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The risk associated with the presence of bacterial and fungal pathogens in recirculating aquaculture systems (RASs) has resulted in an industry‐wide need for low‐cost, safe, and effective disinfectants. The toxicity of peracetic acid (PAA) to Atlantic salmon ( Salmo salar ) eggs, fry, and fingerlings (~16.3 g) in freshwater RAS water has been previously assessed; however, its toxicity to later juvenile life‐stages was yet to be investigated. The 24‐h LC50 value of PAA was determined for parr ( = 47 g), smolt ( = 66.5 g), and post‐smolt ( = 176.7 g) Atlantic salmon in RAS water static PAA treatments. The 24‐h LC50 values were calculated using the trimmed Spearman–Karber (TSK) method and toxicity relationship analysis program (TRAP). TRAP LC50 values for parr, smolt, and post‐smolt were 4.26, 4.27, and 4.78 mg/L PAA, respectively, while TSK LC50 values for parr, smolt, and post‐smolt were 4.27, 3.94, and 4.65 mg/L PAA, respectively. These 24‐h LC50 values provide novel guidance for developing safe PAA treatment protocols for Atlantic salmon parr, smolt, and post‐smolt in freshwater RAS, although the influence of varying water quality scenarios needs to be considered.

There is increasing evidence that predation by harbour seals on out-migrating salmon smolts may be responsible for the low return of adult coho and Chinook salmon in the Salish Sea. However, little attention has been given to understanding where and when this predation occurs and the extent to which it might be conducted by few or many seals in the population. We equipped 17 harbour seals with data loggers to track seal movements and used accelerometry to infer prey encounter events (PEEs) following the release of ~384 000 coho (May 4, 2015) and ~3 million Chinook (May 14, 2015) smolts into the Big Qualicum River. We found a small proportion (5.7%) of all PEEs occurred in the estuary where salmon smolts entered the ocean—and that only one-quarter of the seals actively fed there. PEE counts increased in the estuary after both species of smolts were released. However, the response of the seals was less synchronous and occurred over a greater range of depths following the release of the smaller-bodied and more abundant Chinook smolts. Harbour seals feeding in the estuary appeared to target coho smolts at the beginning of May but appeared to pursue predators of Chinook smolts in mid-May. PEE counts in the estuary increased as tide height rose and were higher at dusk and night—especially during full moonlight. Such fine-scale behavioural information about harbour seals in relation to pulses of out-migrating smolts can be used to design mitigation strategies to reduce predation pressure by seals on salmon populations.

Land‐based recirculating aquaculture systems (RASs) for smolt production are now widely used in the salmon industry, requiring sufficiently high stocking densities to be economically viable. However, elevated densities have often been associated with poor growth and reduced fish condition. Recently, Chinook salmon producers have begun to adopt similar practices, yet the impact of smoltification density on this species at commercially relevant levels remains unstudied. This research evaluated the effects of various smoltification densities (average densities of 20.9–68.5 kg/m 3 ) on growth and survival during smoltification and subsequent seawater transfer. Mortalities were low across all density groups, with the highest density group exhibiting the lowest mortality during the freshwater phase. While slight but significant growth reduction and fin damage were observed at the highest density during smoltification, these effects did not persist after seawater transfer to a lower density that simulated transfer to marine farms. Our findings indicate that Chinook salmon can be smolted at an average density of 55.1 kg/m 3 , with a maximum density of 80.4 kg/m 3 , without adverse effects on growth and with minimal density‐related injuries in freshwater and post‐transfer phases. In cases where freshwater or nursery space is constrained, smoltification at an average density of 68.5 kg/m 3 (up to a maximum density of 95.2 kg/m 3 ) may be feasible. These results provide a basis for optimising Chinook salmon RAS operations, balancing production efficiency with fish welfare.

