Atlantic Salmon Fry Research Articles

Size-related habitat use in juvenile Atlantic salmon: the importance of intercohort competition

In stream-living salmonids, an underlying mechanism for the critical period after emergence has generally been assumed to be size-dependent swimming capacity constraining fry (age-0) to low-velocity habitats with reduced food availability and intense competition. A further plausible mechanism is that intercohort habitat exclusion confines fry to marginal habitats. This possibility was tested using a seminatural stream with 16 test arenas, each comprising one high-velocity, deep habitat and one low-velocity, shallow habitat. We observed groups of newly emerged Atlantic salmon (Salmo salar) fry, either alone or in sympatry with one or two age-1 salmon. Salmon fry used high-velocity areas (42.2 ± 0.4 cm·s−1) most extensively in the absence of intercohort competition, where they obtained more food than in low-velocity areas (3.3 ± 0.3 cm·s−1), even though foraging efficiency was lower (though not significantly so). In sympatry with older cohorts, fry increased their use of the low-velocity habitat, with a reduced foraging activity, suggesting that strong older cohorts in natural populations may have the potential to influence the strength of the recruiting cohort by negative density dependence due to interference competition for habitat.

Assessing the transferability of hydraulic habitat models for juvenile Atlantic salmon

Hydraulic habitat models are logistically and technically challenging and expensive to produce. They are therefore frequently transferred between rivers, often with different environmental conditions, without validation. Although studies have recognised problems with model transfer, few have assessed the consequences for model predictions. This study investigated the local (within sub-catchment) transfer of hydraulic habitat models developed for Atlantic salmon (Salmo salar) fry. Two adjacent reaches were chosen for the study, each containing pool, riffle, glide and run habitats. Detailed topographic surveys were used to develop hydraulic models for the study reaches. Substrate and cover were characterised using transects. Seasonal fish habitat use was characterised by electrofishing. Uniform saturation stocking was employed to ensure standard starting densities across all habitats. Generalised additive models were fitted to fry abundance data. Depth, velocity, dominant substrate and cover were used as predictor variables. The distribution of depth, velocity, dominant substrate and cover differed between the two reaches, but was consistent within reaches across seasons. Substrate exhibited the greatest inter-reach difference. Velocity and depth were the most important individual predictors of fry abundance, with the highest densities observed at moderate velocities (∼0.4ms−1) and low depths (∼0.1m) across all seasons. When models were transferred locally between reaches, those that were adjusted for inter-reach differences in mean fry abundance (i.e. those predicting changes in relative abundance) performed better than those transferred without adjustment. Complex models that included substrate and cover typically explained some of the variation in abundance in the transferred reach but performed less well than models containing hydraulic parameters alone. This potentially reflected inter-reach differences in the distribution of substrate and cover. This study suggests that (1) uniform stocking is useful for examining habitat-abundance relationships free from the influence of patchy egg deposition; (2) habitat models should be developed at sites offering maximum environmental complexity at a local level; (3) scientists and managers should avoid transferring models between locations with different environmental characteristics, especially in the absence of model validation; (4) complex models should be avoided, and those containing hydraulic variables alone should be considered, if predictions of habitat quality are to be made at new sites.

Gene expression comparison of resistant and susceptible Atlantic salmon fry challenged with Infectious Pancreatic Necrosis virus reveals a marked contrast in immune response.

BackgroundInfectious Pancreatic Necrosis (IPN) is a highly contagious birnavirus disease of farmed salmonid fish, which often causes high levels of morbidity and mortality. A large host genetic component to resistance has been previously described for Atlantic salmon (Salmo salar L.), which mediates high mortality rates in some families and zero mortality in others. However, the molecular and immunological basis for this resistance is not yet fully known. This manuscript describes a global comparison of the gene expression profiles of resistant and susceptible Atlantic salmon fry following challenge with the IPN virus.ResultsSalmon fry from two IPNV-resistant and two IPNV-susceptible full sibling families were challenged with the virus and sampled at 1 day, 7 days and 20 days post-challenge. Significant viral titre was observed in both resistant and susceptible fish at all timepoints, although generally at higher levels in susceptible fish. Gene expression profiles combined with gene ontology and pathway analyses demonstrated that while a clear immune response was observed in both resistant and susceptible fish, there were striking differences between the two phenotypes. The susceptible fish showed marked up-regulation of genes related to cytokine activity and inflammatory response that evidently failed to protect against the virus. In contrast, the resistant fish demonstrated a less pronounced immune response including up-regulation of genes relating to the M2 macrophage system.ConclusionsWhile only the susceptible phenotype shows appreciable mortality levels, both resistant and susceptible fish can become infected with IPNV. Susceptible fish are characterized by a much larger, yet ineffective, immune response, largely related to cytokine and inflammatory systems. Resistant fish demonstrate a more moderate, putative macrophage-mediated inflammatory response, which may contribute to their survival.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2600-y) contains supplementary material, which is available to authorized users.

