Jean-Luc Baglinière

Aspects of parr-smolt transformation in anadromous and resident forms of brown trout (Salmo trutta) in comparison with Atlantic salmon (Salmo salar)

This study established the existence of a parr-smolt transformation in the anadromous form of brown trout but no such change in the resident form when reared under ambient photoperiod and temperature. Smolting occurred in March–April in the larger trout of the anadromous form and in April–May in salmon. Silvering, a peak of gill Na+,K+-ATPase activity and a simultaneous decrease in plasma prolactin were observed in both salmon and the anadromous form of trout. Bimodality in length frequency and a surge in growth hormone were observed only in Atlantic salmon. No physiological or morphological changes were observed in smaller (<13 cm) trout of the anadromous form or in the resident form. Hypo-osmoregulatory ability was greatest at the time of peak gill Na+,K+-ATPase activity and increased in spring in all trout, irrespective of smolt status. It is concluded that smolting is not as well developed in brown trout as in Atlantic salmon, and is not necessary for seawater adaptation of brown trout. It is also dependent on both stock origin and fish size.

Determinants of hierarchical genetic structure in Atlantic salmon populations: environmental factors vs. anthropogenic influences.

Disentangling the effects of natural environmental features and anthropogenic factors on the genetic structure of endangered populations is an important challenge for conservation biology. Here, we investigated the combined influences of major environmental features and stocking with non‐native fish on the genetic structure and local adaptation of Atlantic salmon (Salmo salar) populations. We used 17 microsatellite loci to genotype 975 individuals originating from 34 French rivers. Bayesian analyses revealed a hierarchical genetic structure into five geographically distinct clusters. Coastal distance, geological substrate and river length were strong predictors of population structure. Gene flow was higher among rivers with similar geologies, suggesting local adaptation to geological substrate. The effect of river length was mainly owing to one highly differentiated population that has the farthest spawning grounds off the river mouth (up to 900 km) and the largest fish, suggesting local adaptation to river length. We detected high levels of admixture in stocked populations but also in neighbouring ones, implying large‐scale impacts of stocking through dispersal of non‐native individuals. However, we found relatively few admixed individuals suggesting a lower fitness of stocked fish and/or some reproductive isolation between wild and stocked individuals. When excluding stocked populations, genetic structure increased as did its correlation with environmental factors. This study overall indicates that geological substrate and river length are major environmental factors influencing gene flow and potential local adaptation among Atlantic salmon populations but that stocking with non‐native individuals may ultimately disrupt these natural patterns of gene flow among locally adapted populations.

Natural recolonization of the Seine River by Atlantic salmon (Salmo salar) of multiple origins

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-distanc...

Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency.

While the stocking of captive-bred fish has been occurring for decades and has had substantial immediate genetic and evolutionary impacts on wild populations, its long-term consequences have only been weakly investigated. Here, we conducted a spatiotemporal analysis of 1428 Atlantic salmon sampled from 1965 to 2006 in 25 populations throughout France to investigate the influence of stocking on the neutral genetic structure in wild Atlantic salmon (Salmo salar) populations. On the basis of the analysis of 11 microsatellite loci, we found that the overall genetic structure among populations dramatically decreased over the period studied. Admixture rates among populations were highly variable, ranging from a nearly undetectable contribution from donor stocks to total replacement of the native gene pool, suggesting extremely variable impacts of stocking. Depending on population, admixture rates either increased, remained stable, or decreased in samples collected between 1998 and 2006 compared to samples from 1965 to 1987, suggesting either rising, long-lasting or short-term impacts of stocking. We discuss the potential mechanisms contributing to this variability, including the reduced fitness of stocked fish and persistence of wild locally adapted individuals.

Effect of water temperature and density of juvenile salmonids on growth of young‐of‐the‐year Atlantic salmon Salmo salar

A von Bertalanffy growth model for young-of the-year Atlantic salmon Salmo salar in a small French coastal stream was fitted using water temperatures and densities of juvenile salmonids (S. salar and brown trout Salmo trutta) as covariates influencing daily growth rate. The Bayesian framework was used as a template to integrate prior information from external data sets. The relative influence of the covariates on parr growth was quantified and results showed that growth of S. salar juveniles depended on both water temperatures and densities, but that most of the spatiotemporal variability of growth resulted from local spatiotemporal variations of 0+ age salmonid (S. salar and S. trutta) densities. Further analysis revealed that the fluctuations in young-of-the-year salmonid densities are likely to dominate the effects of potential future warming of water temperature due to climate change. It is concluded that factors that could affect salmonid densities might well have a greater effect on S. salar population dynamics than factors influencing water temperatures.

Understanding admixture patterns in supplemented populations: a case study combining molecular analyses and temporally explicit simulations in Atlantic salmon

Genetic admixture between wild and introduced populations is a rising concern for the management of endangered species. Here, we use a dual approach based on molecular analyses of samples collected before and after hatchery fish introduction in combination with a simulation study to obtain insight into the mechanisms of admixture in wild populations. Using 17 microsatellites, we genotyped pre‐ and post‐stocking samples from four Atlantic salmon populations supplemented with non‐native fish to estimate genetic admixture. We also used individual‐based temporally explicit simulations based on realistic demographic and stocking data to predict the extent of admixture. We found a low admixture by hatchery stocks within prestocking samples but moderate to high values in post‐stocking samples (from 12% to 60%). The simulation scenarios best fitting the real data suggested a 10–25 times lower survival of stocked fish relative to wild individuals. Simulations also suggested relatively high dispersal rates of stocked and wild fish, which may explain some high levels of admixture in weakly stocked populations and the persistence of indigenous genotypes in heavily stocked populations. This study overall demonstrates that combining genetic analyses with simulations can significantly improve the understanding of admixture mechanisms in wild populations.

