Effect of hatchery environment on cranial morphology and developmental stability of Atlantic salmon (Salmo salar L.) from North‐West Russia

The study addresses the effect of hatchery rearing on morphological variation and developmental stability of Atlantic salmon parr from North‐West Russia. Totally, we collected nine samples. Four wild samples were collected from each of the rivers Kola, Umba, Keret’ and Shuia. Five samples of hatchery‐reared parr were the first‐generation progeny of wild adults from these rivers reared separately at the four hatcheries (one hatchery was represented by two samples). Ten meristic and 48 morphometric cranial characters were analysed. We studied the morphological divergence between wild and hatchery fishes of the same river of origin. To analyze developmental stability we used fluctuating asymmetry (random deviations from perfect bilateral symmetry). It was found that hatchery‐reared parr significantly differ from wild parr in both meristic characters and the shape of cranial bones. Different hatcheries caused similar effect on morphological variation in all populations. Fluctuating asymmetry in morphometric characters was significantly higher in hatchery fish than in wild from the Shuia River, indicating a higher level of developmental instability. However, wild parr from the Keret’ River had significantly higher fluctuating asymmetry than cultivated parr of the same origin, possible due to a high infection pressure of the parasite Gyrodactylus salaris Malmberg which has led to significant decline of the wild salmon population in this river, or from genetic changes caused by cultivation. The obtained results indicate a notable effect of hatchery environment on Atlantic salmon’s phenotype.     

Food consumption and growth of Atlantic salmon Salmo salar parr in sub-Arctic rivers: empirical support for food limitation and competition

The quantitative food consumption and somatic growth of Atlantic salmon Salmo salar parr were compared between three sub-Arctic rivers in northern Norway and Finland, addressing the potential occurrence of resource limitation and interspecific competition. In one of the rivers, previous resource partitioning studies have suggested severe dietary competition between juvenile S. salar and a dense population of alpine bullheads Cottus poecilopus . It was hypothesized that S. salar parr in this river would have restricted food consumption and growth rates compared to the S. salar populations in the other two rivers where interspecific competition was less likely to occur. The feeding and growth performance differed significantly between the S. salar populations. The lowest food acquisition and growth rates were in the S. salar parr population living in sympatry with C. poecilopus , confirming a restricted food supply for the S. salar parr and providing empirical support for the presence of resource limitation and interspecific food competition in this river system. The study reveals that S. salar parr in sub-Arctic rivers may experience food limitations resulting in diminished growth rates.     

Size variability of juvenile Atlantic salmon: links to environmental conditions

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.     

Natural hybrids between Atlantic salmon, Salmo salar L., and trout, Salmo trutta L., in juvenile salmonid populations in south-west England

Electrophoretic analysis of juvenile salmonids from south-west England revealed the presence of natural hybrids between Atlantic salmon, Salmo salar L., and brown trout, Salmo rrurra L., within three of five rivers. Amongst 409 juvenile 'salmon', 1.2% were hybrids, and of 150 juvenile 'trout' sampled, 2.0% were natural hybrids. In one river, similar hybridization levels in 'salmon' parr samples were found in two successive years. Levels of hybridization are high when compared with most similar studies, especially others within the United Kingdom. Possible factors influencing this are discussed.     

Interaction between hatchery and wild Pacific salmon in the Far East of Russia: A review

We review studies of interactions between hatchery and wild Pacific salmon in the Russian Far East. This includes the role of hatchery practices that result in premature migration to the sea and increased mortality, and data on feeding and territorial competition between juveniles of hatchery and wild origin. In the course of downstream migration many juvenile hatchery salmon are eliminated by wild salmon predation. During the marine period, Japanese hatchery chum salmon (Oncorhynchus keta) distribution overlaps the distribution of Russian wild salmon. Consequently, replacement of wild populations by hatchery fishes, as a result of abundant juvenile hatchery releases combined with extensive poaching in spawning grounds, is apparent in some Russian rivers. Interactions between the populations occur in all habitats. The importance of conservation of wild salmon populations requires a more detailed study of the consequences of interactions between natural and artificially reared fishes.     

