88 research outputs found
Life-history phenology strongly influences population vulnerability to toxicants: a case study with the mudsnail Potamopyrgus antipodarum.
International audienceOne of the main objectives of ecological risk assessment is to evaluate the effects of toxicants on ecologically relevant biological systems such as populations or communities. However, the effects of toxicants are commonly measured on selected subindividual or individual endpoints due to their specificity against chemical stressors. Introducing these effects into population models is a promising way to predict impacts on populations. The models currently employed are very simplistic, and their environmental relevance needs to be improved to establish the ecological relevance of hazard assessment. The present study with the gastropod Potamopyrgus antipodarum combines a field experimental approach with a modeling framework. It clarifies the role played by seasonal variability of life-history traits in the population's vulnerability to the alteration of individual performance, potentially due to toxic stress. The present study comprised 3 steps: 1) characterization of the seasonal variability in life-history traits of a local population over 1 yr by using in situ experiments on caged snails, coupled with a demographic follow-up; 2) development of a periodic matrix population model that visualizes the monthly variability of population dynamics; and 3) simulation of the demographic consequences of an alteration in life-history traits (i.e., fertility, juvenile, and adult survival). The results revealed that demographic impacts strongly depend on the season when alterations of individual performance occur. Model analysis showed that this seasonal variability in population vulnerability is strongly related to the phenology of the population. The authors emphasize that improving the realism of population models is a major objective for ecological risk assessment, and that taking into account species phenology in modeling approaches should be a priority
Adaptive vibrational configuration interaction (A-VCI): a posteriori error estimation to efficiently compute anharmonic IR spectra
International audienceA new variational algorithm called adaptive vibrational configuration interaction (A-VCI) intended for the resolution of the vibrational Schrödinger equation was developed. The main advantage of this approach is to efficiently reduce the dimension of the active space generated into the configuration interaction (CI) process. Here, we assume that the Hamiltonian writes as a sum of products of operators. This adaptive algorithm was developed with the use of three correlated conditions i.e. a suitable starting space ; a criterion for convergence, and a procedure to expand the approximate space. The velocity of the algorithm was increased with the use of a posteriori error estimator (residue) to select the most relevant direction to increase the space. Two examples have been selected for benchmark. In the case of H 2 CO, we mainly study the performance of A-VCI algorithm: comparison with the variation-perturbation method, choice of the initial space, residual contributions. For CH 3 CN, we compare the A-VCI results with a computed reference spectrum using the same potential energy surface and for an active space reduced by about 90 %
Efficient basis selection for the computation of vibrational spectrum
International audienceWe propose here an efficient method to define an approximation subspace to compute the first vibrational frequencies of the molecular Hamiltonian which are those of interest in the experimental results
Optimisation of the variational method for vibrational Hamiltonian eigenvalues computation
International audienceWe propose here an efficient method to define a representative approximation subspace to compute the first eigenvalues of the vibrational Hamiltonian which are those of interest in the experimental results
Décomposition en valeurs singuliÚres randomisée et positionnement multidimensionel à base de tùches
The multidimensional scaling (MDS) is an important and robust algorithm for representing individual cases of a dataset out of their respective dissimilarities. However, heuristics, possibly trading-off with robustness, are often preferred in practice due to the potentially prohibitive memory and computational costs of the MDS. The recent introduction of random projection techniques within the MDS allowed it to be become competitive on larger testcases. The goal of this manuscript is to propose a high-performance distributed-memory MDS based on random projection for processing data sets of even larger size (up to one million items). We propose a task-based design of the whole algorithm and we implement it within an efficient software stack including state-of-the-art numerical solvers, runtime systems and communication layers. The outcome is the ability to efficiently apply robust MDS to large datasets on modern supercomputers. We assess the resulting algorithm and software stack to the point cloud visualization for analyzing distances between sequencesin metabarcoding.Le positionnement multidimensionnel (MDS) est un algorithme important et robuste pour reprĂ©senter les cas individuels dâun ensemble de donnĂ©es en fonction de leurs