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In this study, radio telemetry was used to examine the upstream spawning migration behaviour of anadromous brown trout (sea trout), Salmo trutta L., in a boreal river system, the River Isojoki, western Finland. The aim was to study the movement activity and migration characteristics of trout during the upstream spawning migration, as well as to locate the important spawning habitats and study the spawning characteristics. Furthermore, the authors analysed how flow conditions and a hydropower dam, with adjacent fishways, affected the upstream spawning migration. Tagged trout spawned in both the main stem and four tributaries, with spawning taking place from early October to November. The movement activity of radio-tagged trout was influenced by a hydropower dam (Perus dam), with spring migrators spending prolonged periods at the dam area, postponing the migration upstream. Flow conditions affected the total time spent at the dam area, as well as the movement activity in the free-flowing sections above the dam, with increasing flow stimulating activity. In addition, time of river ascent and location of spawning area had a significant effect on the movement activity of tagged trout. These results are further evidence that synergistic effects of flow and migratory obstacles can negatively influence migrations of anadromous fish, regardless of constructed fishways. The management of flow regimes and the efficiency of fishways are vital, as climate change will likely influence the flow and increase the water temperature of boreal river systems, further aggravating issues caused by obstacles.

Hydropower is a flexible form of electricity generation providing both baseload and balancing power to accommodate intermittent renewables in the energy mix. However, hydropower also generates various externalities. This study investigates individuals’ preferences for policies aiming to reduce short-term regulations (i.e., hydropeaking in regulated rivers) while accounting for associated externalities with a discrete choice experiment. This is the first valuation study focusing on hydropeaking that considers both negative and positive externalities. The results imply that most individuals prefer stronger restrictions on short-term regulations to mitigate local environmental impacts. Individuals especially value improvements in recreational use, fish stocks, and the ecological state. On the other hand, potential increases in CO2 emissions are linked with a clear disutility. The estimated benefits obtained from an improved state of the river environment due to such restrictions probably exceed the disutility caused by increased CO2 emissions. The results also reveal unobserved preference heterogeneity among individuals, which should be accounted for in the willingness-to-pay (WTP) estimation using a model specification with correlated utility coefficients. Overall, the findings can inform policy-makers and environmental managers on the economic value of hydropeaking externalities and further guide the sustainable management of rivers regulated for hydropower generation.

Multispecies bio-economic models are useful tools to give insights into ecosystem thinking and ecosystem-based management. This paper developed an age-structured multispecies bio-economic model that includes the food web relations of the grey seal, salmon, and herring, along with salmon and herring fisheries in the Baltic Sea. The results show that the increasing seal population influences salmon fisheries and stock, but the impacts on the harvest are stronger than on the stock if the targeted management policies are obeyed. If seal population growth and a low herring stock occur simultaneously, the salmon harvest could face a serious threat. In addition, scenarios of the multispecies management approach in this paper reveal a benefit that our model can evaluate the performance of different fisheries with identical or different management strategies simultaneously. The results show the most profitable scenario is that both fisheries pursuit aggregated profits and reveal a trade-off between herring fisheries and salmon fisheries. Our model indicates that the herring harvest level and the approaches to managing herring fisheries can influence the performance of salmon fisheries. The study also demonstrates a way to develop a multispecies bio-economic model that includes both migratory fish and mammalian predators.

Anadromous salmonid fishes frequently exhibit strong geographic population structuring. However, population genetic differentiation of Atlantic salmon (Salmo salar) at fine geographic scales differs across equivalent spatial extents in different regions. So far, fine-scale genetic differentiation has not been assessed in rivers of the Baltic Sea, a region that contains an evolutionarily distinct Atlantic salmon lineage. Thus, Baltic salmon are currently managed on the river level, without focus on potential genetic structure and diversity within rivers. Here, we used microsatellites to characterize the genetic structure of wild juvenile salmon sampled throughout the interconnected, northern Baltic Tornio and Kalix Rivers. We found genetic differentiation within the two rivers, but not between them: salmon in the upper reaches differed from individuals in the lower reaches, regardless of river system. Further, examining smolts migrating from the river to the sea and adults returning from the sea to spawn, we found an association between the genetic structure and seasonal migration timing. Out-migrating smolts genetically assigned to upper river reaches were older and tended to reach the sea later in the season than smolts from the lower reaches. In contrast, mature adults originating from the upper reaches returned to the river early in the season. Our observation of genetic population structuring between downstream and upstream reaches of the large Tornio and Kalix rivers, and its association with migration timing, implies that careful temporal management of the northern Baltic fisheries would help to preserve the diversity and sustainability of the wild salmon stocks of these rivers.

