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Atlantic salmon (Salmo salar) populations throughout the North Atlantic have declined in recent decades largely due to reduced marine survival, yet our understanding of marine distribution patterns and migratory routes remains limited. Here, we assigned archived individual samples (n = 3891) collected over a half century (1968–2018) throughout the North Atlantic to region of origin using range-wide genetic assignment. In the Northwest Atlantic, the distribution of assignments reinforced the importance of the Labrador Sea as an aggregation area, with 73% of all reporting groups detected. Moreover, individuals from six European reporting groups were identified in the Northwest Atlantic, and detections decreased with decreasing latitude spanning an area from Greenland to southern Newfoundland. In the Northeast Atlantic, six North American reporting groups were detected in samples from around the Faroe Islands. Based on the distribution of samples, estimates of trans-Atlantic migration distance averaged 3861 and 2889 km for North American and European salmon respectively. Our analysis highlights the widespread importance of the Labrador Sea and Faroe Islands to the species marine distribution patterns, and the prevalence of long-distance trans-Atlantic migration. Ultimately, the results suggest that environmental conditions experienced by many Atlantic salmon populations span much of the North Atlantic Ocean.

Electrofishing is a commonly used technique to assess freshwater fish population abundance, and in many programs, there has been a shift in the sampling methodologies towards less laborious techniques. These new techniques usually only provide an index of abundance and require calibration with other sampling methods such as successive removal to be used for absolute abundance estimation. Using data for juvenile Atlantic salmon (Salmo salar) collected in 400 sites sampled over 21 years in two large Canadian river catchments with a single sampling protocol, we developed a hierarchical Bayesian model to account for effort, day of sampling, area of the site, and catchment effects on the relationship between the single-pass index of abundance and the fish densities, thereby illustrating the importance of carrying out a calibration exercise on a regular basis. Our work indicates that calibration relationships can change over time even with standardized sampling protocols and that these directional changes in important components of the sampling procedure can bias the estimate of population abundance and misinform the understanding of population dynamics.

BackgroundThe experimental effects of surgically implanting fish with acoustic transmitters are likely to have negative effects on survival and behaviour. Measuring the extent of these negative effects is important if we wish to extrapolate inferences from tagged animals to un-manipulated animals. In this study, we examine the effect of surgery and post-tagging recovery time on the survival and migration rate of acoustically tagged wild Atlantic Salmon (Salmo salar)smolts through freshwater, estuarine and ocean phases of migration. Four treatment groups were used: pre-smolt captured in the fall that overwintered in a hatchery and were tagged either 75 days prior to release (winter hatchery) or within 24 h prior to release (spring hatchery) and smolt captured during the spring smolt run, tagged 24 h prior to release and released during the day (day-released) or night (night-released).ResultsThe spring hatchery treatment group served as a reference treatment group such that recovery time (comparison to winter hatchery treatment) and hatchery effects (comparison to day-released and night-released treatments) could both be discerned. The hatchery effect increased migration rate, whereas short recovery times and captivity in a hatchery negatively affected survival. These effects were most pronounced within the first 5 days and/or 48 km downstream post-release, however, the residual recovery time effects appeared to persist during the transition from the estuary into salt water.ConclusionsEven with smolts originating from the wild and spending relatively little time within the hatchery environment, post-release survival was still negatively affected. Migration speed was faster for hatchery smolts, but is likely only due to their larger size. Recovery time effects were most prominent during the initial migration period in freshwater and again in the transition from the estuary to saltwater which may be due to added stress during these transitional zones. As surgery-related bias will likely never be completely removed from telemetry studies, it is important to quantify and account for these effects in situ when making inferences on the un-manipulated component of the population.

