A microsatellite linkage map for Atlantic salmon (Salmo salar)

A linkage map of the Atlantic salmon is described here consisting of 15 linkage groups containing 50 microsatellite loci with a 14 additional unlinked markers (including three allozymes). The map shows the largest sex-specific recombination rate differences so far found in any vertebrate species (3.92:1 female:male). Homologies with previous linkage mapping studies of Atlantic salmon and rainbow trout are described. An in silico search of the Genbank database carried out using the microsatellites used in the mapping process identified significant matches between the flanking regions of the microsatellite SS11 and the calcium-binding mitochondrial carrier protein, 'Aralar1'.     

Heart rate as an indicator of metabolic rate and activity in adult Atlantic salmon, Salmo salar

Telemetered heart rate (f_H) was examined as an indicator of activity and oxygen consumption rate (VO₂) in adult, cultivated, Atlantic salmon, Salmo salar L. Heart rate was measured during sustained swimming in a flume for six fish at 10° C [mean weight, 1114 g; mean fork length (f. l.), 50·6 cm] and seven fish at 15° C (mean weight, 1119 g; mean f. l., 50·7 cm) at speeds of up to 2·2 body lengths/s. Semi–logarithmic relationships between heart rate and swimming speed were obtained at both temperatures. Spontaneously swimming fish in still water exhibited characteristic heart rate increases associated with activity. Heart rate and Vo₂ were monitored simultaneously in a 575–1 circular respirometer for six fish (three male, three female) at 4° C (mean weight, 1804 g; mean F. L., 62· cm) and six fish (three male, three female) at 10° C (mean weight, 2045 g; mean f. l., 63·2 cm) during spontaneous but unquantified activity. Linear regressions were obtained by transforming data for both f_H and Vo₂ to log values. At each temperature, slopes of the regressions between f_H and Vo₂ for individual fishes were not significantly different, but in some cases elevations were. All differences in elevation were between male and female fish. There were no significant differences in regression slope or elevation for fish of the same sex at the two temperatures and so regressions were calculated for the sexes, pooling data from 4 and 10° C. There was no significant difference in the mean ± S. D. Vo₂ between the sexes at 4° C (male, 66·0 ± 59·6 mgO₂ kg^?1 h^?1; female, 88·0 ± 60·1 mgO₂ kg^?1 h^?1) or 10° C (male, 166·2 ± 115·4 mgO₂ kg^?1 h^?1; female, 169·2 ± 111–1 mgO₂ kg^?1h^?1). Resting Vo₂ (x?± s. d.) at 4°C was 36·7 ± 8.4 mgO₂ kg^?1 h^?1, and 10° C was 72·8 ± 11·9 mgO₂ kg^?1 h^?1. Maximum Vo₂ (x?± S. D.) at 4° C was 250·6 ± 40·2 mgO₂ kg^?1 h^?1, and at 10° C was 423·6 ± 25·2 mgO₂ kg^?1 h^?1. Heart rate appears to be a useful indicator of metabolic rate over the temperature range examined, for the cultivated fish studied, but it is possible that the relationship for wild fish may differ.     

Genetic assessment of Atlantic salmon Salmo salar and sea trout Salmo trutta stocking in a Baltic Sea river

Microsatellite DNA variation was used to assess the outcome of stocking Atlantic salmon Salmo salar and migratory trout Salmo trutta in River Sävarå, N Sweden. No information on pre‐stocking genetic composition of S. salar and S. trutta in River Sävarå was available. In 2 year‐classes of S. salar smolt, microsatellite data indicated that post‐stocking genetic composition differed markedly (F_ST= 0·048) from the main donor strain, Byskeälven S. salar, and from other Gulf of Bothnia S. salar stocks (F_ST 0·047 and 0·132). The STRUCTURE programme failed to detect any substructuring within Sävarå salmon. It was concluded that only minor introgression estimated to a proportion of 0·11 (95% CI 0·07–0·16) has occurred in S. salar. Salmo trutta showed overall low differentiation among populations with maximum F_ST of 0·03 making analysis more cumbersome than in S. salar. Still, the SävaråS. trutta deviated significantly from potential donor populations, and STRUCTURE software supported that majority of trout in Sävarå formed a distinct genetic population. Admixture was more extensive in S. trutta and estimated to 0·17 (95% CI 0·10–0·25).     

