A Bayesian framework to objectively combine metrics when developing stressor specific multimetric indicator

In the context of the European Water Framework Directive (WFD), monitoring programs and related indicators have been developed to assess anthropogenic impacts on various components of aquatic ecosystems. While great precautions are usually taken when selecting and calculating relevant core metrics, little attention is generally paid to the generation of the multimetric indicator, i.e. the combination of the different core metrics. Indeed, most multimetric indicators are generated by simply averaging or summing metrics, without taking into account their sensitivity and their variability. Moreover, few indicators provide a rigorous estimate of the uncertainty of the assessments, while this estimation is essential for managers. In this context, we developed a Bayesian framework to build multimetric indicators aiming at improving those two weaknesses. This framework is based on two phases. First, pressure-impact statistical models are developed to quantify the impact of pressure on various fish metrics. Then the Bayesian theorem is applied to estimate probabilities of being at a certain anthropogenic pressure level from fish observation and pressure-impact models outputs. The Bayesian theorem allows to combine objectively the different core metrics, taking into account their sensitivity and their variability, and to provide rigorous uncertainty quantification, which is especially valuable in the WFD context. The method is applied as illustrative example on transitional French water bodies to demonstrate its relevance, especially in the Water Framework Directive context though the method is generic enough to be applied in various contexts

Synchrony in whitefish stock dynamics: disentangling the effects of local drivers and climate

Synchronic variations in abundance in populations of the same species are common phenomena encountered in various environments, including lakes, and different taxa of freshwater fishes. This phenomenon can be caused by similar environmental conditions across physically separated populations. In the context of the ongoing climate change, it is essential to test this hypothesis, identify the factors driving the synchrony and elucidate the mechanisms, in the attempt to improve fisheries management. This study investigates synchronic variations in European whitefish (Coregonus spp.) populations in five peri-alpine lakes. The hypothesis suggests that shared biotic or abiotic factors contribute to similar trends in whitefish landings. Environmental and seasonal variables impacting the early life stages of the species were analyzed, and the Euclidean distances between the multivariate time series were calculated to identify similarities or dissimilarities in lake environmental parameters. We found that regional winter and spring temperatures were consistent across the lakes, but these factors did not fully account for variations in landings statistics. Wind intensity, water level and zooplankton abundance showed lake-specific patterns that could better explain local conditions and dynamics. Linear models did not reveal a coherent correlation with a common environmental variable across all lakes. However, distinct relationships were found in four of the lakes, with local factors significantly contributing to abundance variations. The spring abundance of Daphnia spp., a primary food source for whitefish larvae, was the main factor correlated with fish landing trends in Lake Geneva and Lake Bourget. Higher availability of Daphnia spp. may decrease intraspecific competition and density-dependent mortality. In Lake Neuchâtel, winter water temperature was negatively correlated with fish abundance proxies, suggesting that warmer winters may compromise reproduction success. Lake Annecy saw an increase in whitefish landings following a substantial reduction in fishing efforts during the late 2000s. A significant negative correlation was found between whitefish landings and fishing efforts. No relationship was found for Lake Aiguebelette, maybe due to a lack of zooplankton data. In conclusion, the observed synchrony in the European whitefish population is likely driven by a combination of interacting environmental and anthropogenic factors rather than a single common variable. Further research and a more detailed dataset are needed to better understand these complex relationships.   Article cover image: Whitefish (Credit: Rémi Masson

Silver eel downstream migration in fragmented rivers: use of a Bayesian model to track movements triggering and duration

Obstacles in rivers are considered to be one of the main threats to diadromous fish. As a result of the recent collapse of the European eel, the European Commission introduced a Regulation, requiring to reduce all sources of anthropogenic mortality, including those caused by passing through hydropower turbines. Improving knowledge about migration triggers and processes is crucial to assess and mitigate the impact of obstacles. In our study, we tracked 97 tagged silver eels in a fragmented river situated in the Western France (the River Dronne). Using the movement ecology framework, and implementing a Bayesian state-space model, we confirmed the influence of river discharge on migration triggering and he distance travelled by fish. We also demonstrated that, in our studied area, there is a small window of opportunity for migration. Moreover, we found that obstacles have a significant impact on distance travelled. Combined with the small window, this suggests that assessment of obstacles impact on downstream migration should not be limited to quantifying mortality at hydroelectric facilities, but should also consider the delay induced by obstacles, and its effects on escapement. The study also suggests that temporary turbines shutdown may mitigate the impacts of hydropower facilities in rivers with migration process similar to those observed here

Marquage-recaptures et évaluation de l’efficacité de rampes à anguille sur des ouvrages littoraux

[Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASAREA mark-recapture protocol have been developed to assess the efficiency of elvers ladders and the influence of environmental factors on this efficiency. This protocol have been applied to two differents ladder: in Pas-du-Bouc on the "canal des Étangs" river and in Saujon on the Seudre river. The results, and more specifically a mark-recapture model, demonstrates that the efficiency of the two ladders is moderate, though a bit superior in Saujon. Regarding environmental factors, tidant range appears to be the hey factor influencing recapture rates in Saujon, while the river flow is determinant in Pas-du-Bouc. Those results may lead to management measures, i.e. maintaining a minimum river flow during the migration season or at least during some periods. Finally, a high predation rates on elvers is suspected on the two sites. First experiments have been carried out that Visible Implant Elastomers may be used as predation tracers to quantify predation rates in the future.Afin d'évaluer l'efficacité de dispositifs de franchissement visant à faciliter la colonisation des eaux continentales sur les jeunes stades d'anguilles, un protocole, basé sur du marquage-recaptures par VIE (Visible Implant Elastomer), a été développé et appliqué sur deux sites: le site du Pas-du-Bouc sur le Canal des Étangs et le site de Saujon sur la Seudre. L'analyse des résultats et plus particulièrement l'ajustement d'un modèle de marquage-recaptures, a permis de quantifier l'efficacité des dispositifs et l'influence de certains paramètres environnementaux. Il en ressort une efficacité modérée des dispositifs, celui de Saujon semblant plus efficace que celui du Pas-du-Bouc dans les conditions rencontrées lors des expérimentations. Concernant l'influence des facteurs environnementaux, le coefficient de marée joue un rôle clé à Saujon, obstacle soumis à marée, alors que le débit d'attrait est le principal facteur jouant sur le taux de recapture au Pas-du-Bouc. Cela pourrait aboutir à des recommandations de gestion en maintenant un débit suffisant pendant la période de migration, ou pendant certaines périodes. Enfin, sur les deux sites, des résultats laissent supposer une prédation importante de civelles bloquées en aval de l'ouvrage ou lors de leur franchissement de la rampe. Afin de quantifier l'impact de la prédation, des premiers tests ont été menés qui montrent que les marques VIE pourraient être utilisées comme traceurs de la prédation

Écologie du mouvement, dynamique des populations - trajectométrie, modèles complexes : faire une interface entre écologie et méthodes

Les anguilles tempérées, un symbole du changement global. Les modèles à espace d'états : des outils flexibles. Analyse bibliographique de la production. Bilan : qu'est-ce qu'un écolisateur

Suivi par radiopistage de la dévalaison de l’anguille argentée sur la Dronne (2011-2012)

[Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASAREAfter a large research and development program carried out from, the « Pole Ecohydraulique » iniated a radiotracking experiment on the river Dronne to improve the knowledge on (i) the silver eel migration speed and (ii) environmental signals inducing the migration. This experiment is carried out jointly with an experiment carried out by Epidor and Onema aiming at quantifying the number of migrating eels in the context of the French index river. The radiotracking experiment started has been carried out from autumn 2011 to spring 2012. Unfortunately, this period was characterised by low river flow and consequently, it has not been possible to apply the experiment protocol and few migrations have been observed. However, the experiment is repeated in 2012/2013 with a protocol adapted according to 2011/2012 observations.A la suite du programme de recherche et développement anguilles, il est apparu nécessaire de mener de nouvelles expérimentations afin de mieux caractériser la cinétique de dévalaison de l'anguilles argentées et le déclenchement de cette migration. Pour cela, une campagne de radiopistage a été entamée sur la Dronne, qui vient compléter les expérimentations menées par Epidor et l'Onema dans le cadre de la rivière index et qui visent à quantifier le flux dévalant. Le radiopistage a commencé à l'automne 2011 et s'est poursuivi jusqu'au printemps 2012. Malheureusement, les très faibles débits rencontrés sur la Dronne au cours de cette période n'ont pas permis la capture du nombre escompté d'anguilles, et les anguilles marquées ont très peu bougées. L'expérimentation est renouvelée pour la saison 2012/2013, le protocole ayant été adapté en fonction des observations déjà réalisées

Développement et ajustement d'un modèle de dynamique des populations structuré en longueur et spatialisé appliqué au stock Nord de merlu (Merluccius merluccius)