Utilization of acid hydrolysed phosphorous from herring bone by-products in feed for Atlantic salmon (Salmo salar) start-feeding fry

The aim of this study was to test the efficacy of a new marine P ingredient from the bone fraction of herring by-products by evaluating the dietary impacts on growth, mineralization and skeletal development in Atlantic salmon fry. Five experimental diets were produced from a fish meal based diet, only differing in the dietary P source and level; low P control (5.5g/kg soluble P), intermediate P (6.5g/kg soluble P) and high P (8.0g/kg soluble P) from either fish bone hydrolysate (FBH1, FBH2) or from NaH2PO4 (NaP1, NaP2). The diets were given for 168days from start of feeding (0.17g fish) until 24weeks of feeding (33g). Weight and specific growth rate did not reveal diet dependent differences except in the initial 10week feeding period where fish fed FBH1 showed lower growth as compared to fish fed the Na–P diets. Mineralization of fish evaluated by whole body and bone ash and mineral contents showed diet dependent differences that were related to dietary P level, but not to P source. Fish fed the low P diet showed clear P deficiency signs with significantly reduced tissue ash and mineral content, reduced whole body Ca:P ratio and morphological deviation from the normal. Histological evaluation of the vertebrae after 19weeks of feeding (15g) revealed stagnation in cartilage development, with accumulation of mature chondrocytes in fish fed low P control and FBH1 diet. FTIR showed that fish fed FBH1 had lower mineralization and increased cross binding in the vertebral end plates. Fish fed FBH2 resembled the positive NaP1 control. Real time qPCR analyses confirmed the histological results, by showing up-regulating of col10a1 (a marker for mature cartilage) in fish fed low P diet and FBH1. Osteocalcin (a marker for mineralization) was also activated in fish fed the low P diet and FBH1, possibly indicating a compensatory regulation in response to inadequate P. The dietary impacts on histology, FTIR and qPCR analyses in the FBH1 fed fish disappeared at 24weeks of feeding (33g). In conclusion, the results showed that P solubilized from bone fraction of herring can be efficiently utilized for growth, mineralization and bone development in Atlantic salmon fry. However, in the initial weeks of feeding, the FBH was a less efficient P source compared to NaP. Overall, the data suggest that P from fish bone hydrolysate is more suited for fish of minimum 15g size. Statement of relevanceThe phosphate (P) rock reserve is a limited resource worldwide. Increased efficiency in the utilization of P and improved recycling of P from waste and manures are examples that could reduce the industry's vulnerability to the limited P supply while also reducing the negative environmental impacts. Recycling of P from fishery offal and development of new available P ingredients to farmed fish will significantly improve the sustainability of the aquaculture industry and reduce the environmental loss. In this paper we show that P hydrolysed from herring bone by-product is as efficient and good for salmon fry as commercially available NaP-salts.

Oral vaccination of first-feeding Atlantic salmon, Salmo salar L., confers greater protection against yersiniosis than immersion vaccination

Yersinia ruckeri is a ubiquitous pathogen of finfish capable of causing major mortalities in farmed fish stocks. It can be transmitted vertically from parent to progeny as well as horizontally in the water column from both clinically infected fish and asymptomatic carriers, and is consequently capable of infecting fish at early stages of development. Immunisation strategies that can protect small fry are therefore critical for the effective management of fish health, as is the ability to detect covertly infected fish. In this study, first-feeding Atlantic salmon fry (<0.5g) were immunised either by oral administration of a microencapsulated Y. ruckeri vaccine formulation (0.38g initial weight), or via immersion in bacterin suspension (0.26g), with and without a booster immersion vaccination at 1g size. Protection in groups receiving only immersion immunisation did not differ significantly from untreated controls when challenged with Y. ruckeri at approximately 5g size, while orally immunised fish were significantly better protected than untreated controls (F=4.38, df=4,10, P=0.026), with RPS varying between 29.4% (ORAL) and 51% (ORAL+DIP). A quantitative real-time PCR assay was used to successfully detect covertly infected fish among challenge survivors, indicating more than 50% of surviving fish in each group were infected with no significant differences between immunised fish and untreated controls.