Counterintuitive migration patterns by Atlantic salmon Salmo salar smolts in a large lake

What little is known about the seaward migration of Salmo salar smolt migration through standing waters indicates that it is both slow and results in high mortality rates, compared with riverine migration. This may be partly because smolts in lakes need to swim more actively and require more complex directional cues than they do in rivers. In this telemetry study of smolt migration through Loch Lomond, S. salar smolts made repeated movements in directions away from the outflowing river, which considerably increased migration time.     

Fine-scale genetic structure of Atlantic salmon (Salmo salar) using microsatellite markers: effects of restocking and natural recolonization

1. An important goal of conservation biology is to preserve the evolutionary potential of a species by maintaining natural levels of genetic diversity. Here, we assess the population differentiation in the Atlantic salmon, Salmo salar, listed in Annex II of the European Habitats Directive, to provide valuable information for its conservation in Normandy (France).
2. Samples collected from 10 natural sites revealed that 13 of 14 microsatellite loci were polymorphic. Significant differentiation among populations was detected ( F _ST = 0.054, P  <   0.001), and all F _ST pairwise comparisons except one were significant. A genetic split was observed between populations inhabiting streams with limestone geology compared to those inhabiting streams with siliceous geology, which could reflect adaptative differences.
3. Hatchery stocks used for the restocking of two rivers were genetically distinct from native stocks.
4. Analysis of three stream habitats restored in 1995 showed that all were recolonized naturally by wild salmon from geographically close populations and no founder effects were detected. Allelic richness was similar between recolonized and wild populations.
5. From a management perspective, our study revealed that restoration of habitat is very effective to recreate new populations in rivers from which salmon have disappeared and that natural recolonization can be fast and effective in terms of genetic diversity.     

Ecological determinants and temporal stability of the within-river population structure in Atlantic salmon (Salmo salar L.)

A gene diversity analysis was performed using microsatellite loci in order to (i) describe the extent and pattern of population structure in Atlantic salmon (Salmo salar L.) within a river system; (ii) establish the importance of quantifying the signal:noise ratio in accurately estimating population structure; and (iii) assess the potential usefulness of two evolutionary models in explaining within-river population structure from the ecological and habitat characteristics of Atlantic salmon. We found weak, yet highly significant microscale spatial patterning after accounting for variance among temporal replicates within sites. Lower genetic distances were observed among temporal samples at four sampling sites whereas no evidence for temporal stability was observed at the other three locations. The component of genetic variance attributable to either temporal instability and/or random sampling errors was almost three times more important than the pure spatial component. This indicates that not considering signal:noise ratio may lead to an important overestimation of genetic substructuring in situations of weak genetic differentiation. This study also illustrates the usefulness of the member-vagrant hypothesis to generate a priori predictions regarding the number of subpopulations that should compose a species, given its life-history characteristics and habitat structure. On the other hand, a metapopulation model appears better suited to explain the extent of genetic divergence among subpopulations, as well as its temporal persistence, given the reality of habitat patchiness and environment instability. We thus conclude that the combined use of both models may offer a promising avenue for studies aiming to understand the dynamics of genetic structure of species found in unstable environments.     

Metabolic rate, growth and aggressiveness in three Atlantic salmon Salmo salar populations

Standard metabolic rate ( R _S), specific growth rate ( G ) and aggressiveness were investigated in three Finnish populations of Atlantic salmon Salmo salar (Neva, Saimaa and Teno), which were reared in identical hatchery conditions. The populations differed in their geographical origin and native habitat. There was a significant difference between populations in R _S: the southernmost Neva population had higher values in R _S than the northernmost Teno population. No difference was found in G or aggressiveness between the populations. G was found to have a significant positive association with aggressiveness and R _S among the three populations, however, these results were not statistically significant after correction for multiple tests. There was no significant association between R _S and aggressiveness. Higher metabolic rate of the most southern population Neva is suggested to be an adaptation to the more abundant food sources of the southern stream.     

