. Parmi les solutions proposées pour pallier cette problématique du manque d’eau, le recours aux eaux impropres à la consommation humaine (nommées également « eaux non potables » et « eaux non conventionnelles ») est encouragé au niveau communautaire et national.Au niveau communautaire, plusieurs directives ou règlements encouragent et encadrent une utilisation durable des ressources en eaux, notamment :- l’article 12 de la directive 91/271/CEE du Conseil du 21 mai 1991 relative au traitement des eaux urbaines résiduaires mentionne que les eaux usées traitées (EUT) peuvent être réutilisées chaque fois que cela se révèle approprié ;- la directive 2000/60/CE du Parlement européen et du Conseil du 23 octobre 2000 établissant un cadre pour une politique communautaire dans le domaine de l'eau, promeut une utilisation durable des ressources en eaux et contribue à atténuer les effets des inondations et des sécheresses ;- le règlement (UE) 2020/741 du Parlement européen et du Conseil du 25 mai 2020, relatif aux exigences minimales applicables à la réutilisation des EUT, rappelle que cette réutilisation vise à contribuer aux objectifs de développement durable de l’Union européenne, en particulier l’objectif 6 sur la disponibilité et la gestion durable de l’eau et de l’assainissement pour tous, et l’objectif 12 sur la consommation et la production durable. Si ce règlement s’applique à la réutilisation des eaux urbaines résiduaires traitées à des fins d’irrigation agricole, il précise, au considérant 29, que « le présent règlement ne devrait pas empêcher les États-membres d’autoriser l’utilisation d’eau de récupération à d’autres fins, y compris à des fins industrielles, environnementales et de services collectifs, dans la mesure jugée nécessaire en fonction des circonstances et des besoins au niveau national, à condition qu’un niveau élevé de protection de l’environnement et de la santé humaine et animale soit garanti ». (extrait) [Saisines liées n° 2014-SA-0177 et 2015-SA-0146