The migration dynamics and inter-annual variation in early at-sea survival of Atlantic salmon (Salmo salar) smolts over 14 years of study are reported for four river populations located in the Gulf of St. Lawrence (Canada). Acoustically tagged smolts were monitored at three points along their migration from freshwater to the Labrador Sea, a migration extending more than 800 km at sea and a period of 2 months. A hierarchical state-space version of the Cormack–Jolly–Seber model was used to estimate apparent survival rates from incomplete acoustic detections at key points. There was a positive size-dependent probability of survival through the freshwater and estuary areas; the odds of survival of a 16 cm smolt were 1.5–1.7 times higher than for a 13.5 cm smolt, length at tagging. Length adjusted (centred to the mean fork length of smolts during the study of 14.6 cm) survivals through the estuary and nearshore waters were estimated to range between 67 and 90% for the two river populations migrating through Chaleur Bay in contrast to lower survival estimates of 28–82% for the two populations from the neighbouring Miramichi Bay. Across the 14 years of study, survival estimates varied without trend for the populations of Chaleur Bay, but declined for the populations migrating through Miramichi Bay. Survival through the Gulf of St. Lawrence was variable but generally high among years and rivers, ranging from 96% day−1 to 99% day−1. Long term, replicated studies at multiple sites using acoustically tagged smolts can provide empirical data to examine hypotheses of the location and timing of factors contributing to smolt and post-smolt mortality of salmon at sea.

Differentiating detections of a telemetered fish from those of predators that may have consumed that telemetered fish presents problems and opportunities. Previous efforts to classify predation events quantitatively have had to rely on data from unknown states of fish (i.e., unsupervised learning techniques) with the consequence that model performance cannot be refined or compared with alternate models. We circumvent this limitation by analysing acoustic telemetry track data to differentiate movement patterns of tagged striped bass (Morone saxitilis) from those of Atlantic salmon (Salmo salar) smolts, which were known to not have been predated by striped bass over a 3-year period in the Miramichi River estuary. A random forests classification model (i.e., supervised learning technique) was used to differentiate the movement patterns of these two species and the model was applied to Atlantic salmon smolt movement characteristics to provide an index of striped bass predation-derived mortality. The optimized random forests model inferred that predation rates by striped bass were highly variable between years for two smolt stocks, ranging from 1.9% to 17.5%. Spatial and temporal overlap of the two species is a likely factor defining the between stock and annual variation of predation rate estimates.

International audience; A major challenge in understanding the response of populations to climate change is to separate the effects of local drivers acting independently on specific populations, from the effects of global drivers that impact multiple populations simultaneously and thereby synchronize their dynamics. We investigated the environmental drivers and the demographic mechanisms of the widespread decline in marine survival rates of Atlantic salmon (Salmo salar) over the last four decades. We developed a hierarchical Bayesian life cycle model to quantify the spatial synchrony in the marine survival of 13 large groups of populations (called stock units, SU) from two continental stock-groupings (CSG) in North America (NA) and Southern Europe (SE) over the period 1971-2014. We found strong coherence in the temporal variation in post-smolt marine survival among the 13 SU of NA and SE. A common North Atlantic trend explains 37% of the temporal variability of the survivals for the 13 SU and declines by a factor 1.8 over the 1971-2014 time series. Synchrony in survival trends is stronger between SU within each CSG. The common trends at the scale of NA and SE capture 60% and 42% of the total variance of temporal variations, respectively. Temporal variations of the post-smolt survival are best explained by the temporal variations of sea surface temperature (SST, negative correlation) and net primary production indices (PP, positive correlation) encountered by salmon in common domains during their marine migration. Specifically, in the Labrador Sea/Grand Banks for NA populations 26% and 24% of variance is captured by SST and PP, respectively and in the Norwegian Sea for SE populations 21% and 12% of variance is captured by SST and PP, respectively. The findings support the hypothesis of a response of salmon populations to large climate induced changes in the North Atlantic simultaneously impacting populations from distant continental habitats.

