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International audience; La végétation riveraine ligneuse le long des rivières et des ruisseaux remplit de multiples fonctions bénéfiques pour les communautés de macroinvertébrés aquatiques . Ils retiennent les sédiments fins, les nutriments et les pesticides, améliorent l'hydromorphologie des canaux, contrôlent la température de l'eau et la production primaire grâce à l'ombrage et fournissent des feuilles, des brindilles et du gros bois.Dans un modèle conceptuel récent (Feld et al., 2018), les fonctions riveraines ligneuses ont été considérées soit comme indépendantes des facteurs de stress liés à l'utilisation des terres à grande échelle (p. rétention des nutriments et des pesticides).Nous avons testé ce concept en utilisant des données à haute résolution sur la couverture végétale riveraine ligneuse et des données empiriques provenant de 1017 sites d'échantillonnage de macroinvertébrés dans les ruisseaux de plaine et de montagne allemands. Les métriques des macroinvertébrés indicatives des fonctions individuelles ont été utilisées comme variables de réponse dans les modèles d'équations structurelles (SEM), représentant la structure hiérarchique entre les différents facteurs de stress considérés à différentes échelles spatiales : bassin versant, riverain en amont, riverain local et occupation du sol locale ainsi que l'hydromorphologie et la qualité de l'eau .L'analyse n'a confirmé que partiellement le modèle conceptuel : l' intégrité biotique et la qualité de l'eau étaient fortement liées aux facteurs de stress à grande échelle comme prévu (effet total absolu de 0,345 à 0,541), mais contre les attentes, la rétention de sédiments fins, considérée comme dépendant de l'échelle dans le modèle conceptuel, a été mal expliquée par les facteurs de stress à grande échelle (effet total absolu 0,027-0,231). Alors que la plupart des fonctions considérées comme indépendantes de l'utilisation des terres à grande échelle s'expliquaient en partie par l'occupation des sols riveraine (effet total absolu 0,023–0,091), elles étaient néanmoins également affectées par l'occupation des sols du bassin versant (effet total absolu 0,017–0,390).Alors que de nombreuses études de cas empiriques à des échelles spatiales plus petites documentent clairement les effets positifs de la restauration de la végétation riveraine ligneuse, nos résultats suggèrent que la plupart des effets de la couverture d'utilisation des terres riveraines sont peut-être superposés par des facteurs de stress à plus grande échelle. Cela n'annule pas les effets localisés de la végétation riveraine ligneuse, mais aide à contextualiser les limites des mesures de restauration réussies ciblant la communauté de macroinvertébrés.

International audience; Pesticides are priority concerns in aquatic risk assessment due to their widespread use, ongoing development of new molecules, and potential effects from short- and long-term exposures to aquatic life. Water quality assessments are also challenged by contrasting pesticide behaviors (e.g., mobility, half-life time, solubility) in different environmental contexts. Furthermore, monitoring networks are not well adapted to the pesticide media transfer dynamics and therefore fail at providing a reliable assessment of pesticides. We present here a Bayesian belief network that was developed in a cooperative process between researchers specializing in Bayesian modelling, soil sciences, agronomy, and diffuse pollutants to provide a tool for stakeholders to assess surface water contamination by pesticides. It integrates knowledge on dominant transfer pathways according to basin physical context and climate for different pesticides properties, such as half-life duration and affinity to organic C, to develop an assessment of risks of contamination for every watershed in France. The resulting model, ARPEGES (Analyse de Risque PEsticide pour la Gestion des Eaux de Surface; trans. Risk analysis of contamination by pesticides for surface water management), was developed in R. A user-friendly R interface was built to enable stakeholders to not only obtain ARPEGES' results, but also freely use it to test management scenarios. Though it is applicable to any chemical, its results are illustrated for S-Metolachlor, a pesticide that was widely used on cereals crops worldwide. In addition to providing contamination potential, ARPEGES also provides a way to diagnose its main explaining factors, enabling stakeholders to focus efforts in the most potentially affected basins, but also on the most probable cause of contamination. In this context, the Bayesian belief network allowed us to use information at different scales (i.e., regional contexts for climate, pedology at the basin scale, pesticide use at the municipality scale) to provide an expert assessment of the processes driving pesticide contamination of streams and the associated uncertainties. Integr Environ Assess Manag 2020;00:1-14. (c) 2020 SETAC

Defining mathematical terms and objects is a constant issue in ecology; often definitions are absent, erroneous, or imprecise. Through a bibliographic prospection, we show that this problem appears in macro‐ecology (biogeography and community ecology) where the lack of definition for the sigmoid class of functions results in difficulties of interpretation and communication. In order to solve this problem and to help harmonize papers that use sigmoid functions in ecology, herein we propose a comprehensive definition of these mathematical objects. In addition, to facilitate their use, we classified the functions often used in the ecological literature, specifying the constraints on the parameters for the function to be defined and the curve shape to be sigmoidal. Finally, we interpreted the different properties of the functions induced by the definition through ecological hypotheses in order to support and explain the interest of such functions in ecology and more precisely in biogeography., The sigmoid class of functions is a mathematical entity commonly used in ecology but yet poorly defined. We propose a definition of this mathematical object as well as a list of functions commonly used in ecology belonging to this class. We finally discuss properties of sigmoid functions from the point of view of the underlying ecological hypotheses.