Alginate Microencapsulation for Oral Immunisation of Finfish: Release Characteristics, Ex Vivo Intestinal Uptake and In Vivo Administration in Atlantic Salmon, Salmo salar L.

This study examined the feasibility of alginate microcapsules manufactured using a low-impact technology and reagents to protect orally delivered immunogens for use as immunoprophylactics for fish. Physical characteristics and protein release kinetics of the microcapsules were examined at different pH and temperature levels using a microencapsulated model protein, bovine serum albumin (BSA). Impact of the microencapsulation process on contents was determined by analysing change in bioactivity of microencapsulated lysozyme. Feasibility of the method for oral immunoprophylaxis of finfish was assessed using FITC-labelled microcapsules. These were applied to distal intestinal explants of Atlantic salmon (Salmo salar) to investigate uptake ex vivo. Systemic distribution of microcapsules was investigated by oral administration of FITC-labelled microcapsules to Atlantic salmon fry by incorporating into feed. The microcapsules produced were structurally robust and retained surface integrity, with a modal size distribution of 250-750 nm and a tendency to aggregate. Entrapment efficiency of microencapsulation was 51.2 % for BSA and 43.2 % in the case of lysozyme. Microcapsules demonstrated controlled release of protein, which increased with increasing pH or temperature, and the process had no significant negative effect on bioactivity of lysozyme. Uptake of fluorescent-labelled microcapsules was clearly demonstrated by intestinal explants over a 24-h period. Evidence of microcapsules was found in the intestine, spleen, kidney and liver of fry following oral administration. Amenability of the microcapsules to intestinal uptake and distribution reinforced the strong potential for use of this microencapsulation method in oral immunoprophylaxis of finfish using sensitive immunogenic substances.

A laboratory experiment to determine the dispersal response of Atlantic salmon (Salmo salar) fry to street light intensity

Summary The effect of a range of ecologically relevant broader spectrum street light intensities on the dispersal timing of Atlantic salmon (Salmo salar) fry was investigated to assess the efficacy of a proposed management tool, the dimming of lamp brightness, for reducing the ecological consequences of artificial night light on aquatic ecosystems. Dispersal timing under treatment street light intensities of 8, 4, 2 and 1 lux was compared to that under a control night light intensity of 0.1 lux, representative of approximately half that experienced from a full moon. Dispersal timing was significantly delayed (by 1.4 to 2.2 days), and its diel pattern significantly disrupted under the treatment street light intensities. However, the dose–response for both delay and disruption effects was not linear, with a strong effect apparent at 1 lux, and little or no additional impact seen when the light intensity was increased further. Under control conditions, the mean time of dispersal was 3:58 h after dusk, with very few fry (&lt;4%) dispersing during daylight hours. For the treatment street light intensities, the mean time of dispersal of fry was significantly later (5:31 h after dusk at 1 lux) at night, and a much wider distribution of fry dispersal times was apparent with many more fry (19% at 1 lux) dispersing during daylight hours. Survival to dispersal in aquarium conditions was high (≥97.8%) and comparable in the control and treatment street light intensities. However, in the wild, the period between fry dispersal and the establishment of feeding territories is considered to be of critical importance in the dynamics of salmonid populations and any disruption may significantly increase predation and reduce fitness. The findings of this aquarium‐based investigation suggest that the dimming of lamp brightness has little potential as a successful management strategy to reduce the disruptive impact of street lighting surrounding freshwater ecosystems. We therefore recommend that the best course of action is to maintain and increase natural unlit areas.

Effects of emergence time and early social rearing environment on behaviour of Atlantic salmon: consequences for juvenile fitness and smolt migration.