This is the peer reviewed version of the following article: "Circumpolar patterns of Arctic freshwater fish biodiversity: A baseline for monitoring", which has been published in final form at https://doi.org/10.1111/fwb.13405. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions Climate change, biological invasions, and anthropogenic disturbance pose a threat to the biodiversity and function of Arctic freshwater ecosystems. Understanding potential changes in fish species distribution and richness is necessary, given the great importance of fish to the function of freshwater ecosystems and as a resource to humans. However, information gaps limit large‐scale studies and our ability to determine patterns and trends in space and time. This study takes the first step in determining circumpolar patterns of fish species richness and composition, which provides a baseline to improve both monitoring and conservation of Arctic freshwater biodiversity. Information on species presence/absence was gathered from the Circumpolar Biodiversity Monitoring Program's Freshwater Database and used to examine patterns of freshwater fish γ‐, α‐, and β‐diversity across 234° of longitude in the Arctic. The metrics of diversity provided information on species richness and composition across hydrobasins, ecoregions, and Arctic zones. Circumpolar patterns of fish species biodiversity varied with latitude, isolation, and coarse ecoregion characteristics; patterns were consistent with historic and contemporary barriers to colonisation and environmental characteristics. Gamma‐diversity was lower in the high Arctic compared to lower latitude zones, but α‐diversity did not decrease with increasing latitude below 71°N, reflecting glacial history. Alpha‐diversity was reduced to a single species, Arctic charr Salvelinus alpinus, in ecoregions above 71°N, where γ‐diversity was the lowest. Beta‐diversity indicated little variation in the composition and richness of species across the High Arctic; at lower latitudes, ecoregions contained more species, although species composition turned over across large spatial extents. In an analysis of five ecoregions in the circumpolar Arctic, physical isolation, and ecoregion area and topography were identified as strong drivers of γ‐, α‐, and β‐diversity. Physical isolation reduced the γ‐ and α‐diversity, and changes in β‐diversity between adjacent locations were due mainly to losses in species richness, rather than due to differences in species composition. Heterogeneity of habitats, environmental gradients, and geographic distance probably contributed to patterns of fish dissimilarity within and across ecoregions. This study presents the first analysis of large‐scale patterns of freshwater fish biodiversity in the circumpolar Arctic. However, information gaps in space, time, and among taxonomic groups remain. Future inclusion of extensive archive and new data will allow future studies to test for changes and drivers of the observed patterns of biodiversity. This is important given the potential impacts of ongoing and accelerating climate change, land use, and biotic exchange on Arctic fish biodiversity.

The implementation challenge of ecosystem-based (fisheries) management (EB(F)M) has entailed calls for integrated governance (IG) approaches in the marine field. We arranged an expert workshop to study the preconditions and applicability of IG, and to suggest how IG could be arranged in practice. Focusing on the management of the dioxin problem shared by the herring and salmon fisheries in the Baltic Sea, and using a coupled ‘insight network’- SWOT (strengths, weaknesses, opportunities, threats) methodology, we evaluated two scenarios: 1) IG of herring and salmon fisheries to benefit from collaboration between these fisheries that suffer from the same problem, and 2) IG between the fisheries sector and the food/public health sector to incorporate food safety in fisheries governance. Our results demonstrate that a variety of societal, political, institutional, operational, instrumental, and biological factors affect the applicability of IG in marine contexts, and work as preconditions for IG. While societal needs for IG were obvious in our case, as major challenges for it we identified the competing cross-sectoral objectives, path dependencies, and limitations of experts to think and work across fields. The study suggests that establishing an IG framework by adding new aspects upon the current governance structures may be easier to accept and adapt to, than creating new strategic or advisory bodies or other new capacities. Viewing IG as a framework for understanding cross-sectoral issues instead of one that requires a defined level and form of integrated assessment and management may be a way towards social learning, and thereby towards the implementation of more sophisticated, open and broad EB(F)M frameworks. The implementation challenge of ecosystem-based (fisheries) management (EB(F)M) has entailed calls for integrated governance (IG) approaches in the marine field. We arranged an expert workshop to study the preconditions and applicability of IG, and to suggest how IG could be arranged in practice. Focusing on the management of the dioxin problem shared by the herring and salmon fisheries in the Baltic Sea, and using a coupled ‘insight network’- SWOT (strengths, weaknesses, opportunities, threats) methodology, we evaluated two scenarios: 1) IG of herring and salmon fisheries to benefit from collaboration between these fisheries that suffer from the same problem, and 2) IG between the fisheries sector and the food/public health sector to incorporate food safety in fisheries governance. Our results demonstrate that a variety of societal, political, institutional, operational, instrumental, and biological factors affect the applicability of IG in marine contexts, and work as preconditions for IG. While societal needs for IG were obvious in our case, as major challenges for it we identified the competing cross-sectoral objectives, path dependencies, and limitations of experts to think and work across fields. The study suggests that establishing an IG framework by adding new aspects upon the current governance structures may be easier to accept and adapt to, than creating new strategic or advisory bodies or other new capacities. Viewing IG as a framework for understanding cross-sectoral issues instead of one that requires a defined level and form of integrated assessment and management may be a way towards social learning, and thereby towards the implementation of more sophisticated, open and broad EB(F)M frameworks.