International audience; Active biomonitoring permits the quantification of biological exposure to chemicals through measurements of bioavailable concentrations in biota and biological markers of toxicity in organisms. It enables respective comparison of the levels of contamination between sites and sampling campaigns. Caged gammarids are recently proposed as relevant probes for measuring bioavailable contamination in freshwater systems. The purpose of the present study was to develop a multi-pressure and multiscale approach, considering metallic contamination levels (from data based on active biomonitoring) as a response to pressures (combination of individual stressors). These pressures were anthropogenic land cover, industry density, wastewater treatment plant density, pressures on stream hydromorphological functioning, riverside vegetation and bioavailability factors. A dataset combining active biomonitoring and potentially related pressures was established at the French national scale, with 196 samplings from 2009 to 2016. The links between pressures and metallic contamination were defined and modelled via structural equation modeling (more specifically partial least squares - path modeling). The model enabled the understanding of the respective influences of pressures on metallic bioconcentration in caged sentinel organisms. Beyond validating the local influence of industries and wastewater treatment plants on metallic contamination, this model showed a complementary effect of driving forces of anthropogenic land cover (leading to human activities). It also quantified a significant influence of pressures on stream hydromorphological functioning, presence of vegetation and physico-chemical parameters on metal bioconcentration. This hierarchical multi-pressure approach could serve as a concept on how pressures and contamination (assessed by active biomonitoring) can be connected. Its future application will enable better understanding of environmental pressures leading to contamination in freshwater ecosystems.

International audience; Hierarchical models are used to study the relationship between a response variable and a predictor in structured data. Random effects are meant to capture the structured part of variability among groups of observations. In ecology, random effects are usually incorporated into the intercept. Their application to the other parameters of the curve, especially in nonlinear curves, has been understudied. However, applying random effects to different parameters of the function is of interest, as it allows us to account for variations in the shape of the relationship over groups of observations. Our study was based on Bayesian models linking the local quantity of deadwood to the local species richness of saproxylic beetles in French forests. Our hypothesis was that it was important to account for inter-forest variations of the relationship to better fit the data. Since a sigmoidal curve seemed adapted to studying this relationship from an ecological point of view, we paid special attention to commonly used sigmoidal functions, but also included two new ones for biogeography originating from ecophysiology (one sigmoid with estimated asymptotes and one with estimated asymptotes allowing asymmetry). We applied various settings of random effects to these different mean functions. We compared, evaluated and interpreted the models and results according to several criteria (WAIC, comparison of significance of the difference in terms of LOOic, goodness-of-fit p-values and magnitude of the effect). We first found that models without random effects were systematically the worst and that the best model was not necessarily the one with random effect incorporated into the intercept, as is usually done in ecology. Secondly, we found that, in most cases, for a given mean function, the best model had several random effects, and the model with the most random effects performed nearly as well as the best models. Furthermore, the inclusion of random effects revealed statistically significant relationships between deadwood volume and species richness. Thirdly, we revealed a complementarity between the different assessment criteria, each one giving important information for the selection and interpretation of the models. In conclusion, future forest biodiversity management studies should incorporate random effects into the modeling framework so that more robust conclusions can be made about the relationships, based on complementary post-fitting analysis criteria

International audience; Aquatic ecosystems are exposed to multiple environmental pressures including chemical contamination. Polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs) known as preoccupying substances for the environment. Active biomonitoring (ABM) is a surveillance method for polluted aquatic ecosystems measuring bioavailable contamination. In this work, the aim was to quantify the total links between environmental pressures and bioavailable contamination (for PAHs and PCBs) at the French national scale. Based on 245 sites experimented by ABM from 2017 to 2019, environmental pressures (anthropogenic pressures and environmental parameters) were defined (point source landfill density, point source urban density, point source industry density, point source road density, nonpoint source industry density, nonpoint source road density, nonpoint source urban density, nutrients and organic matter, slope, dams, straightness, coarse sediment, summer precipitation, hydrographic network density and watershed size) and characterized by one or a combination of measures called stressor indicators. The links between environmental pressures and bioavailable POPs contamination (ABM measure) at a large spatial scale were defined and quantified via structural equation modeling. Point source urban density, nutrients and organic matter, summer precipitation, straightness and point source industry density are correlated positively with PAH bioavailable contamination. In contrast, nonpoint source urban density, nonpoint source industry density, nonpoint source road density and watershed size are positively correlated with PCB bioavailable contamination. The dominant pressures linked to PAHs and PCBs were different, respectively local and large-scale pressures were linked to PAH bioavailable contamination, and only large-scale pressures were linked to PCB bioavailable contamination.