Although the North-East Atlantic stock of European hake has been widely studied, certain characteristics of its biology are still relatively poorly known. This is particularly true of its seasonal migrations and growth, which a recent tagging campaign shows was probably largely underestimated. These uncertainties have several consequences both for the quality of the stock assessment using the usual population dynamics models and for management, particularly by limiting the possibilities of evaluating spatial management measures. To improve the estimation of the parameters of these processes, we have developed an integrated spatialized and length-structured population dynamics model based on a state model describing the dynamics of the population and the fishing activity, and on a model describing the observation processes, allowing the writing of a model of the population dynamics, allowing the writing of a likelihood function.A literature review of existing length-structured models highlighted the key role of growth process modelling in this type of model. To ensure the robustness of the model assumptions related to the discretisation of this continuous process and to individual growth variability, we performed a sensitivity analysis of the growth model. This method of numerical exploration of the model is based on (i) the development of experimental designs and (ii) the fitting of statistical models to the model outputs to quantify the impact of these assumptions. This generic approach is transposable to any sensitivity analysis of a discrete model describing a continuous process. In our case, it showed that for North-East Atlantic hake it was preferable to choose a quarterly time step, 1 cm classes, a gamma distribution of growth increments and a uniform distribution of individuals within the classes. During the development of the model, particular attention was paid to writing the likelihood function so that it would be robust and consistent with the observation processes. Different algorithms were also tested to carry out the numerical optimisation of this function. The choice was finally made for a quasi-Newton type algorithm. The fitting of the population dynamics model to the available observations allowed the estimation of migration rates and the growth rate, which is lower than that estimated from the tagging data. tagging data. It also made it possible to establish a diagnosis in terms of the evolution of the spawning biomass that was consistent with the diagnoses previously established using the current assessment model. However, due to its complexity and certainly to the poor quality of some observations, the adjustment of the model However, due to its complexity and certainly to the poor quality of some observations, the adjustment of the model is difficult. The model suffers from some identifiability problems even though the migration and growth parameters do not seem to be affected.Bien que le merlu de l'Atlantique Nord-Est ait été largement étudié, certaines caractéristiques de sa biologie sont encore assez mal connues. C'est en particulier le cas de ses migrations saisonnières et de sa croissance, dont une campagne récente de marquage montre qu'elle était probablement largement sous-estimée. Ces incertitudes ont plusieurs conséquences tant sur la qualité des diagnostics établis à l'aide des modèles de dynamique des populations usuels, que sur la gestion en limitant notamment les possibilités d'évaluation de mesures de gestions spatialisées. Pour améliorer l'estimation des paramètres de ces processus, nous avons développé un modèle de dynamique de population intégré spatialisé et structuré en longueur reposant sur un modèle d'états décrivant la dynamique de la population et de l'activité de pêche, et sur un modèle décrivant les processus d'observation, permettant l'écriture d'une fonction de vraisemblance.Une revue bibliographique des modèles structurés en longueur existants a mis en évidence le rôle clé de la modélisation du processus de croissance dans ce type de modèles. Pour s'assurer de la robustesse des hypothèses du modèle liées à la discrétisation de ce processus continu et à la variabilité individuelle de croissance, nous avons réalisé une analyse de sensibilité du modèle de croissance. Cette méthode d'exploration numérique du modèle repose sur (i) le développement de plans d'expériences et (ii) l'ajustement de modèles statistiques aux sorties du modèle pour quantifier l'impact de ces hypothèses. Cette démarche générique est transposable à toute analyse de sensibilité d'un modèle discret décrivant un processus continu. Dans notre cas, elle a permis de mettre en évidence que pour le merlu de l'Atlantique Nord-Est il était préférable de choisir un pas de temps trimestriel, des classes de 1 cm, une distribution gamma des incréments de croissance et une distribution uniforme des individus au sein des classes. Au cours du développement du modèle, une attention particulière a été portée à l'écriture de la fonction de vraisemblance afin qu'elle soit robuste et cohérente avec les processus d'observation. Différents algorithmes ont également été testés pour réaliser l'optimisation numérique de cette fonction, le choix se portant finalement vers un algorithme de type quasi-Newton. L'ajustement du modèle de dynamique de population aux observations disponibles a permis l'estimation des taux de migration et du taux de croissance, plus faible que celui estimé à partir des données de marquage. Il a permis également d'établir un diagnostic en terme d'évolution de la biomasse féconde cohérent avec les diagnostics préalablement établis à l'aide du modèle actuel d'évaluation. Cependant, du fait de sa complexité et très certainement de la mauvaise qualité de certaines observations, l'ajustement du modèle est difficile. Le modèle souffre de certains problèmes d'identifiabilité même si les paramètres de migration et de croissance ne semblent pas concernés

Implementation of the ecosystem approach to fisheries: a need for a protean fisheries science?

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