Consistent individual differences in behaviour have been well documented in a variety of animal taxa, but surprisingly little is known about the fitness and life-history consequences of such individual variation. In wild salmonids, the timing of fry emergence from gravel spawning nests has been suggested to be coupled with individual behavioural traits. Here, we further investigate the link between timing of spawning nest emergence and behaviour of Atlantic salmon (Salmo salar), test effects of social rearing environment on behavioural traits in fish with different emergence times, and assess whether behavioural traits measured in the laboratory predict growth, survival, and migration status in the wild. Atlantic salmon fry were sorted with respect to emergence time from artificial spawning nest into three groups: early, intermediate, and late. These emergence groups were hatchery-reared separately or in co-culture for four months to test effects of social rearing environment on behavioural traits. Twenty fish from each of the six treatment groups were then subjected to three individual-based behavioural tests: basal locomotor activity, boldness, and escape response. Following behavioural characterization, the fish were released into a near-natural experimental stream. Results showed differences in escape behaviour between emergence groups in a net restraining test, but the social rearing environment did not affect individual behavioural expression. Emergence time and social environment had no significant effects on survival, growth, and migration status in the stream, although migration propensity was 1.4 to 1.9 times higher for early emerging individuals that were reared separately. In addition, despite individuals showing considerable variation in behaviour across treatment groups, this was not translated into differences in growth, survival, and migration status. Hence, our study adds to the view that fitness (i.e., growth and survival) and life-history predictions from laboratory measures of behaviour should be made with caution and ideally tested in nature.

Using novel methodologies to examine the impact of artificial light at night on the cortisol stress response in dispersing Atlantic salmon (Salmo salar L.) fry.

Artificial light at night (ALAN) is gaining recognition as having an important anthropogenic impact on the environment, yet the behavioural and physiological impacts of this stressor are largely unknown. This dearth of information is particularly true for freshwater ecosystems, which are already heavily impacted by anthropogenic pressures. Atlantic salmon (Salmo salar L.) is a species of conservation and economic importance whose ecology and behaviour is well studied, making it an ideal model species. Recent investigations have demonstrated that salmon show disrupted behaviour in response to artificial light; however, it is not yet clear which physiological processes are behind the observed behavioural modifications. Here, two novel non-invasive sampling methods were used to examine the cortisol stress response of dispersing salmon fry under different artificial lighting intensities. Fish egg and embryos were reared under differing ALAN intensities and individual measures of stress were subsequently taken from dispersing fry using static sampling, whereas population-level measures were achieved using deployed passive samplers. Dispersing fry exposed to experimental confinement showed elevated cortisol levels, indicating the capacity to mount a stress response at this early stage in ontogenesis. However, only one of the two methods for sampling cortisol used in this study indicated that ALAN may act as a stressor to dispersing salmon fry. As such, a cortisol-mediated response to light was not strongly supported. Furthermore, the efficacy of the two non-invasive methodologies used in this study is, subject to further validation, indicative of them proving useful in future ecological studies.

Carcass analogues provide marine subsidies for macroinvertebrates and juvenile Atlantic salmon in temperate oligotrophic streams

Summary Anadromous fish populations entering freshwater ecosystems provide organic matter and marine‐derived nutrients during spawning and subsequent mortalities of adults. Dams and other impediments to connectivity in rivers and streams have affected anadromous fish populations in many regions and prevented or reduced this influx of organic materials and nutrients. This study used historical data on the timing of delivery of marine‐derived nutrients; we added a carcass analogue (pellets made from the carcasses of Chinook salmon, Oncorhynchus tschawytcha) to simulate potential effects of restored access of anadromous fish to streams. We used stable isotopes to document the extent of nutrient incorporation of nitrogen and carbon from the carcass analogue by macroinvertebrates and juvenile Atlantic salmon (Salmo salar) in salmon nursery streams. We stocked four headwater streams that historically hosted spawning Atlantic salmon and sea lamprey (Petromyzon marinus) in Maine, U.S.A. with Atlantic salmon fry and simulated timing of nutrient addition by spawning sea lamprey in the early summer and Atlantic salmon in the autumn. Macroinvertebrates and Atlantic salmon assimilated nitrogen (12–57% of total N) and carbon (21–65% of total C) from the added pellets, and the magnitude and duration of enrichment varied temporally and with macroinvertebrate functional feeding group. Assimilation of nutrients from carcass analogues was both direct and indirect, and a nutrient legacy was evident in the second year of sampling. Incorporation of nutrients from the pellets at a range of heights in the food web demonstrated the potential for marine‐derived subsidies to contribute to freshwater ecosystem processes in Atlantic salmon nursery streams.