Iteroparity is a bet-hedging strategy where individuals spread the risk of reproductive failure over time. The occurrence of iteroparity (i.e. proportion of repeat spawners in annual returns) varies among Atlantic salmon (Salmo salar) populations, yet information on its ecological importance is limited. We compiled multi-decadal time series on the spawning history composition of Atlantic salmon annual returns across ten populations of the northwest Atlantic and West Greenland mixed-stock fishery landings to: (i) describe spatio-temporal patterns of iteroparity at the continental scale; (ii) quantify the reproductive contributions of repeat spawners; and (iii) test the hypothesis that iteroparity acts as a population safeguard during periods of low recruitment through repeat spawners’ contributions. Despite high variability in the representation of repeat spawners among populations and years (range: 0–24.7%; average: 5.0%), we identified broad-scale spatio-temporal shifts in iteroparity, with increases in mid-latitudinal and northern populations (from 3.1% to 7.6%) and declines in southern areas (from 4.1% to 2.7%), between the 1971–1992 and 1993–2017 periods. Our findings highlight the potential for increased prevalence of iteroparity when threats are mitigated (e.g. fishing pressure), with measurable benefits to population processes manifested by the high reproductive contributions of repeat spawners, especially in years of low maiden spawner abundance.

The West Greenland Atlantic Salmon (Salmo salar) fishery represents the largest remaining mixed-stock fishery for Atlantic Salmon in the Northwest Atlantic and targets multi-sea-winter (MSW) salmon from throughout North America and Europe. We evaluated stock composition of salmon harvested in the waters off West Greenland (n = 5684 individuals) using genetic mixture analysis and individual assignment to inform conservation of North American populations, many of which are failing to meet management targets. Regional contributions to this fishery were estimated using 2169 individuals sampled throughout the fishery between 2011 and 2014. Of these, 22% were identified as European in origin. Major North American contributions were detected from Labrador (∼20%), the Southern Gulf/Cape Breton (29%), and the Gaspe Peninsula (29%). Minor contributions (∼5%) were detected from Newfoundland, Ungava, and Quebec regions. Region-specific catches were extrapolated using estimates of composition and fishery catch logs and harvests ranged from 300 to 600 and 2000 to 3000 individuals for minor and major constituents, respectively. To evaluate the temporal stability of the observed fishery composition, we extended the temporal coverage through the inclusion of previously published data (1995–2006, n = 3095) and data from archived scales (1968–1998, n = 420). Examination of the complete time-series (47 years) suggests relative stability in stock proportions since the late 1980s. Genetic estimates of stock composition were significantly associated with model-based estimates of returning MSW salmon (individual years r = 0.69, and overall mean r = 0.96). This work demonstrates that the analysis of both contemporary and archived samples in a mixed-stock context can disentangle levels of regional exploitation and directly inform assessment and conservation of Atlantic Salmon in the West Greenland interceptory Atlantic Salmon fishery.

Following advice from the International Council for the Exploration of the Seas and North Atlantic Salmon Conservation Organization, Irish salmon stocks have been managed on a river-by-river basis since 2007 with biological reference points (BRPs) based on maximum sustainable yield (MSY). A method for estimating BRPs at the river scale and the associated variability arising from observed variability in population structures and fecundities is presented here. Calculations of BRPs (referred to as conservation limits, CLs) were updated and their natural variability was included. Angling logbooks provided new river-specific weight data to give sea age and fecundity ranges, and improved estimates of river-wetted areas, to account for available nursery habitat for juveniles and river-specific carrying capacities, were introduced. To transport BRPs, Bayesian stock–recruitment analysis was re-run with an updated list of monitored rivers and smolt ages. Results were converted to salmon numbers per river in Monte Carlo simulations incorporating the variability in sea ages and fecundities. Minimum sample size rules were implemented to reduce sampling error effects. Results showed that average total CL increased by 7%, average one sea-winter (1SW) CL decreased by 5% and average multi-sea-winter (MSW) CL increased by 157%. Differences were attributed to increases in wetted areas, MSW proportions, and changes in both 1SW and MSW fecundities. While some changes were large, we believe that these updated CLs provide more accurate estimates and with associated confidence limits they are more robust, river-specific, and readily incorporated into stock assessments. As a significant improvement on their predecessors, they represent a major development for the conservation and management of salmon stocks. Additionally, the approach described is portable across stocks and has the potential to be implemented in other jurisdictions to improve the management of Atlantic salmon. Finally, this method of incorporating variation has application for the development of BRPs and management of other species.