Mitigation measures for downstream migratory Atlantic salmon smolts (Salmo salar L.) at migration barriers usually turn out to be insufficient to enable safe and quick passage, probably due to a lack of knowledge about their behavioural responses. Combining manual 2D tracking with hydrodynamic modelling has been rarely performed but might be useful to highlight environmental factors influencing smolt behavioural tactics and the choice of a migration route. We investigated the smolt downstream migration at a hydropower plant that offers five migration routes, including a Kaplan turbine and a fish-friendly Archimedes screw. Four behavioural tactics were defined to describe the smolt expressed behaviour, which was mainly complex and hesitant. The majority of the smolts approached more than one migration route before crossing the site and the Kaplan turbine turned out to be the most approached route, contrary to the Archimedes screw. Hydrodynamic modelling highlighted that flow velocity and water depth were used as hydraulic cues in the selection of a migration route, as the smolts preferred higher flow velocities and water depths. The comprehension of the factors influencing the research behaviour at hydropower plants may be useful to design attractive mitigation measures and to guide the smolts efficiently towards safe routes.

We report the development of a multigene gene expression assay on the BioMark HD platform for the evaluation of immune competence (ImCom) in farmed Atlantic salmon. The first version of the assay included 92 genes selected on the basis of transcriptome analyses in 54 trials that challenged the immune system; annotations were taken into account to represent the key pathways of innate and adaptive immunity. ImCom was tested on samples collected from seven independent projects. Fish were reared from the start feeding to eight months in the sea at eight units in different parts of Norway. Several tissues were analyzed. Linear discriminant analysis (LDA) showed that no more than 10 genes were required to separate groups, and a set of 46 immune genes was sufficient for any task. The second version of the assay was tested in the gills of two groups of high-performing healthy smolts and in groups with intermediate and high mortality rates (IM and HM, respectively). A set of 645 gill samples from clinically healthy Atlantic salmon was used as a reference. The IM group showed general suppression of immunity. All HM group salmon were above the threshold by the squared deviation from the reference. This group showed marked upregulation of genes involved in acute stress and inflammation: mmp-9, mmp-13, hsp70, il-1b, lect2, and cathelicidin. Further work will clarify the boundaries of the norm and explore various cases of impaired immunity.

Brown trout Salmo trutta (L.) is a facultative anadromous species, where a portion of individuals in populations with access to the sea perform migrations to use the richer feeding resources. We investigated the effect of salmon lice Lepeophtheirus salmonis (Krøyer 1837) infestation on the survival and behaviour of wild trout post-smolts (average fork length = 180 mm) during their marine migration. Comparisons of the marine migratory behaviour were made between an artificially infested group (n = 74) and a control group (n = 71) in an area with low natural lice infestation pressure. Artificial infestation was estimated to cause 100% prevalence and a mean intensity of 65 lice fish−1 (mean relative intensity of 2.4 lice g−1 fish). Survival analysis showed limited statistical power but revealed lice-induced mortality, with an estimated hazard ratio of 2.73 (95% CI = 1.04−7.13) compared to the control group, when data from a previous pilot study were included. Surviving individuals in the infested group additionally responded by residing closer to fresh water while at sea, and by prematurely returning to fresh water. On average, infested fish returned to fresh water after only 18 d at sea, while control fish spent on average 100 d at sea. The residency in the inner part of the fjord and the premature return to fresh water represent an adaptive behavioural response to survive the infestation, at the probable cost of reduced growth opportunities and compromised future Fitness. Parasite · Salmon louse · Lepeophtheirus salmonis · Sea trout · Salmo trutta · Epizootic · Acoustic telemetry · Mortality · Behaviour · Field experiment

Captive breeding programs are widely used for the conservation and restoration of threatened and endangered species. Nevertheless, captive-born individuals frequently have reduced fitness when reintroduced into the wild. The mechanism for these fitness declines has remained elusive, but hypotheses include environmental effects of captive rearing, inbreeding among close relatives, relaxed natural selection, and unintentional domestication selection (adaptation to captivity). We used a multigenerational pedigree analysis to demonstrate that domestication selection can explain the precipitous decline in fitness observed in hatchery steelhead released into the Hood River in Oregon. After returning from the ocean, wild-born and first-generation hatchery fish were used as broodstock in the hatchery, and their offspring were released into the wild as smolts. First-generation hatchery fish had nearly double the lifetime reproductive success (measured as the number of returning adult offspring) when spawned in captivity compared with wild fish spawned under identical conditions, which is a clear demonstration of adaptation to captivity. We also documented a tradeoff among the wild-born broodstock: Those with the greatest fitness in a captive environment produced offspring that performed the worst in the wild. Specifically, captive-born individuals with five (the median) or more returning siblings (i.e., offspring of successful broodstock) averaged 0.62 returning offspring in the wild, whereas captive-born individuals with less than five siblings averaged 2.05 returning offspring in the wild. These results demonstrate that a single generation in captivity can result in a substantial response to selection on traits that are beneficial in captivity but severely maladaptive in the wild.