International audience; Many freshwater ecological studies focused on the effects of environmental stressors induced by anthropogenic activities such as land use or alteration of hydromorphology and physico-chemistry conditions. While it is recognized as a potential major driver of ecological alteration, ecotoxicological stress is yet rarely explicitly considered. By combining ecological monitoring and field ecotoxicological approaches, the purpose of this research is to focus on the origin and levels of bioavailable contamination as well as toxicity in freshwater ecosystems taking into account various stream typologies and unraveling the relative impacts of other stressors on these two variables. Datasets of active biomonitoring at the French national scale were established, with 333 sites being investigated from 2009 to 2018. Bioavailable contamination (metallic and persistent organic substances) in freshwater ecosystems was assessed by bioaccumulation measurement in caged Gammarids. Stream toxicity was based on mortality and feeding activity of exposed organisms. For each site, integrated indicators of contamination and toxicity were computed with weighting chemical and biological measurements by national reference values. The link between environmental stressors and ecotoxicological indicators was modeled via Structural Equation Modeling. The model was adjusted according to the source of pollution and is reliable with the consideration of multi-scale and multi-stressor concepts. It enables to understand the role of driving forces (land use, hydromorphology, etc.) and their impact on the two outputs (contamination and toxicity). Its application improves the understanding of contamination and toxicity levels. It can also provide a prediction of risks of contamination and/or toxicity in aquatic environments.

National audience; Nous présentons le cas d'un modèle non-linéaire hiérarchique ayant posé des problèmes d'estimation. Une étude des raisons de ces problèmes d'estimation et une reparamétrisation du modèle passant par les distributions a priori (incorporation de dépendances entre paramètres) améliore grandement l'estimation (voire résout les problèmes).

International audience; Most anthropogenic stressors affecting freshwater systems are qualitatively known. However, the quantitative assessment of contaminant exposure and effects to aquatic communities is still difficult, limiting the understanding of consequences on aquatic ecosystem functioning and the implementation of effective management plans. Here, multisubstance indicators based on caged gammarid bioaccumulated contamination data are proposed (for metals and persistent organic pollutants, POPs) to map the bioavailable contamination level of freshwater ecosystems at a large spatial scale. We assessed the ability of these indicators to highlight the relationships between chemical exposure gradients and alteration in the abundance of macroinvertebrate populations on a data set of 218 watercourses distributed throughout France. We identified spatial regional heterogeneities in the levels of bioavailable contamination of metals (18 compounds) and POPs (43 compounds). Besides this, a degradation of Gammaridae, Ephemeridae, and Hydrobiidae densities with increasing levels of metal contamination are identified relative to Baetidae, Chironomidae, and Hydropsychidae. We show here that active biomonitoring allows the establishment of multisubstance indicators of bioavailable contamination, which reliably quantify chemical exposure gradients in freshwater ecosystems. Our ability to identify species-specific responses to chemical exposure gradients demonstrates the promising possibility to further decipher the effects of chemical contamination on macroinvertebrate assemblages through this type of indicator.

International audience; We investigated the relationships between the ecological status of wadeable rivers and the intensity of various stressors related with hydromorphological alterations, nutrient and organic matter contaminations. The French invertebrate-based multimetric index (I2M2), which efficiently responds to the effects of both physical and chemical and hydromorphological stressors, was used as descriptor of river reach ecological status. We developed a model focusing on the effects of hydromorphological and physical and chemical stressor gradients on the I2M2 in different physiographic contexts. The potential confounding effects of natural geographic conditions and watershed scale pressure gradients were taken into account and neutralized by gathering watersheds into homogeneous clusters integrated as an interaction factor in the model. Whatever effects were considered (general or within-spatial clusters), the I2M2 was impaired similarly by the same stressor types, being negatively influenced by an increase in BOD5, ammonium, nitrite, nitrate and total phosphorus concentrations. The I2M2 was also negatively influenced by variables describing hydromorphology at the reach scale, especially by the 'loss of sinuosity', 'increasing rates of bank erosion', 'flow reductions' and 'alteration of pool/riffle succession'. The I2M2 was generally more strongly impaired by physical and chemical pressures than by hydromorphological alterations.

International audience; The purpose of our approach was to take into account the nested spatial scales driving stream functioning in the description of pressures/ecological status links by analysing the results of a hierarchical model. The development of this model has allowed us to answer the following questions: Does the consideration of the indirect links between anthropogenic pressures and stream ecological status modify the hierarchy of pressure types impacting benthic invertebrates? Do the different nested scales play different roles in the anthropogenic pressures/ecological status relationship? Does this model lead to better understanding of the specific role of hydromorphology in the evaluation of stream ecological status? To achieve that goal, we used the Partial Least Square (PLS) path modelling method to develop a structural model linking variables describing (i) land use and hydromorphological alterations at the watershed scale, (ii) hydromorphological alterations at the reach scale, (iii) nutrients-organic matter contamination levels at the site scale, and (iv) substrate characteristics at the sampling site scale, to explain variation in values of a macroinvertebrate-based multimetric index: the French I2M2. We have highlighted the importance of land use effects exerted on both hydromorphological and chemical characteristics of streams observed at finer scales and their subsequent indirect impact on stream ecological status. Hydromorphological alterations have an effect on the substrate mosaic structure and on the concentrations of nutrients and organic matter at site scale. This result implies that stream hydromorphology can have a major indirect effect on macroinvertebrate assemblages and that the hierarchy of impacts of anthropogenic pressures on stream ecological status generally described in the literature - often determining strategic restoration priorities - has to be re-examined. Finally, the effects of nutrients and organic matter on macroinvertebrate assemblages are lower than expected when all the indirect effects of land use and hydromorphological alterations are taken into account.