Relative production of Atlantic salmon from fluvial and lacustrine habitats estimated from analyses of scale characteristics

Empirical and back-calculated growth of Atlantic salmon parr were compared between fish reared in fluvial and lacustrine habitats of Conne River, Newfoundland. Length at age was significantly higher for lacustrine parr. Various classification and maximum likelihood estimators indicated that 75% or more of the fish used lakes for rearing. Lacustrine use is another aspect of the inherent variability and plasticity of Atlantic salmon life-history traits. As most Newfoundland river systems include lakes, estimates of regional spawning targets and potential smolt production will need to take lake habitat into account.     

Expression of olfactory receptors in different life stages and life histories of wild Atlantic salmon (Salmo salar)

It has been hypothesized that salmonids use olfactory cues to return to their natal rivers and streams. However, the key components of the molecular pathway involved in imprinting and homing are still unknown. If odorants are involved in salmon homing migration, then olfactory receptors should play a critical role in the dissipation of information from the environment to the fish. Therefore, we examined the expression profiles of a suite of genes encoding olfactory receptors and other olfactory-related genes in the olfactory rosettes of different life stages in two anadromous and one non-anadromous wild Atlantic salmon populations from Newfoundland, Canada. We identified seven differentially expressed OlfC genes in juvenile anadromous salmon compared to returning adults in both populations of anadromous Atlantic salmon. The salmon from the Campbellton River had an additional 10 genes that were differentially expressed in juveniles compared to returning adults. There was no statistically significant difference in gene expression of any of the genes in the non-anadromous population (P < 0.01). The function of the OlfC gene products is not clear, but they are predicted to be amino acid receptors. Other studies have suggested that salmon use amino acids for imprinting and homing. This study, the first to examine the expression of olfactory-related genes in wild North American Atlantic salmon, has identified seven OlfC genes that may be involved in the imprinting and homeward migration of anadromous Atlantic salmon.     

Geographical and temporal mitochondrial DNA variability in populations of pink salmon

Pink salmon Oncorhynchus gorbuscha from odd and even year generations in rivers of Sakhalin Island, Kuril Island, Kamchatka Peninsula, and Alaska were investigated with five informative restriction endonucleases for mtDNA variation. The odd and even generations from the same rivers of South Sakhalin differed greatly. The time of divergence between the two broodlines was estimated at 0.9-1.1 Myr. The variability of mtDNA in odd year generations was higher than in even year generations and may have been due to' founder' and/or' bottleneck' effects. The differences among river populations within the Sakhalin region in 1991-1993 were not significant and this confirms the highly migratory nature of pink compared with other Pacific salmon. The mtDNA samples revealed statistically significant differences between regions. The northern populations (Kamchatka, Alaska) were less diverse in number and frequency of haplotypes than the southern populations (Sakhalin). This suggests that pink salmon originated in the Sakhalin-Kuril region and that a founder effect during the spread of this species may have restricted the mtDNA variability in other regions.     

An analysis of the distribution of juvenile Atlantic salmon (Salmo salar) in nature as a function of relatedness using microsatellites

The major objective of this study was to test the hypothesis that juvenile Atlantic salmon kin occupy adjacent territories in their natural habitat in order to profit from the benefits associated with kin-biased behaviours, as has been observed under controlled laboratory conditions. Microsatellites were used to establish the relatedness of salmon fry (in their first summer of life) and parr (in their second and third summer of life) captured in adjacent territories. We did not observe a relationship between the proximity and the relatedness of either parr of the same cohort or fry in their natural habitat. Although many pairs of fry were identified as being related when sampled immediately after emergence, most family groups did not occupy adjacent territories. The high dispersal potential in rivers, the low occupation rate of the habitat and the incidence of half-sibs in nature most probably reduce the opportunity and advantage of kin-biased behaviour, in contrast to laboratory studies conducted in artificial, high-density conditions.     