The role of body size versus growth on the decision to migrate : a case study with Salmo trutta

In a population exhibiting partial migration (i.e. migration and residency tactics occur in the same population), the mechanisms underlying the tactical choice are still unclear. Empirical studies have highlighted a variety of factors that could influence the coexistence of resident and migratory individuals, with growth and body size considered to be key factors in the decision to migrate. Most studies suffer from at least one of the two following caveats: (1) survival and capture probabilities are not taken into account in the data analysis, and (2) body size is often used as a proxy for individual growth. We performed a capture–mark–recapture experiment to study partial migration among juvenile brown trout Salmo trutta at the end of their first year, when a portion of the population emigrate from the natal stream while others choose residency tactic. Bayesian multistate capture–recapture models accounting for survival and recaptures probabilities were used to investigate the relative role of body size and individual growth on survival and migration probabilities. Our results show that, despite an apparent effect of both size and growth on migration, growth is the better integrative parameter and acts directly on migration probability whereas body size acts more strongly on survival. Consequently, we recommend caution if size is used as a proxy for growth when studying the factors that drive partial migration in juvenile salmonid species.

An examination of genetic diversity and effective population size in Atlantic salmon populations.

Effective population size (Ne) is an important parameter in the conservation of genetic diversity. Comparative studies of empirical data that gauge the relative accuracy of Ne methods are limited, and a better understanding of the limitations and potential of Ne estimators is needed. This paper investigates genetic diversity and Ne in four populations of wild anadromous Atlantic salmon (Salmo salar L.) in Europe, from the Rivers Oir and Scorff (France) and Spey and Shin (Scotland). We aimed to understand present diversity and historical processes influencing current population structure. Our results showed high genetic diversity for all populations studied, despite their wide range of current effective sizes. To improve understanding of high genetic diversity observed in the populations with low effective size, we developed a model predicting present diversity as a function of past demographic history. This suggested that high genetic diversity could be explained by a bottleneck occurring within recent centuries rather than by gene flow. Previous studies have demonstrated the efficiency of coalescence models to estimate Ne. Using nine subsets from 37 microsatellite DNA markers from the four salmon populations, we compared three coalescence estimators based on single and dual samples. Comparing Ne estimates confirmed the efficiency of increasing the number and variability of microsatellite markers. This efficiency was more accentuated for the smaller populations. Analysis with low numbers of neutral markers revealed uneven distributions of allelic frequencies and overestimated short-term Ne. In addition, we found evidence of artificial stock enhancement using native and non-native origin. We propose estimates of Ne for the four populations, and their applications for salmon conservation and management are discussed.

Bibliometric analysis of diadromous fish research from 1970s to 2010: a case study of seven species

The aim of this study was to explore the research trends and the evolution of publications covered on diadromous fish from 1970s to 2010. We conducted a bibliometric analysis on seven patrimonial species: Atlantic salmon (Salmo salar), Brown and Sea trout (Salmon trutta), Allis shad (Alosa alosa), Twaite shad (Alosa fallax), Eel (Anguilla Anguilla), Sea lamprey (Petromyzon marinus) and River lamprey (Lampetra fluviatilis). We used bibliometric techniques on the total number of research (articles, books, and conferences) in all country in function of main fields such as growth/age, reproduction, migration, habitat, aquaculture, diseases, diet, abundance, fisheries, climate change, toxicology, dams/fishways, genetics, taxonomy, modelling, resource management, and stocking. The results revealed a clear difference in the evolution of scientific studies by species and by countries. The analysis comparisons showed the intensity of certain topics by species with the emergence of new ones, the economic impact on sciences and the increased support of conservation plan management for certain species, such as salmon and lamprey in France. This study also emerged that French research is not always consistent with the international trend which suggests the dominance of management systems on scientific studies.

A hierarchical bayesian model to quantify uncertainty of stream water temperature forecasts.

Providing generic and cost effective modelling approaches to reconstruct and forecast freshwater temperature using predictors as air temperature and water discharge is a prerequisite to understanding ecological processes underlying the impact of water temperature and of global warming on continental aquatic ecosystems. Using air temperature as a simple linear predictor of water temperature can lead to significant bias in forecasts as it does not disentangle seasonality and long term trends in the signal. Here, we develop an alternative approach based on hierarchical Bayesian statistical time series modelling of water temperature, air temperature and water discharge using seasonal sinusoidal periodic signals and time varying means and amplitudes. Fitting and forecasting performances of this approach are compared with that of simple linear regression between water and air temperatures using i) an emotive simulated example, ii) application to three French coastal streams with contrasting bio-geographical conditions and sizes. The time series modelling approach better fit data and does not exhibit forecasting bias in long term trends contrary to the linear regression. This new model also allows for more accurate forecasts of water temperature than linear regression together with a fair assessment of the uncertainty around forecasting. Warming of water temperature forecast by our hierarchical Bayesian model was slower and more uncertain than that expected with the classical regression approach. These new forecasts are in a form that is readily usable in further ecological analyses and will allow weighting of outcomes from different scenarios to manage climate change impacts on freshwater wildlife.