Ce rapport présente les résultats d'un travail de programmation informatique réalisé en 2017, visant à retranscrire le modèle ARPEGES (Analyse du Risque PEsticides pour la Gestion des Eaux de Surface), initialement développé sur le logiciel propriétaire Netica, dans un format libre de droit, afin de faciliter sa diffusion et son utilisation par les utilisateurs finaux, et de fournir une interface permettant l'utilisation du modèle dans un but de simulation sans devoir écrire des commandes en ligne de code. La plateforme retenue est le logiciel de statistiques R, libre de droit. Ce rapport reprend très brièvement les éléments descriptifs de la démarche ARPEGES, présente rapidement les données d'entrée, puis présente la structure et guide l'utilisateur dans la prise en main de l'interface et de son utilisation dans un but de simulation. La dernière partie de ce rapport est un guide d'installation de l'interface sous R. L'interface est disponible sous forme d'un fichier .zip nommé « Install_Arpeges » auprès de l'Agence Française de la Biodiversité. Les produit finaux des simulations sont des tableaux de résultats, exploitables dans des logiciels de type tableur et permettant le lien vers de nmbreux logiciels statistiques, ainsi que des couches de données de type shape, permettant la cartographie des résultats, à l'échelle des bassins versants des masses d'eau des cours d'eau métropolitains. L'interface est également dotée d'un éditeur de cartes. En complément de ce travail «de programmation », un travail thématique visant à aider les Agences de l'Eau à prendre en main du modèle et à interpréter les résultats a été réalisé en déroulant le modèle sur 15 substances actives prioritaires au regard de la DCE et rapporté dans un guide d'aide à l'interprétation (Adoir et al, 2017).

International audience; In the field of macroecology, climate- and productivity-related factors are frequently identified as the strongest correlates of species-diversity patterns. These variables describe the action of climate on species, either directly by influencing physiological processes, or indirectly by controlling resource productivity or biomass. Being among the most vulnerable ecosystems to climate change, streams and rivers can experience both types of climate-induced effects and their consequences on communities. Here, we gather recent insights from multi-decadal studies investigating long-term responses of invertebrate communities to climatic and trophic changes in France. On the one hand, stream communities have been directly influenced by long-term hydroclimatic changes with a gradual increase in taxa exhibiting resistance and resilience strategies (e.g, small-sized organisms) at the expense of climate-sensitive taxa (e.g, typical from fast-running, cold waters). This general trend followed a latitudinal gradient supporting the predicted northwards colonisation/migration by Mediterranean species. On the other hand, additional long-term variations in invertebrate communities have been induced by trophic resource changes, either corresponding to a climate-induced trophic amplification, especially in headwaters, or related to water quality improvement. In both cases, trophic processes have promoted specialists of different resource types following either a productivity enhancement or a primary production transfer. As a result, these climatic and trophic changes have concomitantly contributed to the overall long-term increase in functional diversity of invertebrate communities throughout France. Nonetheless, beyond these present trends, invertebrate communities are threaten by the expected future warming due to distribution range contractions of the remaining sensitive taxa and/or competitive exclusions by the colonising tolerant taxa. These insights illustrate whether combining long-term and trait-based approaches can help to disentangle direct, indirect and confounding merged effects of environmental drivers on biological communities, with functional relevance for understanding and predicting community dynamics over broad spatial scales.

International audience; La gestion et la protection efficaces des populations d’animaux sauvages reposent sur une bonne compréhension de leurs cycles biologiques. Parce que la dynamique des populations dépend des interactions complexes de processus biologiques et écologiques à différentes échelles, de nouvelles approches sont nécessaires pour expliquer la variabilité des processus démographiques et des paramètres associés dans une hiérarchie d’échelles spatiales. Un modèle bayésien hiérarchique du cycle biologique des truites fario (Salmo trutta) résidentes a été élaboré pour évaluer l’influence relative de déterminants locaux et généraux de la mortalité. Le modèle a été calé sur un vaste ensemble de données provenant de 40 tronçons de rivière, qui combine des données d’abondance et de conditions du milieu (hydraulique, température de l’eau). La mortalité des juvéniles dépendante de la densité augmente à faibles températures et diminue quand la disponibilité d’abris augmente. Des températures de l’eau élevées accroissent la mortalité densité-dépendante chez les adultes. Le modèle pourrait aider à prédire la mortalité mensuelle des juvéniles et des adultes dans des scénarios de réchauffement climatique et de modifications de la disponibilité d’abris découlant de la dégradation ou de la restauration d’habit

International audience

International audience; Floodplain landscapes are highly fragmented by river regulation resulting in habitat degradation and flood regime perturbation, posing risks to population persistence. Climate change is expected to pose supplementary risks in this context of fragmented landscapes, and especially for river systems adaptation management programs are developed. The association of habitat quality and quantity with the landscape dynamics and resilience to human-induced disturbances is still poorly understood in the context of species survival and colonization processes, but essential to prioritize conservation and restoration actions. We present a modelling approach that elucidates network connectivity and landscape dynamics in spatial and temporal context to identify vital corridors and conservation priorities in the Loire river and its tributaries. Alteration of flooding and flow regimes is believed to be critical to population dynamics in river ecosystems. Still, little is known of critical levels of alteration both spatially and temporally. We applied metapopulation modelling approaches for a dispersal-limited tree species, white elm; and a recruitment-limited tree species, black poplar. In different model steps the connectivity and natural dynamics of the river landscape are confronted with physical alterations (dams/dykes) to species survival and then future scenarios for climatic changes and potential adaptation measures are entered in the model and translated in population persistence over the river basin. For the two tree species we highlighted crucial network zones in relation to habitat quality and connectivity. Where the human impact model already shows currently restricted metapopulation development, climate change is projected to aggravate this persistence perspective substantially. For both species a significant drawback to the basin population is observed, with 1/3 for elm and ¼ for poplar after 25 years already. But proposed adaptation measures prove effective to even bring metapopulation strength and persistence up to a level above the current level.