Rivers developed for hydropower production are important electricity generators with an increasing role as a balancing power source in new wind-power dominated energy systems. However, hydropower constructed rivers also provide many ecosystem services, such as habitats for migratory fish species and opportunities for recreational activities. Currently, we see drastic changes in needs from society to use regulated river corridors for multiple purposes, and therefore, new approaches are needed to support the sustainable management of river resources. In our new EcoRiver-project we develop an integrated assessment framework and examine cost and benefits provided by hydropower constructed rivers. We use hydrodynamic modelling to quantify the ecosystem services and variability during short-term regulation practices (hydropeaking). Hydropower and energy markets modelling is used to examine the impacts of increasing demand flexibility on hydropower. Environmental valuation methods are applied to evaluate the ecosystem services monetarily. Finally, we integrate these methods for cost-benefit analysis in order to support well-informed decision making for river management.

Inland fisheries are important sources of ecosystem services contributing to human diet, health, well-being and economies. The evaluation of the importance and value of inland fisheries is one of the biggest challenges for its development. To develop the inland fisheries data collection, we reviewed the current status of data collection in European countries and provided five detailed country examples. The level and methods of inland fisheries data collection in Europe were highly variable. Some countries did not collect any data on recreational fishing, or it was collected only from specific areas, or only the number of licenses sold was recorded. Data collection from catches of diadromous species was most common and harmonized among countries and in particular, Atlantic salmon Salmo salar were recorded. When data from other fish species were also nationally collected, the methods used included postal or telephone recall surveys using a sample of citizens of the country. More detailed surveys were used to assist national surveys, or were used independently, in specific sites of importance using various methods, like postal surveys targeted to fishing license holders, online reporting of catches, or catch reports and logbooks. Many countries provided fishing license buyers with catch return forms or logbooks to be filled at fishing occasions and/or returned in the end of the fishing season. Commercial inland fisheries did not exist, or were very limited, in many European countries. In countries where commercial fishing was important, in most cases the fishers were registered and obliged to report their catches. The reliability of self-reporting of commercial catches was questioned in some cases. There was a trend towards webbased online reporting of inland fisheries data, which some countries were already using. The specific country examples give detailed description of data collection, focusing on: 1) country-wide postal survey (Finland) and 2) web-based survey and development of citizen science approach (Denmark). Example 3) from Ireland focuses on recreational salmonid fishing and conservation limits. There are two examples based on logbook returns: 4) one strict system, which is considered to work well (Czech Republic) and 5) one less controlled system, currently not producing reliable results, and under development (Croatia). Case studies were provided in each country example. Finally, the authors discuss the important aspects of inland fisheries data collection and review the methods to provide recommendations.

Knowledge of current fishing mortality rates is an important prerequisite for formulating management plans for the recovery of threatened stocks. We present a method for estimating migration and fishing mortality rates for anadromous fishes that combines tag return data from commercial and recreational fisheries with expert opinion in a Bayesian framework. By integrating diverse sources of information and allowing for missing data, this approach may be particularly applicable in data-limited situations.Wild populations of anadromous sea trout (Salmo trutta) in the northern Baltic Sea have undergone severe declines, with the loss of many populations. The contribution of fisheries to this decline has not been quantified, but is thought to be significant. We apply the Bayesian mark-recapture model to two reared sea trout stocks from the Finnish Isojoki and Lestijoki Rivers. Over the study period (1987–2012), the total harvest rate was estimated to average 0.82 y–1 for the Isojoki River stock and 0.74 y−1 for the Lestijoki River stock. Recreational gillnet fishing at sea was estimated to be the most important source of fishing mortality for both stocks, particularly during the 1980s and 1990s. Our results indicate a high probability of unsustainable levels of fishing mortality for both stocks, and illustrate the importance of considering the effect of recreational fisheries on fish population dynamics.

The survival of Baltic salmon Salmo salar during the first year at sea (post-smolt stage) has declined since the beginning of the 1990s. In this analysis, we complement previous studies on possible causes of this decline by considering a suite of environmental parameters, potential change in predation pressure, and post-smolt growth. Marine survival estimates were found to be negatively correlated with temperature, indicating that warming conditions have not favoured survival. Survival was also found to be positively correlated with dissolved oxygen levels and regionally related to shifts in salinity. These relationships were further studied in context to the potential predation on post-smolts by one of the main piscivores in the Baltic, Eastern Baltic cod (Gadus morhua callarias). Concomitant with changes in environmental conditions, Baltic cod has changed its latitudinal range, moving northward in the Baltic, possibly in response to warming conditions. These changes lead us to hypothesize that predation pressure on salmon may have increased in recent years as cod has now occupied habitats used by salmon post-smolts during their southward feeding migrations. This predation may have been intensified as a result of anoxic conditions in the central basin by concentrating predation interactions in coastal waters and/or the upper water column typically occupied by salmon post-smolts. Indicators of post-smolt growth were applied to test the alternate hypothesis that mortality is growth-mediated; these indicators lacked a time series trend, which supports the contention that shifting predation pressure rather than feeding opportunities is responsible for the decline in post-smolt survival in Baltic salmon.