Physical mapping of three minisatellite sequences in the Atlantic salmon (Salmo salar) genome

We have determined the localization of three minisatellite loci SsBglIIL.6 , SsBglIIU.20 and SsPstL.26 in the Atlantic salmon ( Salmo salar ) genome by fluorescent in situ hybridization (FISH). FISH analysis of the SsBglIIL.6 and SsBglIIU.20 minisatellites revealed that they are both located in single chromosome pairs allowing their direct identification; in contrast, the SsPstIL.26 probe hybridizes to four different chromosomal pairs. The analysis of chromosomal location of minisatellite sequences could be very useful for studying structural changes that have taken place during chromosome evolution in the karyotype of Salmo salar .     

Evidence of a genetic component in the seasonal return pattern of Atlantic salmon, Salmo salar L.

We tested the null hypothesis that differences in the seasonal return patterns between stocks of Atlantic salmon, Salmo salar L., are a result of a direct response to the environment, and not under genetic control. Two stocks were used in the experiments, originating from the R. Figga and R. Imsa, respectively. In their native habitat fish from the former are known to return to the home stream as adult salmon early in the summer, while from the latter return during late summer and autumn. By rearing these stocks in the same hatchery and releasing smolts of both stocks together at three sites in southern Norway, it was demonstrated that salmon from the R. Figga stock returned earlier to coastal Norway than salmon from the R. Imsa stock, as maturing adults. Thus, we reject the hypothesis that these stocks are genetically identical in this trait. Within both stocks, multi-sea-winter fish returned earlier than one-sea-winter fish. Within stocks, there was no significant difference in time of return between salmon released as 1- and 2-year-old smolts, or between fish reared from parents ascending the R. Imsa early or late in the season.     

The influence of metabolic rate on otolith increment width in Atlantic salmon parr, Salmo salar L.

The influence of metabolic rate on otolith accretion in Atlantic salmon parr was investigated by comparing oxygen consumption rate and increment width in fast and slow growing individuals. Increment width was found to be positively correlated to mean daily oxygen consumption in both fast growing (S1) and slow growing (S2) parr. The results support previous suggestions that a process related to metabolic rate, rather than somatic growth, governs the rate of otolith accretion.     

Migratory behaviour of wild and farmed Atlantic salmon (Salmo salar) during spawning

Migratory behaviour at spawning of wild and newly-escaped farmed Atlantic salmon was analysed by radio telemetry in the River Alta, North Norway. Spawning areas were located by aerial surveys. Farmed females moved significantly more than wild females ( P <0.01). There was no such difference between the two groups of males. About 83% of the wild fish stayed within identified spawning areas for 1 day or longer. The corresponding figure for farmed salmon was only 43% ( P <0.05). Wild salmon stayed 8.1 days inside spawning areas and farmed salmon 5.2 days. The present results suggest that escaped farmed salmon had reduced spawning success compared with wild fish.     

Spawning behaviour of a farmed escaped female Atlantic salmon (Salmo salar)

Excavation of stranded redds revealed differences in spawning behaviour between farmed and wild Atlantic salmon. The redd of a farmed fish contained more egg pockets (nine v . average of two) and fewer eggs per pocket (averages: 459 v . 707). No other pocket measures differed.     

Thyroid hormone levels in Atlantic salmon (Salmo salar) during the return migration from the ocean to spawn

Serum thyroid hormone levels were determined in adult Atlantic salmon ( Salmo salar ) of both sexes caught in the ocean and at a sequence of locations on their return migration to spawn. Tri-iodothyronine (T₃) levels were greatest in fish caught in coastal or estuarine waters or in a river near head-of-tide. T₃ levels were lower in fish caught in rivers throughout the angling season and lowest in those captured entering a tributary near spawning. Thyroxine (T₄) levels were lowest in immature fish captured in the ocean in winter but raised in fish captured in spring; many of the latter group showed endocrine evidence of their becoming sexually mature. T₄ levels were greatest in fish captured in coastal waters and progressively lower in fish captured in an estuary, near head-of-tide and in rivers. T₄ levels in fish captured at tributary entry near spawning exceeded those in fish caught in rivers earlier in the year. In general, these data support the hypothesis that motor activity level in migrant fish is a determinant of thyroid status.     

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.     