International audience; Taking the nested scales of stream functioning into account in analysing the links between pressures and ecological status calls for the development of hierarchical models on the monitoring datasets. We aimed at answering the following questions: Does the indirect links between pressures and ecological status modify the classically observed impact hierarchy of pressures? Do the different nested scales play a different role in the pressures-ecological status relationship? Do hydromorphological alterations play a specific role in ecological status evaluation? To achieve that goal, we used the PLS path modelling method to develop a structural model linking latent variables built on (i) land use, and hydromorphological pressures descriptors at watershed scale, (ii) hydromorphological alterations assessed at reach scale, (ii) nutrients-organic matter contamination levels, and (iv) substrate samples to explain the score variation in the French monitoring macroinvertebrate based indicator I2M2. This method allows one to express the total effect of a variable as the sum of its direct and indirect effects. As a first important result, we have highlighted the importance of land use effect exerted on both hydromorphology and physico-chemistry and their translation as an indirect effect on biological condition of streams. We have also demonstrated that hydromorphological alterations had an effect on substrates structure and nutrients and organic matter concentrations. This study also reveals that hydromorphology has a major effect on macroinvertebrates indicator, thus indirect. Comparatively, nutrients and organic matter total effect on macroinvertebrates communities appears lower than expected since we take into account all the indirect effects of land use and hydromorphological alterations.

La mise en œuvre de la directive cadre sur l’eau impose la realisation d’un etat des lieux des milieux aquatiques en 2013. En l’absence de methode harmonisee sur le niveau national, et a fortiori sur le plan europeen, la methode Arpeges (pour : analyse de risque pesticides pour la gestion des eaux de surface) a ete developpee dans ce contexte pour evaluer le risque de contamination globale par les pesticides des masses d’eau de surface de France metropolitaine. Cette methode repose sur le croisement de la vulnerabilite du milieu aux differents types de transferts hydriques et de la pression phytosanitaire. La vulnerabilite est estimee a partir de parametres lies au milieu physique et a son utilisation (notamment les sols, le climat et les zones tampons) et la pression phytosanitaire est caracterisee par les proprietes et les quantites de substances appliquees. Le croisement est realise grâce a un reseau bayesien construit par dire d’experts, qui permet d’organiser et de formaliser les connaissances sur les processus dominants en integrant les incertitudes, liees notamment a la disponibilite des donnees.

International audience; Ecological status is a summary measurement of the modification of river communities due to interactions between the natural context of the river (geology, climate) and the impacts of anthropogenic pressures that can be either inherited or on-going. Reaching the WFD goals means being able to find an acceptable trade-off between the human benefits from water and giving rivers a sufficient ability to function. Thus, pressures-impacts studies are still developed to understand how human activities (at different scales) impact and alter different inter-connected compartments of the river functioning (hydromorphological, physico-chemical, ecological). Moreover, climate change is predicted to have major impacts on both hydrological and thermic regimes that have deep influence on river ecology. It is therefore necessary to develop methodologies that introduce these new uncertainties in pressures-impacts relations to ensure sufficient adaptation/resilience.

1. Assuming that recruitment variation is one of the main sources of fish population and assemblage changes, it is necessary to understand how natural variations in the environment influence 0+ fish abundance. Temperature regimes play an important role in enhancing both spawning activity and survival during early larval fish development. Flow regime variation, which is a powerful source of stream disturbance, is another factor to be taken into account. 2. Responses to these variables need to be assessed using long-term datasets, since standard statistical approaches fail to provide a causal structure or to quantify the different effects. We therefore used a 26-year dataset to evaluate the respective effects of seven derived independent variables describing the effects of temperature and flow regimes on the 0+ juvenile abundance of eight fish species in the River Rhone. 3. A clustering procedure using the Kendall tau rank correlation coefficient was implemented and identified three groups of fish according to their synchronic variations in juvenile abundance; i.e. varying with decreasing juvenile abundance, slightly increasing juvenile abundance and increasing juvenile abundance. These clusters provided the basis for building hierarchical log-Poisson generalized linear models. The Bayesian paradigm gives a reliable framework for model selection, and the best model was determined using the Bayes Factor. 4. The posterior distribution of the regression parameters was coherent with what was expected based on knowledge of the biology of the different species. It indicates that temperature regime drives 0+ juvenile abundance but that flow regime also plays an important regulating role. The models thus detected evidence of the consequences of specific flow events such as larval drift and an increase in available habitat during higher flow discharges. 5. Our study illustrates the advantages of using a hierarchical modelling approach to quantify ecological effects by improving discrimination between the different sources of uncertainty, leading to better precision when estimating regression parameters.