dissimilaritĂ©s respectives. Cependant, les heuristiques, qui peuvent ĂȘtre un compromis avec la robustesse, sont souvent prĂ©fĂ©rĂ©es en pratique en raison de sa consommation mĂ©moire et de ses coĂ»ts potentiellement prohibitifs. Lâintroduction rĂ©cente de techniques de projection alĂ©atoire dans le MDS lui a permis de devenir compĂ©titif sur des cas test plus importants. Lâobjectif de ce manuscrit est de proposer un MDS haute performance basĂ© sur la projection alĂ©atoire pour le traitement dâensembles de donnĂ©es de taille encore plus grande (jusquâĂ un million dâĂ©lĂ©ments). Nous proposons une conception de lâalgorithme et nous lâimplĂ©mentons dans une pile logicielle efficace, comprenant des solveurs numĂ©riques de pointe ainsi des systĂšmes dâexĂ©cution et des couches de communication optimisĂ©s. Lâaboutissement de ce travail rĂ©sultat est la capacitĂ© dâappliquer efficacement le MDS robuste Ă de grands ensembles de donnĂ©es sur des super-ordinateurs modernes. Nous Ă©valuons lâalgorithme etla pile logicielle rĂ©sultants Ă la visualisation de nuages de points pour lâanalyse des distances entre sĂ©quences de metabarcoding
ModÚles ecologiques pour l'extrapolation des effets écotoxicologiques enregistrés lors de biotests in situ cheZ Gammarus
[Departement_IRSTEA]Eaux [TR1_IRSTEA]BELCAInternational audienceEvaluating the effects of chemical contamination on populations and ecological communities still constitutes a challenging necessity in environmental management. However the toxic effects of contaminants are commonly measured by means of organism-level responses. Linking such effects measures with ecological models is a promising way to apprehend population-level impacts. In this way, population models are currently increasingly used in predictive risk assessment procedures, but their use in environmental diagnostic framework remains limited due to their lack of ecological realism. The present study with the crustacean amphipod Gammarus fossarum, a sentinel species in freshwater monitoring, combines a dual field and laboratory experimental approach with a population modelling framework. In this way, we developed an ecologically-relevant periodic matrix population model for Gammarus. This model allowed us to capture the population dynamics in the field, and to understand the particular pattern of demographic sensitivities induced by Gammarus life-history phenology. The model we developed provided a robust population-level assessment of in situ-based effects measures recorded during a biomonitoring program on a French watershed impacted by past mining activities. Thus, our study illustrates the potential of population modelling when seeking to decipher the role of environmental toxic contamination in ecological perturbations
Modelling and change of scales in ecotoxicological risk assessmment : methodological developments for two freshwater macroinvertebrates, Gammarus pulex (crustacean) and Potamopyrgus antipodarum (gastropod)
Les rĂ©glementations conduisent Ă multiplier les Ă©valuations du risque Ă©cologique liĂ© au rejet des substances chimiques dans les milieux aquatiques avec pour objectif de protĂ©ger les populations naturelles. Cependant, ce niveau de protection visĂ© ne peut ĂȘtre utilisĂ© facilement pour Ă©tablir un lien direct entre une contamination et ses effets. Pour palier cette difficultĂ©, les approches multi-Ă©chelles basĂ©es sur l'Ă©tude des effets des contaminations sur des marqueurs individuels puis sur l'extrapolation de ces effets au niveau des poipulations Ă partir de modĂšles de dynamique de population reprĂ©sentent des dĂ©marches prometteuses et commencent Ă ĂȘtre bien acceptĂ©es dans les dĂ©marches prĂ©dictives.Cependant, leur utilisation pour le diagnostic de la qualitĂ© des milieux aquatiques reste pour le moment trĂšs rare, d'une part en raison de la forte variabilitĂ© des rĂ©ponses des marqueurs individuels in situ liĂ©e Ă l'influence de divers facteurs environnementaux confondants pour l'Ă©valuation de la toxicitĂ©, et d'autre part Ă cause du manque de pertinence environnementale des modĂšles actuellement proposĂ©s. CentrĂ© sur l'utilisation de deux espĂšces couramment observĂ©es dans les cours d'eau europĂ©ens et prĂ©sentant des caractĂ©ristiques Ă©cologiques et phylogĂ©niques contrastĂ©es : le crustacĂ© Gammarus fossarum et le mollusque Potamopyrgus antipodarum, ce travail doctoral a permis : 1- de proposer une mĂ©thodologie pour prendre en compte l'influence des facteurs de confusion dans le but d'amĂ©liorer la lecture des bioessais in situ basĂ©s sur la mesure des marqueurs individuels sur des organismes encagĂ©s et 2- de dĂ©velopper des modĂšles de dynamique de population Ă©cologiquemnt pertinents.The regulatory framework lead to increase the assessments of the ecological risk linked to the dischaarge of chemical substances in aquatic environment with the aim to protect natural populations. However, this target level of protection cannot be used so easily to etablish a direcet link between a contamination and its effects. In order to overcome this difficulty, the multi-scale approaches based on the study of the effects of the contaminations on individual markers and then on the extrapolation of these effects at the population level with population dynamic models reprensent promising tools and start to bewell