Allelic and haplotypic diversity at the major histocompatibility class II within domesticated Australian Atlantic salmon (Salmo salar L.)

Variation within the major histocompatibility (MH) class II alpha gene ( Sasa-DAA ) was compared between domesticated Australian Atlantic salmon and their ancestral Canadian population. The level of Sasa-DAA and MH class II beta gene ( Sasa-DAB ) sequence variation was also examined within the Australian population and compared with that published for European Atlantic salmon populations. In contrast to variation previously reported for non-coding microsatellite loci, a high level of MH class II allelic variation has been maintained within the domesticated Australian populations. Furthermore, a high level of Sasa-DAA and Sasa-DAB allele sequence diversity was also observed and exceeded that reported for other cultured Atlantic salmon populations. The number of Sasa-DAB allele sequences (14) surpassed the number of Sasa-DAA allele sequences (9) to produce 14 unique class II haplotypes. We conclude that the Australian Atlantic salmon populations show high MH class II allelic and haplotypic variation compared with both its ancestral Canadian population and other cultured Atlantic salmon populations.     

Genetic diversity and effective size of the Atlantic salmon Salmo salar L. inhabiting the River Eo (Spain) following a stock collapse

Historic angling records suggest the occurrence of a drastic decline in the River Eo (Spain) Atlantic salmon population size during the past two decades, as a result of overexploitation and habitat deterioration. In recent years, the population has been apparently recovering, and the present study is aimed to report information on the level of genetic diversity and the effective size of the current population as these may have immediate consequences for its conservation. Eighty-six salmon from two temporal groups (1998–1999 and 2004–2006), representing three generations, were genotyped using a panel of eight microsatellites. Inspite of the recent decline in census numbers and the detection of the signs of a population bottleneck, the population exhibits a high level of genetic diversity, similar to that from other populations, and almost unchanged during the period of study [average allelic richness ( A ) = 14·0 and 13·9, and average heterozygosity ( H _e) = 0·843 and 0·851 in 1998–1999 and 2004–2006, respectively]. The effective population size ( N _e) estimated by two different temporal methods showed a consistent value around 80 salmon, whereas the estimates from the linkage disequilibrium (LD) method provided a value around 165 individuals for either sample. The recent growing number of salmon, as indicated by fisheries records, the relatively large estimates of the ratio N _e/ N (with range 0·23–0·44 for the temporal estimates and 0·31–0·59 for the LD estimates) and the high levels of diversity found suggest that the population has not been greatly affected by the historical census declines and can be expected to recover in the future.     

Analysis of microsatellite DNA from old scale samples of Atlantic salmon Salmo salar: a comparison of genetic composition over 60 years

Microsatellite analysis was applied to scale samples of Atlantic salmon collected up to 60 years ago. Samples from the 1930s, from a now endangered Danish population, were compared with recent samples (1989), to test if the present population consists of descendants from the original one. Allele frequencies had changed over time, but individuals from the two samples caught about 60 years apart clustered together when compared with the closest neighbouring population and another reference population. However, fewer alleles were detected in the recent sample from the endangered population, most likely due to a population bottleneck or sampling artefacts.     

Muscle development in Atlantic salmon (Salmo salar) embryos and the effect of temperature on muscle cellularity

Salmon eggs were incubated at 5, 8 or 11° C from fertilization to hatching. At Gorodilov stages 25, 27, 29, 31 and 33 transverse sections of whole embryos (at somite level 10–15) were prepared for histochemistry and electron microscopy. At every stage up to hatching, cross–sectional areas of the embryos were not different between temperatures, and from stage 27 onwards there was also no difference in the ratio of white to red muscle. However, there were more muscle fibres but of smaller average diameter in both the red and white muscle for the colder temperature embryos. At hatching there were also more nuclei (per cross–section) in the colder embryos but more nuclei per muscle fibre in the warmer embryos. In all cases the 8° C embryos were intermediate between 5 and 11° C embryos in their muscle parameters. Fast and slow muscle fibres could only be distinguished in the embryos by alkali–stable ATPase reactions. Succinic dehydrogenase activity was low in embryonic fish. No differences between the temperature groups were detected in the histochemical reactions for either ATPase or succinic dehydrogenase activities.