National audience; Le changement climatique s’est traduit par une rapide évolution des régimes thermiques, mais aussi hydrologiques ces dernières décennies. Il est important de comprendre comment ces changements influencent le fonctionnement des écosystèmes aquatiques. Un modèle hiérarchique est développé pour analyser la réponse de l’assemblage de juvéniles de cyprinidés du Haut-Rhône aux évolutions de ces deux régimes depuis 1980. Un facteur latent est introduit pour représenter les sources communes de variations tant des données environnementales que biologiques : il est conjointement une combinaison linéaire des variables de l’environnement enregistrant leurs variations, et une variable explicative d’une régression logistique dans un modèle multinomial expliquant les variations de proportions relatives des espèces de poissons échantillonnées. L’inférence est réalisée sous le paradigme bayésien à l’aide de méthodes MCMC.

International audience; Rivers are complex systems for which it is hard to make reliable assessments of causes and responses to impairments. We present a holistic risk-based framework for river ecosystem assessment integrating all potential intervening processes and functions. Risk approaches allow us to deal with uncertainty both in the construction of indicators for magnitude of stressors and in the inference of environmental processes and their impairment. Yet, here we go further than simply replacing uncertainty by a risk factor. We introduce a more accurate and rigorous notion of risk with a transcription of uncertainty in causal relationships in probability distributions for the magnitude of impairment and the weight of different descriptors, with an associated confidence in the diagnostic. We discuss how Bayesian belief networks and Bayesian hierarchical inference allow us to deal with this risk concept to predict impairments and potential recovery of river ecosystems. We developed a comprehensive approach for river ecosystem assessment, which offers an appealing tool to facilitate diagnosis of the likely causes of impairment and predict future conditions. The ability of the risk approaches to integrate multi-scale quantitative and qualitative descriptors in the identification of multiple stressor sources and pathways in the stream network, and their impairment of specific processes and structures is illustrated for the national-level risk analysis for hydromorphology and pesticide pollution. Not only does the risk-based framework provide a more complete picture of environmental impairments, but it also offers a comprehensive, user-friendly tool to instruct the decision process.

[Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASARE; We estimated the spatial distribution of 6 Mustelidae species in France using the data collected by the French national hunting and wildlife agency under the "small carnivorous species logbooks" program. The 1500 national wildlife protection officers working for this agency spend 80% of their working time traveling in the spatial area in which they have authority. During their travels, they occasionally detect dead or living small and medium size carnivorous animals. Between 2002 and 2005, each car operated by this agency was equipped with a logbook in which officers recorded information about the detected animals (species, location, dead or alive, date). Thus, more than 30000 dead or living animals were detected during the study period. Because a large number of detected animals in a region could have been the result of a high sampling pressure there, we modeled the number of detected animals as a function of the sampling effort to allow for unbiased estimation of the species density. For dead animals -- mostly roadkill -- we supposed that the effort in a given region was proportional to the distance traveled by the officers. For living animals, we had no way to measure the sampling effort. We demonstrated that it was possible to use the whole dataset (dead and living animals) to estimate the following: (i) the relative density -- i.e., the density multiplied by an unknown constant -- of each species of interest across the different French agricultural regions, (ii) the sampling effort for living animals for each region, and (iii) the relative detection probability for various species of interest.

Connectivity may be structural , based on adjacency of landscape features, or functional , based on how that adjacency translates to movement of organisms. We present a modelling approach that elucidates both aspects of connectivity to identify vital corridors and conservation priorities in a river network. For the dendritic network structure of river systems, at first a graph theoretic structure is developed to model the river network at the segment scale. To derive functional connectivity, a Bayesian hierarchical modelling of species dispersal is applied to infer the influence of riparian corridor characteristics to the species colonization. The integration of the functional and structural component is realized with a graph-theoretic connectivity measure. With this approach, the European otter colonization of the Loire river basin over 25 years is modelled on the basis of large datasets on riparian corridor land use and hydromorphological characteristics of a 17,000 km river network. Channel straightening and riparian forest fragmentation are determined to be key elements to the functional connectivity. Road infrastructure is distinguished as a critical habitat factor, but not so much an obstacle for the species movement in the riparian corridor. Integration of the Bayesian model posterior colonization probability in the integrated connectivity analysis reveals the importance of the river network density to the otter colonization and locates conservation priorities mainly in the lower parts of the river basin. Synthesis and applications Both functional and structural connectivity are essential elements in the contexts of ecological network identification for species conservation and recovery. We successfully developed an integrated modelling of both components of connectivity that highlighted the importance of the downstream basin for a well-connected ecological network for the otter.