International audience; A hierarchical Bayesian life cycle model is presented that considers spatial covariation of marine life history traits of Atlantic salmon (Salmo salar) populations in the North Atlantic. The model is based on a collective analysis of the dynamics of 13 stock units (SUs) from two continental stock groups (CSGs) in North America and Southern Europe in a single hierarchical model over the period 1971–2014. The model sets up a new assessment framework for Atlantic salmon stocks. It also provides a framework to investigate the drivers of changes in Atlantic salmon population dynamics including disentangling the effects of fisheries from those of environmental factors in a hierarchy of spatial scales. It is used to test the hypothesis of a strong spatial synchrony in marine life history dynamics of Atlantic salmon populations. The trends in two key parameters associated with the early marine phase of the life cycle are estimated: (i) the marine survival during the first summer–autumn spent at sea and (ii) the proportion of fish maturing after the first winter at sea. The results provide evidence of a decline in the marine survival together with an increase in the proportion of fish that mature after the first winter at sea, common to all SUs. Our results show an increased coherence in the covariations of trends in these two marine life history traits related to geographic proximity of SUs which support the hypothesis of a coherent response of geographically proximate Atlantic salmon populations that likely share similar migration routes.

Interceptory fisheries represent an ongoing threat to migratory fish stocks particularly when managed in the absence of stock specific catch and exploitation information. Atlantic salmon from the southern portion of the North American range may be subject to exploitation in the commercial and recreational salmon fisheries occurring in the French territorial waters surrounding St. Pierre and Miquelon off southern Newfoundland. We evaluated stock composition of Atlantic salmon harvested in the St. Pierre and Miquelon Atlantic salmon fishery using genetic mixture analysis and individual assignment with a microsatellite baseline (15 loci, 12,409 individuals, 12 regional groups) encompassing the species western Atlantic range. Individual salmon were sampled from the St. Pierre and Miquelon fishery over four years (2004, 2011, 2013, and 2014). Biological characteristics indicate significant variation among years in the size and age distribution. Nonetheless, estimates of stock composition of the samples showed consistent dominance of three regions (i.e., Southern Gulf of St. Lawrence, Gaspe Peninsula, and Newfoundland). Together salmon from these regions accounted for more than 70% of annual harvest over the decade examined. Comparison of individual assignments and biological characteristics revealed a trend of declining fresh water age with latitude of assigned region. Moreover, locally harvested Newfoundland salmon were ten times more likely to be small or one sea winter individuals whereas Quebec and Gaspe Peninsula salmon were two-three times more likely to be harvested as large or two sea winter salmon. Estimates of region specific catch were highest for salmon from the southern Gulf of St. Lawrence region ranging from 242 to 887 individuals annually. This work illustrates how genetic analysis of interceptory marine fisheries can directly inform assessment and management efforts in highly migratory marine species.

Fisheries targeting mixtures of populations risk the overutilization of minor stock constituents unless harvests are monitored and managed. We evaluated stock composition and exploitation of Atlantic salmon (Salmo salar) in a subsistence fishery in coastal Labrador, Canada, using genetic mixture analysis and individual assignment with a microsatellite baseline (15 loci, 11 829 individuals, 12 regional groups) encompassing the species’ western Atlantic range. Bayesian and maximum likelihood mixture analyses of fishery samples over 6 years (2006–2011; 1772 individuals) indicate contributions of adjacent stocks of 96%–97%. Estimates of fishery-associated exploitation were highest for Labrador salmon (4.2%–10.6% per year) and generally

Dixon, H. J., Power, M., Dempson, J. B., Sheehan, T. F., and Chaput, G. 2012. Characterizing the trophic position shift in Atlantic salmon (Salmo salar) from freshwater to marine life-cycle phases using stable isotopes. – ICES Journal of Marine Science, 69: 1646–1655. Marine survival and recruitment of Atlantic salmon (Salmo salar) are commonly thought to be influenced by linkages between marine temperature and growth. Salmon are opportunistic feeders that are likely to be affected by the quality and quantity of prey available. During the marine phase, salmon often target larger zooplankton and fish, with a preference for fish over crustaceans. European salmon recruitment appears to be linked to forage abundance, which affects post-smolt growth critically during the first summer at sea, but similar linkages have not been shown for North American populations. Here, trophic differences within and among populations and life stages of Atlantic salmon during the freshwater and marine life-history phases are investigated. Stable isotope methods were used to characterize trophic dynamics by sampling smolts and returning adult survivors from rivers spanning a broad geographic range in Canada (southern Labrador to the Bay of Fundy), as well as non-maturing salmon sampled at West Greenland. Analyses indicate that salmon undergo a marked change in feeding as they migrate from freshwater and show the expected high reliance on pelagic foodwebs in the marine environment. Documented changes in ocean climate, pH, and the possibility of regime shifts are likely to have significant impacts on pelagic feeding fish, including Atlantic salmon. Due to the similar marine feeding ecology suggested here for adults from different age groups, these changes could have a widespread effect on multiple life-history stages of Atlantic salmon.