accepted in predictive processes. Yet, their use for the diagnosis of water quality remainsrare for the moment, on the one hand, because of the important varaibility of answers of individual makers in situ linked to the influence of diverse confounding environmental factors for the assessments of toxicity and, on the other hand, because pf the lack of environmental relevance of models currently proposed. Focused on the use of 2 species widely observed in European rivers and presenting contrastingecological and phylogenetic characteristics : the Grammar fossarum crutacean and the Potamopyrgus antipodarum mollusc, this doctoral degree first propose a methodology to consider the influenceof confounding factors in order to improve the reading of biological in situ tests based on the measurment of individual markers on caged organisms and second, to develop ecologically relevant population models. Thus, this work allowed to underline the importance of the consideration of confounding factors (i.e. temperature), in different in situ tests based on the measurment of individul markers on caged organisms. Moreover, population models for both species have been defined in order to test the influence of life histories and seasonal variations on demographic sensitivity of populations
Modélisation et changements d'échelles pour l'évaluation écotoxicologique : application à deux macroinvertébrés aquatiques, Gammarus fossarum (crustacé amphipode) et potamopyrgus antipodarum (mollusque gastéropode)
The regulatory framework lead to increase the assessments of the ecological risk linked to the dischaarge of chemical substances in aquatic environment with the aim to protect natural populations. However, this target level of protection cannot be used so easily to etablish a direcet link between a contamination and its effects. In order to overcome this difficulty, the multi-scale approaches based on the study of the effects of the contaminations on individual markers and then on the extrapolation of these effects at the population level with population dynamic models reprensent promising tools and start to bewell accepted in predictive processes. Yet, their use for the diagnosis of water quality remainsrare for the moment, on the one hand, because of the important varaibility of answers of individual makers in situ linked to the influence of diverse confounding environmental factors for the assessments of toxicity and, on the other hand, because pf the lack of environmental relevance of models currently proposed. Focused on the use of 2 species widely observed in European rivers and presenting contrastingecological and phylogenetic characteristics : the Grammar fossarum crutacean and the Potamopyrgus antipodarum mollusc, this doctoral degree first propose a methodology to consider the influenceof confounding factors in order to improve the reading of biological in situ tests based on the measurment of individual markers on caged organisms and second, to develop ecologically relevant population models. Thus, this work allowed to underline the importance of the consideration of confounding factors (i.e. temperature), in different in situ tests based on the measurment of individul markers on caged organisms. Moreover, population models for both species have been defined in order to test the influence of life histories and seasonal variations on demographic sensitivity of populations.Les rĂ©glementations conduisent Ă multiplier les Ă©valuations du risque Ă©cologique liĂ© au rejet des substances chimiques dans les milieux aquatiques avec pour objectif de protĂ©ger les populations naturelles. Cependant, ce niveau de protection visĂ© ne peut ĂȘtre utilisĂ© facilement pour Ă©tablir un lien direct entre une contamination et ses effets. Pour palier cette difficultĂ©, les approches multi-Ă©chelles basĂ©es sur l'Ă©tude des effets des contaminations sur des marqueurs individuels puis sur l'extrapolation de ces effets au niveau des poipulations Ă partir de modĂšles de dynamique de population reprĂ©sentent des dĂ©marches prometteuses et commencent Ă ĂȘtre bien acceptĂ©es dans les dĂ©marches prĂ©dictives.Cependant, leur utilisation pour le diagnostic de la qualitĂ© des milieux aquatiques reste pour le moment trĂšs rare, d'une part en raison de la forte variabilitĂ© des rĂ©ponses des marqueurs individuels in situ liĂ©e Ă l'influence de divers facteurs environnementaux confondants pour l'Ă©valuation de la toxicitĂ©, et d'autre part Ă cause du manque de pertinence environnementale des modĂšles actuellement proposĂ©s. CentrĂ© sur l'utilisation de deux espĂšces couramment observĂ©es dans les cours d'eau europĂ©ens et prĂ©sentant des caractĂ©ristiques Ă©cologiques et phylogĂ©niques contrastĂ©es : le crustacĂ© Gammarus fossarum et le mollusque Potamopyrgus antipodarum, ce travail doctoral a permis : 1- de proposer une mĂ©thodologie pour prendre en compte l'influence des facteurs de confusion dans le but d'amĂ©liorer la lecture des bioessais in situ basĂ©s sur la mesure des marqueurs individuels sur des organismes encagĂ©s et 2- de dĂ©velopper des modĂšles de dynamique de population Ă©cologiquemnt pertinents
Finalisation I2M2, chantier Diagnostic multi-EQB et développement d'un indice pour les grands cours d'eau. Rapport final
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