Effects of species, culture history, size and residency on relative competitive ability of salmonids

The relative competitive ability of juvenile farm and wild salmonids was investigated to provide insight into the potential effects of introduction of cultured salmon on wild Pacific salmonid ( Oncorhynchus ) species. Aquarium experiments involving equal contests ( i.e. size matched, simultaneously introduced individuals) indicated that two wild coho salmon Oncorhynchus kisutch populations were competitively equal to a farm coho salmon population. In equal contests between farm Atlantic salmon Salmo salar (Mowi strain) and these wild coho salmon populations or coastal cutthroat trout Oncorhynchus clarki clarki , Atlantic salmon were subordinate in all cases. When Atlantic salmon were given a residence advantage, however, they were competitively equal to both wild coho salmon populations, but remained subordinate to coastal cutthroat trout. When Atlantic salmon were given a 10–30% length advantage, they were competitively equal to one wild coho salmon population but remained subordinate to the other. In equal contests in semi-natural stream channels, both wild coho and farm Atlantic salmon grew significantly more in the presence of the other species than when alone. It appears that coho salmon obtain additional food ration by out competing Atlantic salmon, whereas Atlantic salmon were stimulated to feed more in the presence of coho salmon competitors. These results suggest that wild coho salmon and cutthroat trout should out compete farm Atlantic salmon of a similar size in nature. As the relative competitive ability of Atlantic salmon improves when they have a size and residence advantage, should feral populations become established, they may exist on a more equal competitive footing owing to the long freshwater residence of Atlantic salmon.     

Gene diversity analysis of mitochondrial DNA, microsatellites and allozymes in landlocked Atlantic salmon

This study investigates the patterns of genetic diversity detected in allozymes, mtDNA, and microsatellites, in order to assess their relative efficacy to differentiate sympatric landlocked salmon populations and to estimate changes in genetic diversity between wild and first-generation hatchery fish. Overall, the three genetic markers indicated a genetic differentiation between two sympatric populations of Lake Saint-Jean, Québec. MtDNA and microsatellites also showed significant differences between wild and first-generation hatchery fish originating from the same river. Allozyme analysis was the most limited approach due to the low genetic diversity detected and the necessity to kill specimens. Although low polymorphism was found in mtDNA, it was the most discriminant marker between wild populations. Microsatellite analysis appears to be a promising approach due to its high sensitivity in differentiating wild populations, in detecting changes in allele composition between wild and first-generation hatchery fish and its potential for increased resolution by augmenting the number of polymorphic loci. Given the benefits and disadvantages of the three methods, the combination of mtDNA and microsatellite analyses will best address our research objectives.     

Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon

The high level of escapes from Atlantic salmon farms, up to two million fishes per year in the North Atlantic, has raised concern about the potential impact on wild populations. We report on a two-generation experiment examining the estimated lifetime successes, relative to wild natives, of farm, F(1) and F(2) hybrids and BC(1) backcrosses to wild and farm salmon. Offspring of farm and "hybrids" (i.e. all F(1), F(2) and BC(1) groups) showed reduced survival compared with wild salmon but grew faster as juveniles and displaced wild parr, which as a group were significantly smaller. Where suitable habitat for these emigrant parr is absent, this competition would result in reduced wild smolt production. In the experimental conditions, where emigrants survived downstream, the relative estimated lifetime success ranged from 2% (farm) to 89% (BC(1) wild) of that of wild salmon, indicating additive genetic variation for survival. Wild salmon primarily returned to fresh water after one sea winter (1SW) but farm and 'hybrids' produced proportionately more 2SW salmon. However, lower overall survival means that this would result in reduced recruitment despite increased 2SW fecundity. We thus demonstrate that interaction of farm with wild salmon results in lowered fitness, with repeated escapes causing cumulative fitness depression and potentially an extinction vortex in vulnerable populations.     

Functions of restored wetlands for juvenile salmon in an industrialized estuary

The Duwamish estuary is an industrialized waterway located in Seattle, WA, USA. Despite a history of habitat loss, naturally produced juvenile Chinook salmon use the estuary. In addition to experiencing degraded habitat in the estuary, wild salmon growth may be affected by competition with more than three million hatchery fish released yearly into the river. Restoring habitat to benefit salmon in the Duwamish River is a priority for trustees of public resources, and a number of wetland restoration sites have been created there. We tested the function of restored sites in the Duwamish estuary for juvenile Chinook salmon by comparing fish densities from enclosure nets or beach seines at three paired restored/un-restored sites and by applying environmental and diet data to a bioenergetics model. We also examined temporal and diet overlap of wild juvenile Chinook salmon with other salmon species and with hatchery-reared Chinook salmon using non-metric multidimensional scaling (NMDS). At a brackish upstream site with a relatively large opening to the river, we found higher densities of juvenile Chinook salmon at the restored site. NMDS results indicated that juvenile Chinook salmon fed on different taxa at the restored sites than at the reference sites. However, modeled growth was similar at restored and reference sites. Co-occurring juvenile chum and Chinook salmon fed differently, with chum eating smaller prey, and Chinook salmon eating larger prey. Co-occurring hatchery and wild juvenile Chinook salmon had similar diets, indicating that they may compete for prey. However, modeled growth was positive and did not differ between hatchery and wild fish, suggesting that food was not limiting. Bioenergetics models indicated that overall juvenile Chinook salmon growth potential at the brackish water site was consistently higher than at more saline sites. Our results suggest that restoration sites in the Duwamish estuary that have larger access openings and are located in brackish water may have increased function over other configurations.     