This paper compares two fisheries management objectives recognized in the literature and applied in practice: maximum sustainable yield (MSY) and maximum economic yield (MEY). The European Union Common Fisheries Policy (CFP) sets the minimum target of fish populations at the MSY level, defined as the stock level that maximizes the fish catch. Although MSY is useful in nudging over-harvested stocks back to biologically sustainable levels, the CFP requires the harvested stocks to be maintained above levels that can produce MSY without addressing the exact definition of “above MSY”. One possibility for maintaining fish stocks above MSY is to apply the maximum economic yield (MEY) that maximizes the discounted net present value of the fishery. Comparison of the economic and ecological outcomes of the two objectives in the Northern Baltic salmon fishery is conducted by applying a dynamic optimization model coupled with age-structured salmon stock dynamics. The results are further tested for the changes in stock-recruitment parameters, and related to the precautionary management target of reaching 75% smolt production capacity. A sensitivity analysis for the economic parameter values is conducted. The results show that as a target, MEY performs better than MSY in both conserving the stocks and providing economic viability for the fishers. Targeting MEY while keeping MSY at hand as a minimum biological objective was found to be a pragmatic objective that is in line with the goals of the CFP and the EU Blue Growth Strategy.

This article studies how accounting for the benefits of recreational fisheries affects the formation and stability of an international fisheries agreement (IFA) on the management of Baltic salmon stocks. The interaction between four countries is modelled through a partition function game, under two scenarios. In the first scenario, countries take their participation decision for the IFA based only on the net present value of profits from commercial fisheries. In the second scenario, the net present value of the recreational benefits from angling is also considered. The results show that accounting for recreational benefits leads to the formation of the grand coalition, whereas only partial cooperation occurs when payoffs are confined to profits from commercial fisheries.

The phenotypic divergence between natural salmon stocks and the corresponding hatchery-reared stocks was investigated in two Atlantic salmon (Salmo salar) populations from the Tornionjoki and Simojoki Rivers, where hatchery reared smolts of local origin were released during the second half of the last century. The reared salmon were larger as smolts and also heavier at sea than wild salmon in both stocks. The recapture rate was highest for wild Tornionjoki salmon (mean 2.8%) and lowest for reared Simojoki salmon (mean 1.2%). During 1999–2008, survival was higher in wild than reared fish, while the overall survival of tagged smolts declined. Survival was close to similar in Tornionjoki and Simojoki salmon when the year, background (wild or reared) and smolt length were taken into account. Migration distances differed between wild and reared stocks. In the second winter at sea, the majority of wild salmon (94–96%) were captured in the southern part of the Baltic Sea, while the reared salmon, especially those of the Simojoki stock, remained closer to their native river in the northern parts of the Baltic. Rearing also decreased the duration of the sea migration before the first maturation in Simojoki salmon, but not in Tornionjoki salmon. Of the wild Simojoki salmon, 64% returned to their home river as multi-sea-winter (MSW) fish compared to 40% of the reared fish. The population and rearing background, but not smolt length, explained the probability of maturing as one-sea-winter instead of MSW fish. Rearing produced 1.60 times more grilse than occurred among wild salmon. The reared salmon showed different life-history patterns from wild fish, and especially in the Simojoki River, the salmon stock as a whole presently deviates from previously documented wild rivers. Even though population sizes appear to be recovering, it may take time before the stocks regain their adaptive potential following the period of collapse and supportive releases.

We introduce a Bayesian probability model for making inferences about the unknown number of individuals in a sample, based on known sample weight and on information provided by subsamples with known weights and corresponding counts. Inherent in the Bayesian approach, the model allows for an incorporation of prior information that is often available about the sample size and other uncertain parameter values. As a result, the model provides an estimate of the number of individuals in the sample in the form of a posterior probability distribution that includes both the prior information and the interpretation of the observed data. Such a result cannot be obtained using the frequentist approach. The model presented here can be applied to a wide range of similar problems. Here our main focus is stock assessment, where the task is the conversion of the catch weight into the number of individuals in the catch. The model is easy to use due to availability of general purpose MCMC simulation software, and it can be used either in a standalone fashion or embedded into more complex probability models.

The Atlantic salmon, Salmo salar L., in the Tornio River in the Northern Baltic Sea basin accommodates a monogenean ectoparasite, Gyrodactylus salaris. The aim of the study was to understand the population structure of apparently co-adapted host-parasite system: no parasite-associated mortality has been reported. The parasite burden among salmon juveniles (parr) was monitored along 460km of the river in 2000-2009. Among the parr, 33.0% were infected (nfish=1913). The genetic structure of the parasite population was studied by sequencing an anonymous nuclear DNA marker (ADNAM1, three main genotypes) and mitochondrial CO1 (three clades, six haplotypes). During the ten years, the parasite population was strongly and stably genetically differentiated among up- and downstream nurseries (nADNAM1=411, FST=0.579; nCO1=443, FST=0.534). Infection prevalence among the smolts migrating to sea was higher than in the sedentary parr populations (82.2%, nfish=129). The spatial differentiation observed among the sedentary juveniles was reflected temporally in the smolt run: parasite genotypes dominating the upper part of the river arrived later than downstream dwellers (medians June 4 and June 2) to the trap 7km from the river mouth. The nuclear and mitochondrial markers were in stable disequilibrium which was not relaxed in the contact zone or among the smolts where the parasite clones often met on individual fish. Only five parasite specimens on smolts (nworms=217) were putative recent sexual recombinants. The contribution of extant salmon hatcheries into the infection was negligible. The host salmon population in Tornio River is known to show significant spatial differentiation (FST=0.022). The stable spatial genetic structure of the parasite against the high physical mobility suggested a possibility of local co-adaptation of the host-parasite subpopulations.

