Genetic variation in immune parameters and associations to survival in Atlantic salmon

Lysozyme activity, haemolytic activity, total level of IgM, and levels of antibodies against A-layer from Aeromonas salmonicida and O-antigen from Vibrio salmonicida , respectively, were determined in 77 full-sib groups of Atlantic salmon in order to evaluate their possible use as immune parameters for indirect selection to improve disease resistance. Fish from parallel full-sib groups had previously been challenged with Aeromonas salmonicida (causing furunculosis), Renibacterium salmoninarum (causing bacterial kidney disease, BKD) and Vibrio salmonicida (causing cold-water vibriosis). Heritabilities were estimated for each of the immune parameters and correlations between the least square means of the full-sib groups for the different immune parameters and survival rates in the parallel full-sib groups were determined. A significant genetic variation in lysozyme activity was found, as well as an apparent genetic association between low lysozyme activity and high survival rates. Low heritabilities and low univariate correlations with survival in the full-sib groups were estimated for all of the other immune parameters. An analysis of the multivariate associations between the full-sib mean values of the complete set of immune parameters, and survival rates in the parallel full-sib groups in each of the challenge tests, revealed that, at low levels of lysozyme activity and with low antibody titres against V. salmonicida O-antigen, increased IgM levels seemed to increase survival from furunculosis.     

Genetic variation in Atlantic salmon, Salmo salar L., within the Tamar catchment in south-west England

Electrophoretic analysis of enzymes in 383 juvenile Atlantic salmon, Salmo salar L., within the Tamar catchment (south-west England) revealed significant genetic differences at the IDHP-3* locus between the three tributaries studied. Aspects of temporal and spatial variation, and management policy within catchments, are discussed.     

Genetic variation at enzyme loci in the southernmost European populations of Atlantic salmon

Genetic variation was studied at 8 allozyme loci in six severely endangered wild Spanish populations of Salmo salar located at the southernmost geographical limit of European Atlantic salmon. Low levels of variation were detected and no significant deviations from Hardy–Weinberg equilibrium were found.     

Genetic changes in an Atlantic salmon population resulting from escaped juvenile farm salmon

The study was undertaken on three adjacent rivers in NW Ireland, on one of which an Atlantic salmon Salmo salar freshwater juvenile rearing unit is situated. Two markers which distinguished farm and wild populations were used. An Ava II-B RFLP in the ND1 region of mtDNA was at a frequency of 0.58 in the farm strain but absent in the wild populations. Allele E at minisatellite locus Ssa- A45/2/l was at a frequency of 0.91 in farm samples, but at a maximum of 0.41 in the populations in the two rivers adjacent to the one with the juvenile rearing unit. The farm strain showed a significant reduction in mean heterozygosity (0.281 ± 0.057), over three minisatellite loci examined, compared to wild samples (0.532 ± 0.063). The occurrence of farm genotypes and the independent occurrence of mtDNA and minisatellite markers in several parr samples from the river indicated that escaped juvenile salmon completed their life cycle, bred and interbred with native fish, upon their return to the river. Escaped fish homed accurately, as adults, to the site of escape, i.e. the area adjacent to the hatchery outflow in the upstream part of the river. Breeding of males in the lower part of the river was also indicated but this could have been due to mature male parr which had moved downstream. The return of adults of farm origin to the river to breed was indicated by the presence of the Ava II-B haplotype in adults netted in the estuary.     

Genetic divergence at the NAD +-dependent malic enzyme locus in Atlantic salmon from Europe and North America

The distribution of genetic variation for NAD+ malic enzyme ( ME* ) polymorphism in the Atlantic salmon was assessed in both anadromous and resident populations. The analysis revealed a major allelic divergence between North America and Europe. The *80 variant occurred in 39 of 40 North American samples, ranging in frequency from 0 to 0.515. In contrast, it was detected in only three fish from two of the 35 European locations analysed. Eleven fish from two rivers in north-west France had the * 110 variant. While heterogeneity among North American populations was significant, no regional differentiation was apparent and anadromous and resident salmon were not found to differ.     