Reid, J. E., and Chaput, G. 2012. Spawning history influence on fecundity, egg size, and egg survival of Atlantic salmon (Salmo salar) from the Miramichi River, New Brunswick, Canada. – ICES Journal of Marine Science, 69: 1678–1685. There is an increasing abundance of repeat spawners in the Atlantic salmon (Salmo salar) population in the Miramichi River that, owing to their larger size, can be expected to contribute greater egg depositions and better offspring survival than primarily maiden spawning populations. Currently, there is little information on the reproductive contribution of repeat-spawning salmon. In this study, the fecundity, egg size, and egg survival for 235 maiden and repeat-spawning wild female Atlantic salmon were examined over a period of 3 years. Relative fecundity did not differ among the largest body size group of salmon, but consecutive repeat spawners had a higher fecundity than maiden 2SW salmon and alternate repeat spawners. Egg diameter also increased with body size, but consecutive repeat spawners had significantly smaller eggs, in absolute terms and relative to their body size, than maiden 2SW salmon and alternate repeat spawners. The egg survival rate of consecutive repeat spawners was significantly lower than that of 2SW maiden salmon and alternate repeat spawners. Consecutive repeat spawners are different in that egg diameter and egg survival did not follow the general positive association with female body size, probably because of the short time that they spend reconditioning in the ocean and consequently their available energy reserves.

Chaput, G., and Benoît, H. P. 2012. Evidence for bottom–up trophic effects on return rates to a second spawning for Atlantic salmon (Salmo salar) from the Miramichi River, Canada. – ICES Journal of Marine Science, 69: 1656–1667. Increased return rates of consecutive repeat-spawning Atlantic salmon (Salmo salar) have been noted in the Miramichi River during the past two decades, and the short period for their reconditioning at sea suggests that they occupy the southern Gulf of St Lawrence ecosystem. A 40-year time-series of observations was used to examine linkages between return rates to a second spawning for Atlantic salmon in the Miramichi River and changes in the small fish community of the southern Gulf of St Lawrence that is potential prey for adult salmon. The positive association between the variations in the return rates of repeat spawners and the variations in the small fish biomass index early in the reconditioning year at sea provides evidence that abundant food supplies after return to sea following first spawning may be beneficial for the survival of Atlantic salmon to a second consecutive spawning. In contrast, no association was found between prey availability and return rates of alternate repeat spawners that presumably recondition outside the Gulf of St Lawrence.

Chaput, G. 2012. Overview of the status of Atlantic salmon (Salmo salar) in the North Atlantic and trends in marine mortality. – ICES Journal of Marine Science, 69: 1538–1548. Since the early 1980s, the ICES Working Group on North Atlantic Salmon has collated and interpreted catch data, exchanged information on research initiatives, and provided advice to managers in support of conservation efforts for Atlantic salmon. During the past three decades, the annual production of anadromous Atlantic salmon from more than 2000 rivers draining into the North Atlantic has been less than 10 million adult-sized salmon. This represents a minor component, by number and biomass, of the pelagic ecosystem in the North Atlantic Ocean. Ideally, Atlantic salmon would be assessed and managed based on river-specific stock units, the scale that best corresponds to the spawner to recruitment dynamic. In reality, comparatively few river-specific assessments are available for either the Northwest or the Northeast Atlantic. The marine survival of Atlantic salmon is low and, based on return rates of smolts to adults from monitored rivers, has declined since the mid- to late 1980s. Abundance has declined more severely for the multi-sea-winter components, and especially in the southern areas of the species' range. Common patterns in abundance, inferred at the level of stock complex in the North Atlantic, suggest that broad-scale factors are affecting productivity and abundance and that they are acting throughout the salmon's time at sea.