Mäntyniemi, S., Romakkaniemi, A., Dannewitz, J., Palm, S., Pakarinen, T., Pulkkinen, H., Gårdmark, A., and Karlsson, O. 2012. Both predation and feeding opportunities may explain changes in survival of Baltic salmon post-smolts. – ICES Journal of Marine Science, 69: 1574–1579. The survival of wild and hatchery-reared post-smolts of salmon (Salmo salar) in the Baltic Sea has declined since the 1990s. Direct observations of the processes affecting survival are, however, lacking. Here, the importance of food availability and predation in regulating post-smolt survival is analysed. Based on previous studies, the following explanatory variables were selected: (i) availability of herring (Clupea harengus membras) recruits in the Gulf of Bothnia (Bothnian Sea, Bothnian Bay) in the northern Baltic Sea; (ii) sprat (Sprattus sprattus balticus) and herring abundance in the southern Baltic Sea; and (iii) abundance of grey seal (Halichoerus grypus) along the post-smolt migration route. Bayesian analysis was used to estimate the relative probability of each of the 32 combinations of these variables and revealed that the model including grey seal abundance and herring recruits per post-smolt had the highest posterior probability and a high coefficient of determination. The results suggest that the declining trend in post-smolt survival is explained by the increased number of grey seals, whereas the annual variation in survival coincides with variation in the recruitment of Bothnian Sea herring. However, it remains uncertain whether the observed correlations arise from direct causalities or other mechanisms.

Linnansaari T, Keskinen A, Romakkaniemi A, Erkinaro J, Orell P. Deep habitats are important for juvenile Atlantic salmon Salmo salar L. in large rivers. Ecology of Freshwater Fish 2010: 19: 618–626. © 2010 John Wiley & Sons A/S Abstract – Juvenile Atlantic salmon were studied by underwater video surveillance and self contained underwater breathing apparatus-diving in deep (i.e. >1.0 m), fast flowing areas of two large river systems (River Teno, River Tornionjoki) in northern Finland. Both video and diving data indicated that young-of-the-year (YOY) salmon (0+) and salmon parr (>0+) readily utilised habitats deeper than 1 m. Young-of-the-year salmon and parr were observed through a range of 0.5–1.9 m and 0.4–2.2 m, respectively. A negative linear relationship between the mean abundance of YOY salmon and mean depth was noted from the diving transects. Salmon parr were similarly abundant throughout the range of depths studied. Video data showed that deep habitats were used throughout the summer (June–August). It was concluded that deep, fast-flowing areas in large rivers may constitute a significant habitat resource for juvenile salmon that has not been traditionally accounted for when estimating salmon production.

This paper presents a sequential Bayesian framework for quantitative fisheries stock assessment that relies on a wide range of fisheries-dependent and -independent data and information. The presented methodology combines information from multiple Bayesian data analyses through the incorporation of the joint posterior probability density functions (pdfs) in subsequent analyses, either as informative prior pdfs or as additional likelihood contributions. Different practical strategies are presented for minimising any loss of information between analyses. Using this methodology, the final stock assessment model used for the provision of the management advice can be kept relatively simple, despite the dependence on a large variety of data and other information. This methodology is illustrated for the assessment of the mixed-stock fishery for four wild Atlantic salmon (Salmo salar) stocks in the northern Baltic Sea. The incorporation of different data and information results in a considerable update of previously available smolt abundance and smolt production capacity estimates by substantially reducing the associated uncertainty. The methodology also allows, for the first time, the estimation of stock–recruit functions for the different salmon stocks.

The occurrence of Gyrodactylus salaris in the River Tornionjoki was investigated in 2000-2004. Infection of salmon parr, Salmo salar, was common in the uppermost reach of the river system but decreased downstream and was rare in the lowermost reach. This pattern was consistent across the study period regardless of varying water temperatures. The oldest age groups of parr were more often infected than younger ones throughout the river system, irrespective of their origin (wild or stocked). Parasite-free hatchery-reared 1-year-old parr became infected during their first summer in the wild. Downmigrating salmon smolts had a high prevalence of infection, but their role in the distribution of infection seemed unimportant. On grayling, Thymallus thymallus, we observed only the grayling-specific clade of Gyrodactylus. We found no indication of grayling participating in the epidemiology of infection on salmon. The salmon parr and smolt population in the Tornionjoki has been at its height during the late 1990s and 2000s. Our results indicate that G. salaris infection in this Baltic river has no devastating effects on the salmon population as it has had in salmon rivers flowing into the North Atlantic and White Sea.