Genetic variation within and among domesticated Atlantic salmon broodstocks in British Columbia, Canada

Atlantic salmon have been reared in the British Columbia, Canada aquaculture industry since the early 1980s. No breeding programmes spanned the entire production period and pedigree records were not kept for broodstocks prior to or since importation. Of the three recognized industry strains, two are of European ancestry ('Mowi' from Norway and 'McConnell' from Scotland) and one is of North American heritage ('Cascade' from Gaspe, Quebec). We evaluated the amount and distribution of genetic variation within industry broodstocks by surveying microsatellite variation at 11 loci in 20 broodstock groups sampled from major production facilities. Allelic richness averaged 10.9 (range 5.8-13.8), compared with a value of 20.3 obtained for a North American wild population. Pairwise genetic distances (D(S)) between samples within strains were generally less than those between strains, with samples attributed to the same strain clustering together in a neighbour-joining dendrogram. Nevertheless, average distances between samples within the European strains were high (0.41 for Mowi; 0.71 for McConnell) but lower (0.06) for the Cascade strain. The reduced intra-sample and increased intra-strain genetic variation observed for the BC domesticated samples compared with wild populations was similar to observations for European domesticated Atlantic salmon. Evidence of introgression of the Cascade strain into European broodstocks was provided by the presence of large Ssa202 alleles (confined to North America in wild populations) in some Mowi and McConnell samples. Introgression likely also contributed to the decreased intercontinental genetic distance for the domesticated samples of this study compared with that observed for wild populations.     

Determinants of hierarchical genetic structure in Atlantic salmon populations: environmental factors vs. anthropogenic influences

Disentangling the effects of natural environmental features and anthropogenic factors on the genetic structure of endangered populations is an important challenge for conservation biology. Here, we investigated the combined influences of major environmental features and stocking with non‐native fish on the genetic structure and local adaptation of Atlantic salmon (Salmo salar) populations. We used 17 microsatellite loci to genotype 975 individuals originating from 34 French rivers. Bayesian analyses revealed a hierarchical genetic structure into five geographically distinct clusters. Coastal distance, geological substrate and river length were strong predictors of population structure. Gene flow was higher among rivers with similar geologies, suggesting local adaptation to geological substrate. The effect of river length was mainly owing to one highly differentiated population that has the farthest spawning grounds off the river mouth (up to 900 km) and the largest fish, suggesting local adaptation to river length. We detected high levels of admixture in stocked populations but also in neighbouring ones, implying large‐scale impacts of stocking through dispersal of non‐native individuals. However, we found relatively few admixed individuals suggesting a lower fitness of stocked fish and/or some reproductive isolation between wild and stocked individuals. When excluding stocked populations, genetic structure increased as did its correlation with environmental factors. This study overall indicates that geological substrate and river length are major environmental factors influencing gene flow and potential local adaptation among Atlantic salmon populations but that stocking with non‐native individuals may ultimately disrupt these natural patterns of gene flow among locally adapted populations.     

Cortisol stimulates hypo-osmoregulatory ability in Atlantic salmon, Salmo salar L.

Hypo-osmoregulatory ability in juvenile Atlantic salmon, Sulrno salur L., was improved by cortisol treatment. Implantation of a vegetable shortening pellet containing cortisol (50 mg kg⁻¹) resulted in elevated plasma cortisol titres. Maximum cortisol levels (160–170ngml⁻¹) were observed at days 6 and 12 after the implantation and dropped significantly by day 55. Cortisol-implanted fish in fresh water developed a twofold increase in gill Na⁺/K⁺-ATPase activity at days 6 and 12, and a threefold increase by day 55. Intestinal mucosa Na⁺/K⁺-ATPase activity was not affected by cortisol. Cortisol-implanted fish exposed to 28 ppt sea water for 48 h tended to show an improved ability to regulate their plasma osmolarity and reduce their ionic load. The osmo-regulatory ability attained at days 12 and 55 was further evaluated by exposing fish to 37 ppt sea water for 96 h. While all the control fish died relatively early in these tests, cortisol-implanted fish showed a clear reduction in their mortality rate. These results indicate that cortisol can induce biochemical and organismal changes during winter months that typify preadaptive events normally occurring in the spring.     

