European Union legislation, through the Water Framework Directive (2000/60/ EC), as well as national legislation, such as the 'Grenelle Environnement ' (2007) in France, requires restoration of ecological connectivity in streams to improve free circulation of migratory fish. Different methods (e.g. capture by trap or net, telemetry, hydroacoustics) are used to evaluate the efficiency of fish passes to estimate the migratory species abundance and analyse changes in their within-river distributions. Among these methods, hydroacoustics is non-intrusive, allowing long-term observation and description of fish populations based on physical properties of sound in water. However, the main limit to hydroacoustic tools is their difficulty in identifying species. Initially designed for military purposes, dual-frequency identification sonar (DIDSON) has been used in environmental management for a decade. This acoustic camera uses higher frequencies and more sub-beams than common hydroacoustic tools, which improves image resolution and then enables observation of fish morphology and swimming behaviour. The ability to subtract static echoes from echograms and directly measure fish length improve the species-identification process. However, some limits have been identified, such as automatic dataset recording and the low range of the detection beam, which decreases accuracy, but efficient tools are now being developed to improve the accuracy of data recording (morphology, species identification, direction and speed). The new technological properties of acoustic cameras, such as the video-like visualization of the data, have greatly improved monitoring of diadromous fish populations (abundance, distribution and behaviour), helping river and fisheries managers and researchers in making decisions.
This perspective summarizes our knowledge of the freshwater habitat of Atlantic salmon (Salmo salar). The article is organized by life stage and identifies areas where more research is needed. For example, little is known of the kelt and presmolt life stages despite their importance in stock maintenance. We also believe that further investigation is required to assess the relevance of variables currently used to characterize habitat and that more attention should be focussed on adult and embryo-larva habitat requirements. We also discuss the fact that the majority of research is directed at habitat at the micro (i.e., immediate area around the fish) and macro scales (area of the geomorphological unit), while the influence of habitat at higher spatial scales should also be considered.
We present a hierarchical Bayesian modelling (HBM) framework for estimating riverine fish population size from successive removal data via electrofishing. It is applied to the estimation of the population of Atlantic salmon (Salmo salar) juveniles in the Oir River (France). The data set consists of 10 sampling sites sampled by one or two removals over a period of 20 years (1986–2005). We develop and contrast four models to assess the effect of temporal variations and habitat type on the density of fish and the probability of capture. The Bayes factor and the deviance information criterion are used to compare these models. The most credible and parsimonious model is the one that accounts for the effects of the years and the habitat type on the density of fish. It is used to extrapolate the population size in the entire river reach. This paper illustrates that HBM successfully accommodates large but sparse data sets containing poorly informative data for some units. Its conditional structure enables it to borrow strength from data-rich to data-poor units, thus improving the estimations. Predictions of the population size of the entire river reach can be derived, while accounting for all sources of uncertainty.Nous proposons un cadre de modélisation bayésien hiérarchique (HBM) pour estimer l’abondance d’une population de juvéniles de saumon atlantique (Salmo salar) dans la rivière Oir (France) par la méthode des retraits successifs par pêche électrique. Le jeu de données est composé de 10 sites d’échantillonnage, chacun ayant été échantillonné par un ou deux passages sur une période de 20 ans (1986–2005). Quatre modèles sont développés pour introduire les variations inter-annuelles et les effets du type d’habitat sur la densité et sur la probabilité de capture. Ces modèles sont comparés à l’aide du facteur de Bayes et d’un critère d’information basé sur la déviance. Le modèle retenu est celui qui prend en compte l’effet de l’année et du type d’habitat sur la densité de juvéniles de saumons. Il est utilisé pour extrapoler la population de saumon à l’ensemble du cours d’eau. Cet article illustre que les HBM permettent de traiter des jeux de données de grande taille dont l’information portée par chaque unité échantillonnée est hétérogène. La structure conditionnelle permet d’améliorer les estimations car elle organise un transfert d’information entre les unités. Le modèle permet d’obtenir des prédictions de l’abondance sur l’ensemble du cours d’eau, tout en prenant en compte les différentes sources d’incertitude
The restoration of previously extinct salmon populations is usually achieved with stocking programmes, but natural recolonization can also occur through the straying of individuals from nearby populations. Here we investigated the origin of Atlantic salmon (Salmo salar) that recently recolonized the Seine River (France). The degradation of this river had led to the extinction of the population, but since the 1990s, the water quality has greatly improved. Although no stocking was performed, 162 individual salmon were recently observed by video-counting. Seven fish were sampled for morphological and genetic analyses. These individuals were genotyped at 17 microsatellites markers and their probable source populations were identified using baseline samples from regional and distant populations. Four of the sampled individuals were grilse and three were multi-sea-winter fish. Genetic analyses revealed that the fish partly originated from a nearby stock but also from distant populations, suggesting long-distance straying. This natural recolonization of a large river by strayers from several origins is discussed in terms of population sustainability and management. / La restauration de populations antérieurement éradiquées de saumons se fait ordinairement par des programmes d'empoissonnement, mais il peut aussi exister une recolonisation naturelle par les individus errants des populations avoisinantes. Nous examinons ici l'origine des saumons atlantiques (Salmo salar) qui ont récemment recolonisé la Seine(France). La dégradation du fleuve avait entraıné l'extinction de la population, mais depuis les années 1990, la qualité de l'eau s'est grandement améliorée. Bien qu'aucun empoissonnement n'ait été effectué, 162 saumons individuels ont récemment été observés par comptage vidéo. Sept poissons ont été prélevés pour des analyses morphologiques et génétiques.Nous avons déterminé leur génotype à 17 marqueurs microsatellites et identifié leur population d'origine probable au moyen d'échantillons de référence provenant de populations régionales et éloignées. Quatre des individus prélevés étaient des madeleineaux et trois avait passé plusieurs hivers en mer. Les analyses génétiques montrent que les poissons proviennent en partie d'un stock voisin et en partie de populations lointaines, ce qui indique une errance sur de longues distances. Nous discutons de la recolonisation d'une grande rivière par des poissons errants d'origines diverses, en particulier de la durabilité et de la gestion de la population
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