Males and females share many traits that have a common genetic basis, however selection on these traits often differs between the sexes leading to sexual conflict. Under such sexual antagonism, theory predicts the evolution of genetic architectures that resolve this sexual conflict. Yet, despite intense theoretical and empirical interest, the specific genetic loci behind sexually antagonistic phenotypes have rarely been identified, limiting our understanding of how sexual conflict impacts genome evolution and the maintenance of genetic diversity. Here, we identify a large effect locus controlling age at maturity in 57 salmon populations, an important fitness trait in which selection favours earlier maturation in males than females, and show it is a clear example of sex dependent dominance reducing intralocus sexual conflict and maintaining adaptive variation in wild populations. Using high density SNP data and whole genome re-sequencing, we found that vestigial-like family member 3 (VGLL3) exhibits sex-dependent dominance in salmon, promoting earlier and later maturation in males and females, respectively. VGLL3, an adiposity regulator associated with size and age at maturity in humans, explained 39.4% of phenotypic variation, an unexpectedly high effect size for what is usually considered a highly polygenic trait. Such large effects are predicted under balancing selection from either sexually antagonistic or spatially varying selection. Our results provide the first empirical example of dominance reversal permitting greater optimisation of phenotypes within each sex, contributing to the resolution of sexual conflict in a major and widespread evolutionary trade-off between age and size at maturity. They also provide key empirical evidence for how variation in reproductive strategies can be maintained over large geographical scales. We further anticipate these findings will have a substantial impact on population management in a range of harvested species where trends towards earlier maturation have been observed

Background Fish fin is a widely used, non-lethal sample material in studies using stable isotopes to assess the ecology of fishes. However, fish fin is composed of two distinct tissues (ray and membrane) which may have different stable isotope values and are not homogeneously distributed within a fin. As such, estimates of the stable isotope values of a fish may vary according to the section of fin sampled. Methods To assess the magnitude of this variation, we analysed carbon (δ13C), nitrogen (δ15N), hydrogen (δ2H) and oxygen (δ18O) stable isotopes of caudal fin from juvenile, riverine stages of Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). Individual fins were sub-sectioned into tip, mid and base, of which a further subset were divided into ray and membrane. Findings Isotope variation between fin sections, evident in all four elements, was primarily related to differences between ray and membrane. Base sections were13C depleted relative to tip (~ 1 ‰) with equivalent variation evident between ray and membrane. A similar trend was evident in δ2H, though the degree of variation was far greater (~ 10 ‰). Base and ray sections were 18O enriched (~ 2 ‰) relative to tip and membrane, respectively. Ray and membrane sections displayed longitudinal variation in 15N mirroring that of composite fin (~ 1 ‰), indicating that variation in15N values was likely related to ontogenetic variation. Conclusions To account for the effects of intra-fin variability in stable isotope analyses we suggest that researchers sampling fish fin, in increasing priority, 1) also analyse muscle (or liver) tissue from a subsample of fish to calibrate their data, or 2) standardize sampling by selecting tissue only from the extreme tip of a fin, or 3) homogenize fins prior to analysis.

A Bayesian state–space mark–recapture model is developed to estimate the exploitation rates of fish stocks caught in mixed-stock fisheries. Expert knowledge and published results on biological parameters, reporting rates of tags and other key parameters, are incorporated into the mark–recapture analysis through elaborations in model structure and the use of informative prior probability distributions for model parameters. Information on related stocks is incorporated through the use of hierarchical structures and parameters that represent differences between the stock in question and related stocks. Fishing mortality rates are modelled using fishing effort data as covariates. A state–space formulation is adopted to account for uncertainties in system dynamics and the observation process. The methodology is applied to wild Atlantic salmon (Salmo salar) stocks from rivers located in the northeastern Baltic Sea that are exploited by a sequence of mixed- and single-stock fisheries. Estimated fishing mortality rates for wild salmon are influenced by prior knowledge about tag reporting rates and salmon biology and, to a limited extent, by prior assumptions about exploitation rates.

We introduce a Bayesian probability model for the estimation of the size of an animal population from re- moval data. The model is based on the assumption that in the removal sampling, catchability may vary between indi- viduals, which appears to be necessary for a realistic description of many biological populations. Heterogeneous catchability among individuals leads to a situation where the mean catchability in the population gradually decreases as the number of removals increases. Under this assumption, the model can be fitted to any removal data, i.e., there are no limitations regarding the total catch, the number of removals, or the decline of the catch. Using a published data set from removal experiments of a known population size, the model is shown to be able to estimate the population size appropriately in all cases considered. It is also shown that regardless of the statistical approach, a model that assumes equal catchability of individuals generally leads to an underestimation of the population. The example indicates that if there is only vague prior information about the variation of catchability among individuals, a very high number of suc- cessive removals may be needed to correctly estimate the population size. Resume : Nous utilisons un modele de probabilite bayesien pour estimer la taille d'une population animale a partir de donnees de retrait. Le modele se base sur la presupposition que, dans un echantillonnage par retraits, la capturabilite peut varier d'un individu a un autre, ce qui semble necessaire pour decrire de facon realiste de nombreuses populations biologiques. Une capturabilite individuelle heterogene engendre une situation dans laquelle la capturabilite moyenne de la population decroit graduellement a mesure que le nombre de retraits augmente. Avec cette presupposition, le modele s'ajuste a n'importe quelle serie de donnees de retrait; il n'y a donc pas de limites en ce qui a trait a la capture totale, au nombre de retraits ou au declin de la recolte. L'utilisation de donnees de retrait publiees obtenues sur une popula- tion de taille connue montre que le modele est capable d'estimer la taille de la population de facon adequate dans tous les cas etudies. De plus, independamment de l'approche statistique utilisee, un modele qui presuppose une capturabilite individuelle uniforme sous-estime la population. L'exemple montre que, s'il n'existe que des informations prealables vagues sur la capturabilite individuelle, il faudra peut-etre un nombre tres eleve de retraits successifs pour pouvoir estimer correctement la taille de la population. (Traduit par la Redaction) Mantyniemi et al. 300