Genetic differentiation among natural European populations of Atlantic salmon, Salmo salar L., from drainages of the Atlantic Ocean

Previously published allelic frequencies at four polymorphic protein coding loci were used as a basis for examining genetic relationships among 19 European populations of Atlantic salmon, Salmo salar L.--exclusive of Baltic drainages--from the Barents Sea to Spain. The data did not support a model of distinct ancestral (e.g. Boreal and Celtic) origins, but were consistent with all populations descending from a single ancestral group within this region with genetically diverged populations drawn together through limited local migrations.     

A study of temporal genetic variation in a natural population of Atlantic salmon in the River Bush, Northern Ireland

Temporal genetic variation in River Bush Atlantic salmon was low and much less than among geographically discrete samples reported from elsewhere.     

Genetic variation in haemolytic activity in Atlantic salmon (Salmo salar L.)

Spontaneous and antibody-dependent haemolytic activity against sheep red blood cells (SRBC) has been studied in serum from Atlantic salmon, Salmo salar L. Considerable increase in haemolytic activity was detected when SRBC were sensitized with haemolysin produced in Atlantic salmon. Haemolytic activity was sensitive both to divalent cations and to heat treatment. Significant reduction in haemolytic activity was detected after absorption with SRBC, indicating the presence of natural antibody against SRBC in Atlantic salmon serum. Persistent haemolytic activity of unsensitized SRBC in serum absorbed to remove natural antibodies was found, which suggests the activation of the alternative complement pathway, while the observed increased haemolytic activity in the presence of specific antibody against SRBC suggests activation of the classical complement pathway. Spontaneous and antibody-dependent haemolytic activity were both analysed in absorbed and non-absorbed sera in a family material of Atlantic salmon. The material consisted of 574 fish belonging to 57 fullsib groups within 20 paternal halfsib groups. Fish with signs of sexual maturity generally showed reduced haemolytic activity. Statistically significant effect of sire on the spontaneous haemolytic activity of both absorbed and nonabsorbed serum, and on antibody-dependent activity, provides evidence of significant additive genetic variation in both the alternative and the classical complement activation in Atlantic salmon. Neither on a phenotypical nor on a family basis were the two traits statistically correlated. The estimated heritabilities were 0.2–0.3 with a standard error of approximately 0.1.     

Chromosomal fusion and life history‐associated genomic variation contribute to within‐river local adaptation of Atlantic salmon

Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation, we genotyped 728 juvenile salmon using a 50 K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global F_ST = 0.004) and failed to support hierarchical structure between the river's two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (F_ST = 0.019), and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250‐Kb region of chromosome 9, including the gene six6 that has previously been linked to age‐at‐maturity and run‐timing for this species. Overall, our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.     

Characterization of transferrin‐linked microsatellites in brown trout (Salmo trutta) and Atlantic salmon (Salmo salar)

The transferrin (TF) gene has recently received increased interest in fish given its fitness relevance as a resistance gene against pathogenic bacteria. In this study, we characterized five TF‐linked microsatellites in brown trout (Salmo trutta) and Atlantic salmon (Salmo salar). Interestingly, each marker amplified duplicated loci and linkage analysis revealed that the TF gene has most likely experienced a tandem duplication during salmonid evolution. In addition, the amplification of all five markers across a wide range of salmonid species suggests that they may be of general interest for the genetic analysis of the TF gene(s) in this teleost family.     

