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'.     

Links between patterns of marine growth and survival of Atlantic salmon Salmo salar, L.

The hypothesis that marine survival of Atlantic salmon Salmo Salar is linked to marine growth was explored by using inter-circuli distances and total numbers of circuli existing on scales from a population monitored over nearly four decades. The results suggest that marine growth controls survival, particularly during the late summer and early winter of the first year at sea. Recruitment is strongly linked to growth, described as the total number of circuli, but not to inter-circuli distances. This highlights the potential of patterns of circuli number to be considered as proxies for growth. Indications that hatchery populations might be subject to other mortality events, in addition to those experienced by wild populations, are also presented.     

Territory size and distribution of newly-emerged Atlantic salmon (Salmo salar)

Newly emerged Atlantic salmon (Salmo salar) were observed from May to August 1981 at six isolated redds in Washington County, Maine, USA. Territorial size and distribution were measured. At the end of the emergence period (12 to 28 May), fish maintained positions (stations) at redds where water velocity did not exceed 52 cm s^–1 By 12 June, most salmon (80–96%) had moved off the redds of origin and had established territories 1 to 5 m from the redd. The area defended increased substantially after mid-June, but territorial aggression diminished by 15 July, and the fry dispersed downstream. All fish observed were territorial, and the percentage of time during which stations were held decreased from 89 in mid-May to as low as 40% in mid-June.Cooperators are the Maine Department of Inland Fisheries and Wildlife, University of Maine, U.S. Fish and Wildlife Service, and the Wildlife Management Institute     

Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites

Microsatellite genetic markers are becoming increasing important tools in the investigation of alternate reproductive strategies in wild plants and animals, and in the implementation of optimal breeding programs for endangered species, and managed cultured populations. Overall, little attention is paid to the frequency and impact of scoring errors and mutations on the resolution and accuracy of such analyses. Here, parentage of 792 Atlantic salmon ( Salmo salar ) reared communally were determined using di- and tetranucleotide microsatellites. Over 99·5% of the offspring could be unambiguously matched to one set of parents in the original 12 (1 × 1) experimental cross (each of 12 males uniquely crossed to one of 12 females) and in a simulated 36 (1 × 1) cross (involving additional parents), and over 80% in a 12 × 12 cross (all 12 males crossed to all 12 females). Mutations were rare (≈3·4 × 10⁻⁻⁴), though scoring errors were relatively common (2–3% per allele scored), with the rate of error varying among loci. Approximately 90% of scoring errors (or mutations) are expected to be detected in this analysis, and of those that are not, fewer than 0·5% should lead to a false or incorrect determinations of parentage. Based on several indices, we expect that greater than 99·7% of offspring assayed were matched to their true parents.     

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.     

Type I microsatellite markers from Atlantic salmon (Salmo salar) expressed sequence tags

The detection of simple sequence repeats (SSRs) within expressed sequence tags (ESTs) connects potential microsatellite markers with specific genes, generating Type I markers. Using an in silico approach, we identified 1975 SSRs from the Genome Research on Atlantic Salmon Project EST database. We designed primers to amplify 158 SSRs, of which 65 amplified 76 loci (including 11 duplicated loci). Sixty‐one of the 76 loci were variable in 24 Atlantic salmon from seven populations, and 96% of these markers also amplify DNA from other salmonids. Functions for 16 of the SSR associated ESTs have been determined, confirming them as Type I markers.     

Vertical distribution of Atlantic salmon (Salmo salar) as a function of illumination

The vertical distribution of cultured Atlantic salmon larger than 1 kg was monitored by hydroacoustics in both a shallow (6 m) and a deep (20 m) cage. Surface light levels and fish distribution were registered for three periods throughout the year. The two fish groups were fed calculated rations twice a day. During the winter and spring (including vernal equinox), the fish were distributed at around 5 m depth in both cages when not feeding. Around summer solstice, the fish preferred deeper waters when not feeding. The light dependency of the vertical migration was pronounced, and indicates clearly that even a 20 m deep cage is not deep enough to meet the depth requirements of large Atlantic salmon during summer.     

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.     