A mixed salmon fishery with both natural wild salmon stocks and reared salmon exists in the Baltic Sea. The agreed-upon goal of management is to safeguard the wild stocks, and the practical management objectives have been agreed to attain at least a 50% maximum salmon production capacity in each river. This natural production capacity is, however, largely unknown. Here, a new approach has been used to estimate the salmon maximum production capacity of northern Baltic Sea rivers. A probabilistic salmon production capacity model was built entirely upon expert knowledge. The model describes the external physical and biological factors of the rivers and the juvenile salmon stocks' response to these factors. We found that the experts estimated the carrying capacity to be considerably higher than former estimates. A very high uncertainty was, however, connected with these estimates. We also found considerable disagreement over the general carrying capacity level among the experts; the major uncertainty emerged from the conflicting views of the experts. The result implies that perhaps operational management objectives other than those based on maximal smolt production levels should be considered to decrease the uncertainty connected with evaluation of management success.

River entry of adult Atlantic salmon Salmo salar into the River Tornionjoki, monitored during three migration seasons (1997–1999) by horizontal split-beam hydroacoustics, started early in June when water temperature was c. 9° C and when the discharge varied between 1700 and 2000 m3 s−1. In 1997 and 1999, migration peaked during the latter half of June, 17 days after the peak flood, at water temperatures ranging from 11· 5 to 18·2° C. Few statistically significant correlations were observed between river entry and six measured environmental factors and those that were significant were not persistent over the years. The strongest correlation ( r = −0·60) was between the number of upstream migrants and seawater level, with a time lag of 1 day in 1998. In 1998 and 1999, no clear diurnal migration pattern was observed, although in 1997 the intensity of midday migration was higher than that of the midnight migration. It is concluded that environmental factors have little effect on river entry of Atlantic salmon in a large pristine river located at high latitude.

Since 1980, the abundance of wild Atlantic salmon has been monitored by means of catch records, adult counts, electrofishing and smolt trapping in six rivers flowing into the northern Baltic Sea. River abundance (spawners, parr and smolts) was compared with implemented large-scale and river-specific management measures and with natural factors potentially affecting abundance. Since the 1980s, the wild stocks have recovered in a synchronous cyclical pattern. The recovery occurred mainly in two jumps, first a sudden increase dating back to around 1990 and a second sharp rise in the late 1990s. River abundance of young salmon commonly rose about 10-fold and approached the previously estimated production capacity in some of the rivers. This positive development may be explained by a decline in fishing pressure together with covarying natural factors influencing survival and growth. The offshore fishery started to decline at the time of the first increase, while the reduction in the total allowable catches together with seasonal restrictions on the coastal fishery strengthened the second increase. Improved natural conditions seem to have increased both survival and escapement during the first rise. Spawners producing the second rise were the offspring of the spawners of the first rise. The outbreak of the M74 mortality syndrome among alevins reduced the abundance of several year-classes that hatched during the first half of the 1990s. In most rivers, the fraction of older and female fish in the spawning run has increased over the period, thereby increasing the reproductive capacity of the populations. No distinct effects of variations in river-specific management regimes were observed. Instead, the results emphasize the role of fisheries management in the open sea as well as in coastal waters, and also of non-human factors in controlling overall abundance of wild salmon in northern Baltic rivers.

Interspecific hybridization between Atlantic salmon and brown trout is well documented, but why it should vary so much among populations is not clear. Determining the maternal origin of hybrids can provide insights into the mechanisms underlying interspecific hybridization, but this information is lacking in many studies. Here we present a species-specific mitochondrial DNA marker for the identification of the maternal origin of hybrids. This marker involves only one PCR step followed by fragment analysis, can be integrated within PCR multiplexing for existing nuclear markers for hybrid identification, and is therefore faster and more cost-effective than previous methods.

We developed a Bayesian probability model for mark–recapture data. Three alternative versions of the model were applied to two sets of data on the abundance of migrating Atlantic salmon (Salmo salar) smolt populations, and the results were then compared with those of two widely used maximum likelihood models (Petersen method and a model using stratified data). Our model follows the basic principles of stochastic models presented for stratified data. In contrast to the earlier models, our model can deal with sparse data. Moreover, even weak dependencies between the studied parameters and the possible factors affecting them can be used to improve the plausibility of the estimates. The assumptions behind our approach are more realistic than those of earlier models, taking into account such factors as overdispersion, which is expected to be present in the mark–recapture data of salmon smolts because of their schooling behavior. Our examples also show that assumptions about the model structure can have a substantial impact on the resulting inferences on the size of the smolt run, especially in terms of the precision of the estimate.