Infectious salmon anaemia virus in wild fish from Scotland.

Following the outbreak of infectious salmon anaemia (ISA) at salmon farms in Scotland, UK, a survey was established to determine the extent of infection in wild fish. All fish tested were free from the clinical symptoms of ISA. Isolations of ISAV were made from 5 sea trout within areas where ISA affected salmon farms were located. Evidence for ISAV in other sea trout was provided by ISA RT-PCR diagnostic tests. Results from ISA RT-PCR tests reveal evidence for ISAV being present in salmon parr, adult salmon and juvenile brown trout in rivers distant from salmon farms and indicate that, at the time of the survey (1998-1999), ISAV may have been widely distributed. Nucleotide sequence analysis of segments 2 and 8 showed that for most sequences from wild fish there was 100% homology with ISAV isolated from clinically affected farmed fish although evidence is presented which indicates variability in ISAV sequences from wild fish. Modelling the RT-PCR findings indicates that ISAV among salmonid fish was spatially non-random. Brown trout, sea trout and salmon (adult and parr) show a pattern of occasionally large numbers of positive samples against a background of very low numbers.     

Inclusion of water temperature in a fuzzy logic Atlantic salmon (Salmo salar) parr habitat model

As water temperature is projected to increase in the next decades and its rise is clearly identified as a threat for cold water fish species, it is necessary to adapt and optimize the tools allowing to assess the quantity and quality of habitats with the inclusion of temperature. In this paper, a fuzzy logic habitat model was improved by adding water temperature as a key determinant of juvenile Atlantic salmon parr habitat quality. First, salmon experts were consulted to gather their knowledge of salmon parr habitat, then the model was validated with juvenile salmon electrofishing data collected on the Sainte-Marguerite, Matapedia and Petite-Cascapedia rivers (Québec, Canada). The model indicates that when thermal contrasts exist at a site, cooler temperature offered better quality of habitat. Our field data show that when offered the choice, salmon parr significantly preferred to avoid both cold areas (<15 °C) and warm areas (>20.5 °C). Because such thermal contrasts were not consistently present among the sites sampled, the model was only validated for less than 60% of the sites. The results nevertheless indicate a significant correlation between median Habitat Quality Index and parr density for the Sainte-Marguerite River (R² = 0.38). A less important, albeit significant (F-test; p = 0.036) relationship was observed for the Petite-Cascapedia river (R² = 0.14). In all instances, the four-variable (depth, velocity, substrate size and temperature) model provided a better explanation of parr density than a similar model excluding water temperature.     

Mitochondrial DNA variation in Atlantic salmon, Salmo, salar L., populations

Mitochondrial DNA (mtDNA) variation was examined in 209 Atlantic salmon from two river systems, the R. Itchen in Hampshire (Southern England) and the R. Conwy (North Wales). Within each system, five spawning sites were sampled. Four enzymes (AVA II, HAE III, HINF I and MBO I) revealed restriction fragment polymorphisms that were informative. Ten clonal lines were observed. These clones were differentially distributed between the two river systems and single clonal types were found to predominate at several spawning sites. MBO I variants were found in salmon from the R. Itchen but not the R. Conwy. A significant heterogeneity in frequency distribution of clonal lines between parr and smolt assemblages of the same year class within the R. Itchen was detected. This heterogeneity suggests that differences in survival or migratory behaviour may be identified by changes in mtDNA clonal frequencies.     