Sheehan, T. F., Reddin, D. G., Chaput, G., and Renkawitz, M. D. 2012. SALSEA North America: a pelagic ecosystem survey targeting Atlantic salmon in the Northwest Atlantic. – ICES Journal of Marine Science, 69: 1580–1588. Pelagic ecosystem surveys were conducted in the Labrador Sea during 2008 and 2009 as part of SALSEA North America. In total, 107 Atlantic salmon (Salmo salar) were captured using a pelagic surface trawl and multipanel surface gillnets. Surface trawling provided a broad spatial sampling of the fish and macroinvertebrate communities in the upper 10 m of the water column, but caught few salmon (23). Gillnetting was more effective at capturing post-smolt (60) and adult (24) salmon. Multiple smolt cohorts were captured, indicating that post-smolts and returning adults from different rivers in North America have similar autumnal habitat requirements. Post-smolts were caught at night and in water temperatures exceeding 10°C, both novel results. Post-smolts and adults consumed similar and diverse prey species, although Themisto compressa was the most important prey item. Intestinal macroparasite loads were substantial and could be a significant source of mortality. Concurrent planktonic assemblage and oceanographic conditions were also quantified. A full exploration of these data, historical datasets, and parallel data collected during SALSEA Greenland and SALSEA-Merge will further understanding of the ecology of marine-phase Atlantic salmon and inform investigations into stock-specific differences in marine productivity.

Acoustic telemetry was used to describe the behavior of individual striped bass Morone saxatilis and their use of the Miramichi River estuary during two consecutive spawning seasons in 2004 and 2005. In both years, prespawning striped bass staged in the lower and middle sections of the Miramichi River estuary downstream from the spawning area. Males and females moved in synchrony from the staging area to the spawning grounds in the Northwest Miramichi River. The dates of arrival at the spawning grounds were similar between sexes in both years, but significantly later (by about a week) in 2005. There were no significant differences in average daily water temperature on the dates of arrival at the spawning grounds for male and female striped bass, but water temperatures on the arrival dates were significantly cooler in 2005. Increases in temperature rather than the absolute temperature was the apparent cue initiating the movements of striped bass onto the spawning grounds. Females occupied the spaw...

Friedland, K. D., Chaput, G., and MacLean, J. C. 2005. The emerging role of climate in post-smolt growth of Atlantic salmon. e ICES Journal of Marine Science, 62: 1338e1349. Though it is well established that mortality during the post-smolt year is critical in shaping recruitment patterns in Atlantic salmon (Salmo salar L.), the controlling mechanism for North Atlantic stocks remains elusive. The emerging paradigm is based on relationships between survival and ocean thermal conditions during the early marine phase. The survival of post-smolts from both Europe and North America has been correlated to sea surface temperature conditions during their first month at sea. In addition, data for European fish support the hypothesis that growth mediates survival during that time. Thus, the working model for a salmon recruitment mechanism is analogous to those proposed for other fish species. We present growth data for two stocks, the Girnock Burn, which is a tributary to the River Dee, Scotland, and the Margaree River, Canada. Circuli spacing data for Girnock Burn fish suggest post-smolt growth is negatively correlated with temperature in the migration corridors during the first months at sea, while post-smolt growth of Margaree fish appears to be positively correlated with temperature. Growth is either patterned by a physiological response to an optimal temperature, or is co-varying with some ecosystem effect on growth, and the growth response might affect mortality and maturation of the stocks. Published by Elsevier Ltd on behalf of International Council for the Exploration of the Sea.