Global change calls for an understanding of how temperature and flow regimes influence aquatic ecosystems. Fish assemblages are a major component of river ecosystems and are thought to exhibit more integrative informative responses than single species to environmental variations, whether rare and sudden or gradual and continuous. The use of long-term datasets is thus of primary importance, allied to statistical modeling. For each of three previously identified species clusters, we performed Bayesian variable selection and inference within a hierarchical log Poisson Generalized Linear Model using a spike and slab normal prior to pinpoint which subset of environmental variables is of importance for each fish assemblage. Fish counts from electrofishing experiments are known to provide overdispersed data and, not surprisingly, the contribution of recorded environmental effects is found to be weak compared with those of other intra-assemblage sources of variation. The posterior distribution of the regression parameters is in coherence with what was expected from biological knowledge of the three species clusters. In particular, thermophilic species tend to benefit from warmer waters, whereas the recruitment of cold water species decreases due to global warming effects. Our study provides an example of the advantages of hierarchical modeling for quantifying interspecies ecological effects and selecting common environmental variables of importance.

Existing methods for connectivity analysis still encounter difficulties in explaining functional relationships between network structure and ecological patterns over larger territories or complex structures like dendritic river networks. We propose a method that addresses the problem of scale and resolution in the connectivity analysis of dendritic network structures, illustrated here for the re-colonization of the French Loire river basin by the European otter. The ecological niche factor approach is applied to infer favourable habitat in the river network based on large scale data of land use and hydro-morphology of river segments for the entire river basin. These analyses identified the stressors to the riparian zone of channel straightening, urbanisation and forest fragmentation as the principal factors explaining otter occurrence. Using this estimate of habitat favourability, we used the Integral Index of Connectivity to quantify habitat availability and connectivity in the dendritic river network. When we calculate the integral index of connectivity over different spatial extents by constraining network distances, the scale-sensitivity of the network’s connectivity emerges. Accounting for high mobility by entering larger network distances in the analysis identifies conservation networks and priorities mainly in downstream parts of the river basin, whereas with smaller network distances, more restricted high quality areas in central and upstream parts are highlighted. The presented approach performed better than distribution modelling approaches in explaining species occurrence over the river network and confirms the crucial aspect of connectivity in otter re-colonization.

The well-documented re-colonisation of the French large river basins of Loire and Rhone by European otter and beaver allowed the analysis of explanatory factors and threats to species movement in the river corridor. To what extent anthropogenic disturbance of the riparian zone influences the corridor functioning is a central question in the understanding of ecological networks and the definition of restoration goals for river networks. The generalist or specialist nature of target species might be determining for the responses to habitat quality and barriers in the riparian corridor. Detailed datasets of land use, human stressors and hydro-morphological characteristics of river segments for the entire river basins allowed identifying the habitat requirements of the two species for the riparian zone. The identified critical factors were entered in a network analysis based on the ecological niche factor approach. Significant responses to riparian corridor quality for forest cover, alterations of channel straightening and urbanisation and infrastructure in the riparian zone are observed for both species, so they may well serve as indicators for corridor functioning. The hypothesis for generalists being less sensitive to human disturbance was withdrawn, since the otter as generalist species responded strongest to hydro-morphological alterations and human presence in general. The beaver responded the strongest to the physical environment as expected for this specialist species. The difference in responses for generalist and specialist species is clearly present and the two species have a strong complementary indicator value. The interpretation of the network analysis outcomes stresses the need for an estimation of ecological requirements of more species in the evaluation of riparian corridor functioning and in conservation planning.

Understanding how fis assemblages vary is a major goal of ecology and bioindication. In this PhD thesis, advanced statistical tools were used to identify which descriptors of temperature and flow regimes, that are among the most essential components of fish natural environment, do generate interannual variations of juvenile assemblages of cyprinid fish in the upper River Rhone. By using datasets of water temperature, flow and electric fishing samples over the 1980-2005 period, three groups of species have been determined based on their synchrone response to environmental variations and have been used to develop to types of Bayesian hierarchical models : - a Poisson regression, for which a selection of variable was performed, using the Bayes Factor criterion. this first model allowed for the quantification of the effects of the selected variables on the interannual variations of the different species abundance. - a model with shared latent variable, assuming the existence of a common source of variation for the environmental and the biological data, the Hypersignal. This model underlined the relative importance of the environemental variables in determining the assemblages structure. While their effects are generally treated separately, the joint effect of the temperature and flow regimes on the structure and the interannual variations of juveniles fish assemblages was put forward here., La compréhension des déterminismes des communautés de poissons et de leurs variations est un enjeu majeur, tant en écologie qu'en bioindication. Dans ce travail doctoral, nous avons mis en place des outils de statistiques avancées afin d'identifier les aspects des régimes thermique et hydrique, constituants essentiels de l'environnement naturel des poissons, responsables des variations des assemblages de juvéniles de cyprinidés du haut Rhône. En utilisant des chroniques de températures de l'eau, de débits et d'échantillonnages par pêche électrique sur la période 1980-2005, nous avons déterminé trois groupes d'espèces présentant des réponses synchrones aux variations d'environnement, et développé deux types de modèles hiérarchique, s'appuyant sur ces groupes, selon une perspective bayésienne :- un modèle de régression poissonienne, pour lequel nous avons utilisé une procédure de choix de modèle fondée sur le critère du Facteur de Bayes. Ce premier modèle nous a permis de sélectionner les variables d'intérêt et de quantifier leurs effets sur les variations interannuelles d'abondances des différentes espèces. - un modèle à facteur latent partagé, résumant l'influence commune d'une variable latente, l'hypersignal, sur les variations de l'environnement et des proportions relatives des groupes d'espèces. Nous avons ainsi souligné les importances relatives des variables environnementales dans la structuration des communautés. Alors que leurs effets sont généralement discutés séparément, nous avons mis en évidence l'influence conjointe des régimes thermique et hydrique sur la structuration et les variations interannuelles des assemblages de juvéniles de poissons en grandes rivières.