A novel in vivo model for rapid evaluation of Aliivibrio salmonicida infectivity in Atlantic salmon

Cold-Water Vibriosis (CWV) is a well-known disease which significantly influences the aquaculture industry of the North Atlantic coasts (Egidius et al., 1981). Due to wide implementation of apparently effective vaccines in all farmed Atlantic salmon (Salmo salar) the phenomenon of CWV was not a research focus for nearly two decades (Lillehaug, 1990, 1991). Although prevented by vaccination since the 1980s, CWV was again reported in farmed, vaccinated Atlantic salmon in 2012 (Johansen, 2012). Since CWV emerged as a recognized infection in the early 1980s (Egidius et al., 1981; Sørum et al., 1990), several attempts have been undertaken to identify the initial steps of the pathogenesis of CWV. However, no final explanation to how Aliivibrio (Vibrio) salmonicida enters the host has been reported. In this study, we present a novel and simple model for analyzing the initial steps of CWV. Our results demonstrate that initiation of CWV is more complex than was previously thought. In particular, A. (V.) salmonicida enters the host much faster than was anticipated. To identify the initial pathogenic steps in CWV, Atlantic salmon fry were differentially immersed in a suspension of A. (V.) salmonicida and the number of bacteria entering the host was measured. The putative roles of the gills, skin, rectal and oral routes as well as the role of the fin blood vessels as portals of infection were investigated. Bacterial counts were obtained from freshly collected blood samples, thus representing immediate snapshots of the early stages of host invasion. The results clearly indicated that skin was a major route of infection. The experimental design reported in this study provides a new, rapid and cost-effective model for studying CWV.

Stress-Induced Reversion to Virulence of Infectious Pancreatic Necrosis Virus in Naïve Fry of Atlantic Salmon (Salmo salar L.)

We have studied stress-induced reversion to virulence of infectious pancreatic necrosis virus (IPNV) in persistently infected Atlantic salmon (Salmo salar L.) fry. Naïve fry were persistently infected with a virulent strain (T217A221 of major structural virus protein 2, VP2) or a low virulent (T217T221) variant of IPNV. The fry were infected prior to immunocompetence as documented by lack of recombination activating gene-1, T-cell receptor and B-cell receptor mRNA expression at time of challenge. The fish were followed over 6 months and monitored monthly for presence of virus and viral genome mutations. No mutation was identified in the TA or TT group over the 6 months period post infection. Six months post infection TA and TT infected groups were subject to daily stress for 7 days and then sampled weekly for an additional period of 28 days post stress. Stress-responses were documented by down-regulation of mRNA expression of IFN-α1 and concomitant increase of replication levels of T217T221 infected fish at day 1 post stress. By 28 days post stress a T221A reversion was found in 3 of 6 fish in the T217T221 infected group. Sequencing of reverted isolates showed single nucleotide peaks on chromatograms for residue 221 for all three isolates and no mix of TA and TT strains. Replication fitness of reverted (TA) and non-reverted (TT) variants was studied in vitro under an antiviral state induced by recombinant IFN-α1. The T217A221 reverted variant replicated to levels 23-fold higher than the T217T221 strain in IFN-α1 treated cells. Finally, reverted TA strains were virulent when tested in an in vivo trial in susceptible salmon fry. In conclusion, these results indicate that stress plays a key role in viral replication in vivo and can facilitate conditions that will allow reversion from attenuated virus variants of IPNV.

Street lighting delays and disrupts the dispersal of Atlantic salmon (Salmo salar) fry