Alternative male life-history tactics as potential vehicles for speeding introgression of farm salmon traits into wild populations

Releases of cultured organisms, such as farm Atlantic salmon (Salmo salar L.), threaten native biodiversity and the integrity of natural communities. Salmon escaping from sea farms, however, have relatively poor reproductive success, suggesting that the rate of spread of domesticated traits may be reduced. We now compare the relative reproductive success of males that mature precociously in freshwater (parr) and find that those of farm origin have higher breeding and fertilization success than wild and hybrid individuals. Specifically, hybrid parr had 57% and wild parr 25% the success of farm parr. Early maturing males could thus be important vehicles promoting introgression of domesticated and/or non‐native traits into wild populations and ultimately have long‐term impact on the genetic integrity of native populations.     

Habitat selection by juvenile Atlantic salmon: the interaction between physical habitat and abundance

The effect of physical river habitat variables on the distribution of juvenile Atlantic salmon Salmo salar L. in the Rivière de la Trinité, Québec, Canada, was examined using generalized additive modelling. A survey of Atlantic salmon fry and parr densities and habitat variables (flow velocity, water column depth and substratum size) was conducted in the summer months from 1984 to 1992. Clear patterns of habitat use existed: specific ranges of habitat variables were selected, with parr preferring greater velocities, depths and substratum sizes than fry. There was a large variation, however, in juvenile densities for given velocities, depths or substratum sizes, with this variation being greatest in optimal habitats. On examination of an individual year, interaction between the variables was found to explain some of the variation. On a year‐to‐year basis the juvenile Atlantic salmon population was found to exhibit an 'Ideal Free Distribution', which resulted in greatest variation in optimal habitats with year‐to‐year changes in population abundance.     

Restitution and genetic differentiation of salmon populations in the southern Baltic genotyped with the Atlantic salmon 7K SNP array

Background

Native populations of Atlantic salmon in Poland, from the southern Baltic region, became extinct in the 1980s. Attempts to restitute salmon populations in Poland have been based on a Latvian salmon population from the Daugava river. Releases of hatchery reared smolts started in 1986, but to date, only one population with confirmed natural reproduction has been observed in the Slupia river. Our aim was to investigate the genetic differentiation of salmon populations in the southern Baltic using a 7K SNP (single nucleotide polymorphism) array in order to assess the impact of salmon restitution in Poland.

Methods

One hundred and forty salmon samples were collected from: the Polish Slupia river including wild salmon and individuals from two hatcheries, the Swedish Morrum river and the Lithuanian Neman river. All samples were genotyped using an Atlantic salmon 7K SNP array. A set of 3218 diagnostic SNPs was used for genetic analyses.

Results

Genetic structure analyses indicated that the individuals from the investigated populations were clustered into three groups i.e. one clade that included individuals from both hatcheries and the wild population from the Polish Slupia river, which was clearly separated from the other clades. An assignment test showed that there were no stray fish from the Morrum or Neman rivers in the sample analyzed from the Slupia river. Global F_ST over polymorphic loci was high (0.177). A strong genetic differentiation was observed between the Lithuanian and Swedish populations (F_ST = 0.28).

Conclusions

Wild juvenile salmon specimens that were sampled from the Slupia river were the progeny of fish released from hatcheries and, most likely, were not progeny of stray fish from Sweden or Lithuania. Strong genetic differences were observed between the salmon populations from the three studied locations. Our recommendation is that future stocking activities that aim at restituting salmon populations in Poland include stocking material from the Lithuanian Neman river because of its closer geographic proximity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0121-9) contains supplementary material, which is available to authorized users.     

Genetic implications of hatchery rearing in Atlantic salmon: effects of rearing environment on genetic composition

In an experiment to investigate genetic consequences of hatchery rearing in salmon, allozyme variation at five polymorphic loci was examined in Atlantic salmon of known initial genetic composition, which were reared throughout freshwater life in the hatchery or stocked into the wild as swim-up fry. The genetic composition of the juveniles in the hatchery remained homogeneous from fertilization up to stocking, and from stocking to 2+ in the wild, however, those remaining at the hatchery developed genetic differences among smolting and nonsmolting 1+ parr. These differences were attributed to conditions leading to early smolting at 1+ among the hatchery fish, with 1+ smolts diverging from the gene pool from which they were derived, whereas those stocked into the wild did not smolt until a year later and retained the original genetic composition. The results are discussed in relation to hatchery rearing of salmon and implications for the use of reared fish in stocking and enhancement programmes.