International audience; In a context of increasing landscape modifications and climatic changes, scale hierarchy becomes an ever more crucial issue to integrate in the analysis of drivers and stressors of biological communities, especially in river networks. To cope with this issue, we developed (i) spatial hierarchical models of functional diversity of stream invertebrate communities to assess the relative influence of local- vs. regional-scale factors in structuring community assembly, and (ii) analysis of metacommunity elements to determine the ecological processes behind the structuring. The spatial structuring of benthic invertebrate communities was investigated over 568 sites in South-eastern France. Community structure was mainly driven by the altitudinal gradient and spring flow variation at broad scales, with functional diversity gradually decreasing with elevation and being maximized at intermediate levels of flow variability. According to the ‘elements of metacommunity structure’ analysis, the prevailing influence of the altitudinal gradient was also supported by a Clementsian structuration of invertebrate communities. Conversely, the influence of observed climatic changes in temperature and rainfall was weak and observed only at fine scales. As a result, natural environmental filters were stronger drivers of the functional diversity of communities than human-induced stressors (e.g. water pollution and hydromorphological alterations). More broadly, our results suggest that management needs to embrace the possibilities of gathering high spatial and taxonomical resolution data when analysing and predicting flow variation and climate change effects in order to preserve and restore functionally diverse communities. Moreover, to develop environmental flow schemes or restoration and climate change adaptation strategies for freshwater communities, local and regional processes need to be addressed simultaneously; equally responsible as drivers of community diversity.

International audience; The purpose of our approach was to take account of the nested scales of stream functioning on the links between pressures and ecological status by building and analysing a hierarchical model. The development of this model aimed at answering the following questions: Does the indirect links between pressures and ecological status modify the impact hierarchy of pressures? Do the different nested scales play a different role in the pressures-ecological status relationship? To achieve that goal, we used the PLS path modelling method for developing a structural model linking the latent variables of (i) land use, and hydromorphological alterations at watershed scale, (ii) hydromorphological alterations at reach scale, (ii) nutrients-organic matter contamination levels, and (iv) substrate samples to explain macroinvertebrate based index I2M2 score variation. As a first important result, we have highlighted the importance of land use effect exerted on both hydromorphology and physico-chemistry and their translation as an indirect effect on biological condition of streams. We have also demonstrated that hydromorphological alterations had an effect on substrates structure and nutrients and organic matter concentrations. This result implies that hydromorphology has a major indirect effect on macroinvertebrates.

Understanding how fis assemblages vary is a major goal of ecology and bioindication. In this PhD thesis, advanced statistical tools were used to identify which descriptors of temperature and flow regimes, that are among the most essential components of fish natural environment, do generate interannual variations of juvenile assemblages of cyprinid fish in the upper River Rhone. By using datasets of water temperature, flow and electric fishing samples over the 1980-2005 period, three groups of species have been determined based on their synchrone response to environmental variations and have been used to develop to types of Bayesian hierarchical models : - a Poisson regression, for which a selection of variable was performed, using the Bayes Factor criterion. this first model allowed for the quantification of the effects of the selected variables on the interannual variations of the different species abundance. - a model with shared latent variable, assuming the existence of a common source of variation for the environmental and the biological data, the Hypersignal. This model underlined the relative importance of the environemental variables in determining the assemblages structure. While their effects are generally treated separately, the joint effect of the temperature and flow regimes on the structure and the interannual variations of juveniles fish assemblages was put forward here.; La compréhension des déterminismes des communautés de poissons et de leurs variations est un enjeu majeur, tant en écologie qu'en bioindication. Dans ce travail doctoral, nous avons mis en place des outils de statistiques avancées afin d'identifier les aspects des régimes thermique et hydrique, constituants essentiels de l'environnement naturel des poissons, responsables des variations des assemblages de juvéniles de cyprinidés du haut Rhône. En utilisant des chroniques de températures de l'eau, de débits et d'échantillonnages par pêche électrique sur la période 1980-2005, nous avons déterminé trois groupes d'espèces présentant des réponses synchrones aux variations d'environnement, et développé deux types de modèles hiérarchique, s'appuyant sur ces groupes, selon une perspective bayésienne :- un modèle de régression poissonienne, pour lequel nous avons utilisé une procédure de choix de modèle fondée sur le critère du Facteur de Bayes. Ce premier modèle nous a permis de sélectionner les variables d'intérêt et de quantifier leurs effets sur les variations interannuelles d'abondances des différentes espèces. - un modèle à facteur latent partagé, résumant l'influence commune d'une variable latente, l'hypersignal, sur les variations de l'environnement et des proportions relatives des groupes d'espèces. Nous avons ainsi souligné les importances relatives des variables environnementales dans la structuration des communautés. Alors que leurs effets sont généralement discutés séparément, nous avons mis en évidence l'influence conjointe des régimes thermique et hydrique sur la structuration et les variations interannuelles des assemblages de juvéniles de poissons en grandes rivières.