The paper presents the data, the models, and the approach for the provision of management advice for a high seas mixed stock fishery on Atlantic salmon (Salmo salar L.). The approach incorporates observation errors, model uncertainty, and considers a possible shift in the productivity of Atlantic salmon. The risk analysis framework further incorporates uncertainty in the fishery harvest characteristics and presents the catch advice as probabilities of meeting or exceeding the conservation objectives relative to catch options. There is very strong evidence from the analyses that there has been a phase shift in productivity of Atlantic salmon of North American origin in the Northwest Atlantic. The change in productivity likely resulted from a change in marine survival which occurred in the early 1990s and has persisted to date. When the uncertainties in the input data are considered, the most parsimonious models suggest that there has been a shift in absolute abundance independent of variations in the spawner index contributing to the recruitment. There continues to be a large amount of uncertainty in the measures of abundance and population dynamics of Atlantic salmon. Uncertainty in the understanding of population dynamics does not necessarily equate to uncertainty in management advice. If model results suggest that spawning objectives are unattainable even when harvest rates are zero, then any harvest level will either accelerate the rate of decline if the model prediction is correct or diminish the probability of recovery if the model prediction is wrong.

Hydrometeorological conditions are important determinants of the distribution and productivity of Atlantic salmon Salmo salar in freshwater habitats. Environmental conditions, such as temperature, precipitation, and streamflow, affect an aquatic organism's growth rate, developmental rate, behavior, and ultimate survival. In the Miramichi River, New Brunswick, Canada, climatic and hydrological conditions have been monitored for over 30 years, providing a unique opportunity to examine long-term changes in temperature, precipitation, and streamflow and their effects on juvenile Atlantic salmon. Average air temperature in the Miramichi region increased over time, particularly in spring and summer months. Coincident changes in water temperature were not observed, with only summer water temperature increasing in the Southwest Miramichi River. Extreme summer water temperatures in the Southwest Miramichi River regularly exceeded the upper temperature threshold for growth of Atlantic salmon (22.5°C). Few ...

Atlantic salmon, as a result of their population structure and behaviour, are potentially subject to a complex array of fisheries, ranging from those within rivers harvesting single stocks, to distant-water mixed stock fisheries that harvest fish from different countries, stock complexes, and continents. In addition, estuarine and in-river fisheries may catch fish from more than one stock or stock component, where these are present. One of the main challenges in managing salmon across this range of fisheries is to account for the differing status of stocks with respect to safe biological limits, noting that stocks of differing productivity may require different harvest strategies. Also, the existence of sequential harvest in different fisheries provides unique challenges, because decisions in an individual fishery cannot be made in isolation of the impacts of other fisheries on those stocks. We illustrate the uncertainties and complexities involved in managing mixed stocks of salmon, whether in home-waters or in distant-water fisheries, and examples are given to illustrate how science and management are, or should be, developing to face these challenges.

The probability of achieving the spawning requirement objective of Atlantic salmon (Salmo salar L.) is defined by the stochastic properties of small numbers and biological characteristics of the stock. The uncertainty in achieving the spawning escapement objective is greater for small stocks than for large ones, such that measures of annual performance are more variable for small stocks. Summing individual river spawner requirements into a regional requirement reduces the probability of meeting the objectives simultaneously in all rivers. Variations in productivity among stocks, when not accounted for, can result in under-escapement in areas of lower productivity. The impact of mixed-stock fisheries can be most important for small stocks, and especially if these are of low relative productivity. Increasing the regional spawner requirement in an attempt to compensate for lower productivity may alleviate the problem somewhat, but it is not a guaranteed solution to the challenge of protecting all stocks, specifically those of low productivity in mixed-stock fishery situations. Each mixed-stock fishery situation can be evaluated on a case-by-case basis using Monte Carlo techniques.

Climate change models predict a 2 to 6° C increase in air temperature within the next 100 years in the Maritime Provinces of eastern Canada. Higher air temperatures are expected to contribute to increased water temperatures, alterations in stream flow conditions, and ultimately reductions in fish growth. Mean annual size-at-age of juvenile Atlantic salmon Salmo salar decreased in the Northwest Miramichi and Southwest Miramichi Rivers between 1971-1999. Lengths-at-age of juveniles were significantly correlated between the two rivers. For Atlantic salmon parr, stronger associations between inter-cohort fork length (L F ) than intra-cohort L F were observed, suggesting that environmental conditions in the current year of growth have the more significant effects on size of age 2 year parr than conditions encountered the previous year by age 1 year parr of the same cohort. Fork lengths of parr were significantly and negatively associated with spring air and water temperatures. In the Miramichi River, increases in air and water temperature as predicted from climate change models may adversely affect growth of juvenile Atlantic salmon parr, reducing the overall productivity of the Atlantic salmon populations in this region.