15 pages, 7 figures, 2 tables, Migrations between different habitats are key events in the lives of many organisms. Such movements involve annually recurring travel over long distances usually triggered by seasonal changes in the environment. Often, the migration is associated with travel to or from reproduction areas to regions of growth. Young anadromous Atlantic salmon (Salmo salar) emigrate from freshwater nursery areas during spring and early summer to feed and grow in the North Atlantic Ocean. The transition from the freshwater ('parr') stage to the migratory stage where they descend streams and enter salt water ('smolt') is characterized by morphological, physiological and behavioural changes where the timing of this parr-smolt transition is cued by photoperiod and water temperature. Environmental conditions in the freshwater habitat control the downstream migration and contribute to within- and among-river variation in migratory timing. Moreover, the timing of the freshwater emigration has likely evolved to meet environmental conditions in the ocean as these affect growth and survival of the post-smolts. Using generalized additive mixed-effects modelling, we analysed spatio-temporal variations in the dates of downstream smolt migration in 67 rivers throughout the North Atlantic during the last five decades and found that migrations were earlier in populations in the east than the west. After accounting for this spatial effect, the initiation of the downstream migration among rivers was positively associated with freshwater temperatures, up to about 10 °C and levelling off at higher values, and with sea-surface temperatures. Earlier migration occurred when river discharge levels were low but increasing. On average, the initiation of the smolt seaward migration has occurred 2.5 days earlier per decade throughout the basin of the North Atlantic. This shift in phenology matches changes in air, river, and ocean temperatures, suggesting that Atlantic salmon emigration is responding to the current global climate changes., This study is part of the Norwegian Research Council project nº 183989/S30. J.O. acknowledges additional funding from Norwegian Water and Energy Directorate (NVE).

Fixed location split-beam horizontal echosounding was used to assess the size and timing of the Atlantic salmon (Salmo salar) spawning run in the River Tornionjoki. Four transducers, two on each river bank, were mounted across the river at the study site 4 km upstream from the river mouth. Net weirs were used on both shores to direct the passage of fish through the acoustic beams. Hydroacoustic monitoring covered 40-50% of the river cross-sectional area. Also test fishing and yearly catch statistics of salmon were used as an indication of the size of the spawning run in the river. Altogether, 7 700, 5 300 and 4 300 salmon-sized targets (target strength, TS ≥ -29 dB) moving upstream were detected in 1997, 1998, and 1999, respectively. The fish migration began in all the years by early June and peaked during the second half of the month; the migration period of large salmon lasted until mid-July. The observations made by the echosounding and catch statistics were similar in this respect. In 1998 and 1999, however, more targets of TS ≥ -29 dB were detected during late summer than could be expected by the river catches of salmon. It may be that the large targets in late summer were, in fact, whitefish whose run occurred during the same time. Hydroacoustic estimation of the total salmon run at the study site was found difficult. The numbers of salmon-sized targets detected were almost the same as the numbers of salmon caught each year by fishermen. Therefore, only an index of the run timing and the size of the stock can be produced from the data. It was clear that a considerable amount of fish escaped the acoustic monitoring by using areas uncovered by the beam, such as gaps in the bottom and the surface layers of the water column near the shores. Moreover, it was found that species recognition based on TS only is not adequate in multispecies environments. Assessment of spawning runs remains, however, a key issue in the management of Baltic salmon, and with further development, the hydroacoustic monitoring may be the most viable means of doing it. © 2000 Ifremer/CNRS/INRA/IRD/Cemagref/Editions scientifiques et medicales Elsevier SAS

Males and females share many traits that have a common genetic basis; however, selection on these traits often differs between the sexes, leading to sexual conflict. Under such sexual antagonism, theory predicts the evolution of genetic architectures that resolve this sexual conflict. Yet, despite intense theoretical and empirical interest, the specific loci underlying sexually antagonistic phenotypes have rarely been identified, limiting our understanding of how sexual conflict impacts genome evolution and the maintenance of genetic diversity. Here we identify a large effect locus controlling age at maturity in Atlantic salmon (Salmo salar), an important fitness trait in which selection favours earlier maturation in males than females, and show it is a clear example of sex-dependent dominance that reduces intralocus sexual conflict and maintains adaptive variation in wild populations. Using high-density single nucleotide polymorphism data across 57 wild populations and whole genome re-sequencing, we find that the vestigial-like family member 3 gene (VGLL3) exhibits sex-dependent dominance in salmon, promoting earlier and later maturation in males and females, respectively. VGLL3, an adiposity regulator associated with size and age at maturity in humans, explained 39% of phenotypic variation, an unexpectedly large proportion for what is usually considered a highly polygenic trait. Such large effects are predicted under balancing selection from either sexually antagonistic or spatially varying selection. Our results provide the first empirical example of dominance reversal allowing greater optimization of phenotypes within each sex, contributing to the resolution of sexual conflict in a major and widespread evolutionary trade-off between age and size at maturity. They also provide key empirical evidence for how variation in reproductive strategies can be maintained over large geographical scales. We anticipate these findings will have a substantial impact on population management in a range of harvested species where trends towards earlier maturation have been observed.