There has been a decline in the abundance of Atlantic salmon (Salmo salar) despite significant conservation measures designed to reduce fishing mortality. Populations at the southern edge of their historical distribution, where anthropogenic impacts on the freshwater environment may be greater, have suffered the largest decline. In this investigation, we compared the timing of Atlantic salmon fry dispersal from incubators in an aquarium under control and ecologically relevant broad spectrum street-lit conditions (median night light intensity=12lx). Fry dispersal occurred 2.8days later (F=82.9, df=1,8, p<0.001), and on average the fry were smaller at dispersal (0.017g, se=0.0012, p<0.001, n=730), in the incubators exposed to street lighting. Significant disruption to the diel pattern of fry dispersal was also observed. Dispersal under control conditions was significantly directed around a mean time of 4:17h after dusk (p<0.001, r=0.76, n=1990) with very few fry (<2%) dispersing during daylight hours. Under street lighting, the dispersal of fry was significantly delayed (mean time 6:38h after dusk; p<0.001, r=0.39, n=2413) with a significant proportion (32%) dispersing during daylight hours. Survival to dispersal in the controlled aquarium conditions was not lower under street-lit conditions (p=0.21, n=5000eggs across 10incubators). However, in the wild, the period between fry emergence and the establishment of feeding territories is considered to be of critical importance in the dynamics of salmonid populations and any disruption may reduce fitness.

Sensory complementation and antipredator behavioural compensation in acid-impacted juvenile Atlantic salmon

Prey incorporate multiple forms of publicly available information on predation risk into threat-sensitive antipredator behaviours. Changes in information availability have previously been demonstrated to elicit transient alterations in behavioural patterns, while the effects of long-term deprivation of particular forms of information remain largely unexplored. Damage-released chemical alarm cues from the epidermis of fishes are rendered non-functional under weakly acidic conditions (pH < 6.6), depriving fish of an important source of information on predation risk in acidified waterbodies. We addressed the effects of long-term deprivation on the antipredator responses to different combinations of chemical and visual threat cues via in situ observations of wild, free-swimming 0(+) Atlantic salmon (Salmo salar) fry in four neutral and four weakly acidic nursery streams. In addition, a cross-population transplant experiment and natural interannual variation in acidity enabled the examination of provenance and environment as causes of the observed differences in response. Fish living under weakly acidic conditions demonstrate significantly greater or hypersensitive antipredator responses to visual cues compared to fish under neutral conditions. Under neutral conditions, fish demonstrate complementary (additive or synergistic) effects of paired visual and chemical cues consistent with threat-sensitive responses. Cross-population transplants and interannual comparisons of responses strongly support the conclusion that differences in antipredator responses between neutral and weakly acidic streams result from the loss of chemical information on predation risk, as opposed to population-derived differences in behaviours.

Growth hormone reduces growth in free‐living Atlantic salmon fry

Summary1. Although life‐history theory predicts that juvenile growth rates should be high, there is substantial evidence that most juveniles grow below their physiological maximum. The endocrine system plays an important role in the determination of fundamental life‐history traits, and hormones often serve as a link between an organism’s environment and the expression of a trait. Particularly, growth is a life‐history trait, which is strongly associated with growth hormone (GH) in fish, as well as most vertebrates.2. To elucidate trade‐offs related to elevated GH in fish in a natural environment, we experimentally administrated GH exogenously to juvenile Atlantic salmon using sustained‐release GH implants, at an earlier ontogenetic stage than previously achieved (1·5 months). We assessed the effects on growth, dispersal and survival in contrasting environments.3. Exogenous GH treatment increased the growth rate when fish were fed ad libitum in captivity. However, in a natural stream, GH treatment had a significant negative effect on growth and no apparent effect on survival or dispersal. This contrasts with previous studies conducted at later developmental stages, which show either a positive growth effect or no effect of elevated GH levels.4. This study shows that environmental conditions strongly affect the response to GH and that under some natural conditions, it may also reduce growth. We suggest that the endogenous plasma GH levels may be maximizing growth during early, but not later, juvenile stages in nature.

Stocking experiment with Atlantic salmon and sea trout parr reared on either live prey or a pellet diet

Survival rate and growth parameters of Atlantic salmon fry and sea trout fry were determined after stocking in the wild. Before release (22 May 2009) into the wild the larvae were reared for 10 weeks in the hatchery in three groups: (i) fry fed on live zooplankton, (ii) fry fed on larvae of live nekton, and (iii) fry fed on prepared pellet food. In autumn (15 September 2010) the fish were caught in the wild; the survival rate and growth parameters of both Atlantic salmon and sea trout were the highest in the zooplankton-fed group, whilst the pellet-fed group had the lowest survival rate and growth value parameters. Most effective food for hatchery-reared fishes to be used as stock was the natural living zooplankton. The general conclusion is that the live diet supplied in the rearing period has a positively impact on fish survival in the wild.