Amount and distribution of biochemical-genetic variation among wild populations and a hatchery stock of Atlantic salmon, Salmo salar L., from north-east Ireland

The effects of tributyltin (TBT) compounds on gill morphology were examined in the mummichog, Fundulus heteroclitus , in 96-h LC50 and 6-week sublethal exposures. Morphometry was used for the identification and quantification of effects with the light microscope. A 96-h LC50 of 17.2 μg 1 ¹ was determined. Morphometric analysis of gill tissues revealed hypertrophy of the lamellar epithelium in fish exposed to 17.2 μg 1–1. Relative diffusing capacity was significantly decreased (−41 %); ( P <0.05, ANOVA, Bonferroni t -test). At 35.6 μg 1⁻¹, TBT exposure resulted in a significant reduction (− 40%) in the volume of the lamellar blood channels. Both of these observations occurred in fish that showed signs of acute poisoning including loss of equilibrium. In fish exposed to sublethal concentrations of 0.105–2.000 μg TBT 1⁻¹ for 6 weeks, there were no pathological changes in the gill. There were no treatment-related changes in the surface morphology of the gills of fish from both experiments upon scanning electron microscopic examination. Although gill pathology was observed in acutely toxic exposures, it does not appear to be a major mechanism of TBT toxicity.     

Identification of Atlantic salmon × brown trout hybrids with a nuclear marker useful for evolutionary studies

A new nuclear DNA marker is described to identify Atlantic salmon, brown trout, and their hybrids. Species-specific banding patterns are obtained by digestion of genomic DNA with the restriction endonuclease Sac I and hybridization with a histone DNA probe. FISH analyses in hybrid metaphases illustrate the potential of interspecific hybrids for evolutionary studies.     

The effect of pineal removal on circulating melatonin levels in Atlantic salmon parr

Nocturnal melatonin levels showed a significant decrease in pinealectomized Atlantic salmon parr in comparison with intact control and sham-operated fish.     

A critical review of adaptive genetic variation in Atlantic salmon: implications for conservation

Here we critically review the scale and extent of adaptive genetic variation in Atlantic salmon (Salmo salar L.), an important model system in evolutionary and conservation biology that provides fundamental insights into population persistence, adaptive response and the effects of anthropogenic change. We consider the process of adaptation as the end product of natural selection, one that can best be viewed as the degree of matching between phenotype and environment. We recognise three potential sources of adaptive variation: heritable variation in phenotypic traits related to fitness, variation at the molecular level in genes influenced by selection, and variation in the way genes interact with the environment to produce phenotypes of varying plasticity. Of all phenotypic traits examined, variation in body size (or in correlated characters such as growth rates, age of seaward migration or age at sexual maturity) generally shows the highest heritability, as well as a strong effect on fitness. Thus, body size in Atlantic salmon tends to be positively correlated with freshwater and marine survival, as well as with fecundity, egg size, reproductive success, and offspring survival. By contrast, the fitness implications of variation in behavioural traits such as aggression, sheltering behaviour, or timing of migration are largely unknown. The adaptive significance of molecular variation in salmonids is also scant and largely circumstantial, despite extensive molecular screening on these species. Adaptive variation can result in local adaptations (LA) when, among other necessary conditions, populations live in patchy environments, exchange few or no migrants, and are subjected to differential selective pressures. Evidence for LA in Atlantic salmon is indirect and comes mostly from ecological correlates in fitness-related traits, the failure of many translocations, the poor performance of domesticated stocks, results of a few common-garden experiments (where different populations were raised in a common environment in an attempt to dissociate heritable from environmentally induced phenotypic variation), and the pattern of inherited resistance to some parasites and diseases. Genotype x environment interactions occurr for many fitness traits, suggesting that LA might be important. However, the scale and extent of adaptive variation remains poorly understood and probably varies, depending on habitat heterogeneity, environmental stability and the relative roles of selection and drift. As maladaptation often results from phenotype-environment mismatch, we argue that acting as if populations are not locally adapted carries a much greater risk of mismanagement than acting under the assumption for local adaptations when there are none. As such, an evolutionary approach to salmon conservation is required, aimed at maintaining the conditions necessary for natural selection to operate most efficiently and unhindered. This may require minimising alterations to native genotypes and habitats to which populations have likely become adapted, but also allowing for population size to reach or extend beyond carrying capacity to encourage competition and other sources of natural mortality.