Anadromous Atlantic salmon (Salmo salar) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9142 individuals from 149 sampling locations and data from a medium-density SNP array providing genotypes for >3000 SNPs for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite data set and with neutral SNPs identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNPs did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNPs and outlier SNPs. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNPs only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America.

Atlantic salmon (Salmo salar) management in eastern Canada is based on ensuring that there is sufficient spawning escapement to meet an egg deposition target that maximizes the production of smolts. Using available egg deposition to smolt production data, we show that the present strategy of basing spawning targets on the presence-absence of lacustrine habitat for the rearing of juvenile salmon is a valid approach. We further show that a general smolt production model that accounts for this difference in available habitat when combined with the biological characteristics of the recruiting adults provides river-specific spawning targets. Targets corresponding to maximum yield tend to be less than half the target values currently used. A target representing the egg deposition for 90% of maximum yield serves as an example of a risk-averse strategy. The lower target values relative to those currently used are in large part determined by low sea survivals. The targets that we derived for four example rivers would correspond to the currently used target egg depositions if the long-term sea survivals were 2-3 times those observed in the last 6 years.

We developed a hierarchical Bayesian integrated life cycle model for Atlantic salmon that improves on the stock assessment approach currently used by ICES and provides some interesting insights about the population dynamics of a stock assemblage. The model is applied to the salmon stocks in eastern Scotland. It assimilates a 40-year (1971–2010) time-series of data compiled by ICES, including the catches in the distant water fisheries at Faroes and West Greenland and estimates of returning fish abundance. Our model offers major improvements in terms of statistical methodology for A. salmon stock assessment. Uncertainty about inferences is readily quantified in the form of Bayesian posterior distributions for parameters and abundance at all life stages, and the model could be adapted to provide projections based on the uncertainty derived from the estimation phase. The approach offers flexibility to improve the ecological realism of the model. It allows the introduction of density dependence in the egg-to-smolt transition, which is not considered in the current ICES assessment method. The results show that this modifies the inferences on the temporal dynamics of the post-smolt marine survival. In particular, the overall decrease in the marine survival between 1971 and 2010 and the sharp decline around 1988–1990 are dampened when density dependence is considered. The return rates of smolts as two-sea-winter (2SW) fish has declined in a higher proportion than return rates as one-sea-winter (1SW) fish. Our results indicate that this can be explained either by an increase in the proportion maturing as 1SW fish or by an increase in the mortality rate at sea of 2SW fish, but the data used in our analyses do not allow the likelihood of these two hypotheses to be gauged.

Trial experiments to develop an in situ method for determining effects of short-term exposure to contaminants on salmon during the sensitive smolt stage were carried out. Wild Atlantic salmon ( Salmo salar ) smolts were caged at various estuarine locations in northeast New Brunswick, Canada at different levels of anthropogenic impact in 2000 and 2001. Survival, growth (weight and K ), and feeding ( δ 13 C and δ 15 N) parameters were measured following summer grow-out at a hatchery. A summary of distributions of the four parameters indicated that smolts caged at locations receiving lower levels of industrial and municipal discharges feed and grow better than those caged at sites receiving higher levels. The findings, however, were not repeatable between the 2 years studied. The observed inconsistency between years may be a consequence of the relatively low concentrations of alkylphenolic contaminants (putative causative agents) and overall steroidogenic potency in river water at the time of caging. Differences in temperature and salinity from 2000 to 2001 may have further confounded comparisons across treatments and between years. In future studies, caging in closer proximity to industrial and municipal discharges or in systems with higher concentrations of waterborne contaminants or impoundments would help further the assessment and applicability of this methodology and allow a more robust comparison of smolt feeding and growth among reference and exposure sites.