Ontogenetic selection on hatchery salmon in the wild: natural selection on artificial phenotypes.

Captive rearing often alters the phenotypes of organisms that are destined for release into the wild. Natural selection on these unnatural phenotypes could have important consequences for the utility of captive rearing as a restoration approach. We show that normal hatchery practices significantly advance the development of endangered Atlantic salmon (Salmo salar) fry by 30+ days. As a result, hatchery fry might be expected to face strong natural selection resulting from their developmental asynchrony. We investigated patterns of ontogenetic selection acting on hatchery produced salmon fry by experimentally manipulating fry development stage at stocking. Contrary to simple predictions, we found evidence for strong stabilizing selection on the ontogeny of unfed hatchery fry, with weaker evidence for positive directional selection on the ontogeny of fed fry. These selection patterns suggest a seasonally independent tradeoff between abiotic or biotic selection favoring advanced development and physiological selection linked to risk of starvation in unfed fry. We show, through a heuristic exercise, how such selection on ontogeny may exacerbate problems in restoration efforts by impairing fry productivity and reducing effective population sizes by 13–81%.

Habitat-mediated size selection in endangered Atlantic salmon fry: selectional restoration assessment.

Preservation of adaptive variation is a top priority of many species restoration programs, but most restoration activities are conducted without direct knowledge of selection that might foster or impair adaptation and restoration goals. In this study, we quantified geographic variation in selection on fry size of endangered Atlantic salmon (Salmo salar) during the 6-week period immediately following stocking in the wild. We also used a model selection approach to assess whether habitat variables influence patterns of such selection. We found evidence for significant size-selection in five out of six selection trials. Interestingly, the strength and pattern of selection varied extensively among sites, and model selection suggested that this variation in phenotypic selection was related to geographic variation in the presence of large woody debris and the slope of the stream gradient. The strong selection differentials we observed should be a concern for endangered salmon restoration, whether they reflect natural processes and an opportunity to maintain adaptation, or an indicator of the potentially deleterious phenotypic consequences of hatchery practices.

The susceptibility of Atlantic salmon fry to freshwater infectious pancreatic necrosis is largely explained by a major QTL.

Infectious pancreatic necrosis (IPN) is a viral disease with a significant negative impact on the global aquaculture of Atlantic salmon. IPN outbreaks can occur during specific windows of both the freshwater and seawater stages of the salmon life cycle. Previous research has shown that a proportion of the variation seen in resistance to IPN is because of host genetics, and we have shown that major quantitative trait loci (QTL) affect IPN resistance at the seawater stage of production. In the current study, we completed a large freshwater IPN challenge experiment to allow us to undertake a thorough investigation of the genetic basis of resistance to IPN in salmon fry, with a focus on previously identified QTL regions. The heritability of freshwater IPN resistance was estimated to be 0.26 on the observed scale and 0.55 on the underlying scale. Our results suggest that a single QTL on linkage group 21 explains almost all the genetic variation in IPN mortality under our experimental conditions. A striking contrast in mortality is seen between fry classified as homozygous susceptible versus homozygous resistant, with QTL-resistant fish showing virtually complete resistance to IPN mortality. The findings highlight the importance of the major QTL in the genetic regulation of IPN resistance across distinct physiological lifecycle stages, environmental conditions and viral isolates. These results have clear scientific and practical implications for the control of IPN.

A Bayesian approach to estimating Atlantic salmon fry densities using a rapid sampling technique

Abstract Removal sampling by electric fishing is widely used for assessing fish population size. As it is manpower consuming, less‐demanding techniques have been proposed to increase the number of sites covered with the same human resources. These techniques essentially provide relative abundance measures. To be used for absolute abundance estimation, they need to be inter‐calibrated with another method such as removal sampling. Here, hierarchical Bayesian modelling framework is used for this inter‐calibration because it allows an estimate of absolute abundance from abundance index data alone while accounting for the main sources of uncertainty. It is applied to a 0+ juvenile Atlantic salmon, Salmo salar L. data set from 21 sites on the River Faughan, Northern Ireland. A positive relationship was found between the abundance index (number of fish caught in 5 min of actual electric fishing) and the density. The estimates from the index of abundance alone are fairly imprecise, but still allow differentiation of contrasting levels of fish density.