Disruption to migration is a growing problem for conservation and restoration of animal populations. Anthropogenic barriers along migration paths can delay or prolong migrations, which may result in a mismatch with migration-timing adaptations. To understand the interaction of dams (as barriers along a migration path), seasonally changing environmental conditions, timing of Atlantic salmon ( Salmo salar ) downstream migration, and ultimate migration success, we used 10 years of river temperature and discharge data as a template upon which we simulated downstream movement of salmon. Atlantic salmon is a cool-water species whose downstream migrating smolts must complete migration before river temperatures become too warm. We found that dams had a local effect on survival as well as a survival effect that was spatially and temporally removed from the encounter with the dam. While smolts are delayed by dams, temperatures downstream can reach lethal or near-lethal temperatures; as a result, the match between completion of migration and the window of appropriate migration conditions can be disrupted. The strength of this spatially and temporally removed effect is at least comparable to the local effects of dams in determining smolt migration success in the presence of dams. We also considered smolts from different tributaries, varying in distance from the river mouth, to assess the potential importance of locally adapted migration timing on the effect of barriers. Migration-initiation temperature affected modeled smolt survival differentially across tributaries, with the success of smolts from upstream tributaries being much more variable across years than that of smolts with a shorter distance to travel. As a whole, these results point to the importance of broadening our spatial and temporal view when managing migrating populations. We must consider not only how many individuals never make it across migration barriers, but also the spatially and temporally removed consequences of delays at the barriers for those individuals that successfully navigate them.

Animal migrations are costly and are often characterized by high predation risk for individuals. Three of the most oft‐assumed mechanisms for reducing risk for migrants are swamping predators with high densities, specific timing of migrations and increased body size. Assessing the relative importance of these mechanisms in reducing predation risk particularly for migrants is generally lacking due to the difficulties in tracking the fate of individuals and population‐level characteristics simultaneously. We used acoustic telemetry to track migration behaviour and survival of juvenile sockeye salmon (Oncorhynchus nerka) smolts released over a wide range of conspecific outmigration densities in a river associated with poor survival. The landscape was indeed high risk; smolt survival was poor (˜68%) over 13·5 km of river examined even though migration was rapid (generally <48 h). Our results demonstrate that smolts largely employ swamping of predators to reduce predation risk. Increased densities of co‐migrant conspecifics dramatically improved survival of smolts. The strong propensity for nocturnal migration resulted in smolts pausing downstream movements until the next nightfall, greatly increasing relative migration durations for smolts that could not traverse the study area in a single night. Smolt size did not appear to impact predation risk, potentially due to unique characteristics of the system or our inability to tag the entire size range of outmigrants. Movement behaviours were important in traversing this high‐risk landscape and provide rare evidence for swamping to effectively reduce individual predation risk.

Many salmon populations in both the Pacific and Atlantic Oceans have experienced sharply decreasing returns and high ocean mortality in the past two decades, with some populations facing extirpation if current marine survival trends continue. Our inability to monitor the movements of marine fish or to directly measure their survival precludes experimental tests of theories concerning the factors regulating fish populations, and thus limits scientific advance in many aspects of fisheries management and conservation. Here we report a large-scale synthesis of survival and movement rates of free-ranging juvenile salmon across four species, 13 river watersheds, and 44 release groups of salmon smolts (>3,500 fish tagged in total) in rivers and coastal ocean waters, including an assessment of where mortality predominantly occurs during the juvenile migration. Of particular importance, our data indicate that, over the size range of smolts tagged, (i) smolt survival was not strongly related to size at release, (ii) tag burden did not appear to strongly reduce the survival of smaller animals, and (iii) for at least some populations, substantial mortality occurred much later in the migration and more distant from the river of origin than generally expected. Our findings thus have implications for determining where effort should be invested to improve the accuracy of salmon forecasting, to understand the mechanisms driving salmon declines, and to predict the impact of climate change on salmon stocks.