Ocean migration and recaptures of tagged, triploid, mixed-sex and all-female Atlantic salmon (Salmo salar L.) released from rivers in Ireland

Fiftyfour thousand diploid and triploid Atlantic salmon were tagged with coded-wire micro-tags and released to the sea as smolts from two freshwater sites in Ireland in 1996 and 1997. Over 36,000 were mixed-sex groups in which the triploids (MS3N) were treated batches and the diploids (MS2N) were untreated batches of a single group of fertilized eggs at each site and year class. Over 17,000 were all-females, the triploids (AF3N) being treated batches and the diploids (AF2N) untreated batches of a single group of fertilized eggs at each site and year class. Adult tagged fish were subsequently recovered in the coastal fishery and in freshwater traps and angling fisheries in the rivers of release during 1997, 1998 and 1999. Recoveries from migration ranged from 0.08 to 9.79%. Diploid recoveries were within the normal ranges for salmon ranched from these sites, being between 0.64 and 1.82% at one site and between 3.85 and 9.79% at the other. Triploid recoveries, which occurred in the coastal fishery and in freshwater, ranged from 0.08 to 0.40% at the first site and from 0.98 to 2.05% at the other. Overall, triploid recoveries were between 12 and 24% of their diploid siblings within each release group. There were two peaks of recapture in the coastal fishery, the first in mid-June and the second in mid to late July. All-female diploids appeared to enter the fishery in advance of mixed-sex diploids. Triploids were the latest to arrive. There was no evidence of increased straying in triploids relative to diploids and the mean lengths, weights and condition factors were not significantly different between the ploidy groups. Triploidisation therefore reduced the home water harvest of treated salmon to less than 25% but did not completely eliminate triploid recaptures. The way in which triploidisation may influence the return of salmon from the oceanic feeding grounds is discussed.     

Evidence for multiple sex-determining loci in Tasmanian Atlantic salmon (Salmo salar)

Phenotypic sex in salmonids is determined primarily by a genetic male heterogametic system; yet, sex reversal can be accomplished via hormonal treatment. In Tasmanian Atlantic salmon aquaculture, to overcome problems associated with early sexual maturation in males, sex-reversed females are crossed with normal females to produce all female stock. However, phenotypic distinction of sex-reversed females (neo-males) from true males is problematic. We set out to identify genetic markers that could make this distinction. Microsatellite markers from chromosome 2 (Ssa02), to which the sex-determining locus (SEX) has been mapped in two Scottish Atlantic salmon families, did not predict sex in a pilot study of seven families. A TaqMan 64 SNP genome-wide scan suggested SEX was on Ssa06 in these families, and this was confirmed by microsatellite markers. A survey of 58 families in total representing 38 male lineages in the SALTAS breeding program found that 34 of the families had SEX on Ssa02, in 22 of the families SEX was on Ssa06, and two of the families had a third SEX locus, on Ssa03. A PCR test using primers designed from the recently published sdY gene is consistent with Tasmanian Atlantic salmon having a single sex-determining gene that may be located on at least three linkage groups.     

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.     

Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar)

Evidence of selection acting on major histocompatibility complex (MHC) genes has been illustrated with the analysis of their nucleotide sequences and allele frequency distribution. Comparing the patterns of population differentiation at neutral markers and MHC genes in the wild may provide further insights about the relative role of selection and neutrality in shaping their diversity. In this study, we combine both methods to assess the role of selection on a MHC gene in Atlantic salmon. We compare variation at a MHC class II B locus and microsatellites among 14 samples from seven different rivers and seven subpopulations within a single river system covering a variety of habitats and different geographical scales. We show that diversifying selection is acting on the sites involved in antigen presentation and that balancing selection maintains a high level of polymorphism within populations. Despite important differences in habitat type, the comparison of the population structure at MHC and microsatellites on large geographical scales reveals a correlation between patterns of differentiation, indicating that drift and migration have been more important than selection in shaping population differentiation at the MHC locus. In contrast, strong discrepancies between patterns of population differentiation at the two types of markers provides support for the role of selection in shaping population structure within rivers. Together, these results confirm that natural selection is influencing MHC gene diversity in wild Atlantic salmon although neutral forces may also be important in their evolution.     

The effects of prior residence on behavior and growth rates in juvenile Atlantic salmon (Salmo salar)

It is well documented that prior residence confers advantagesin territorial disputes, but its impact on other aspects ofbehavior and fitness is less understood. We tested how priorresidence influences the subsequent feeding behavior and growthperformance of dispersing Atlantic salmon fry (Salmo salar)using experimental manipulations of residence in a seminaturalstream tank. In replicated trials, groups of seven "primary"fish were released into the stream tank 3 days ahead of seven"secondary" fish. Standardized behavioral observations were madeon each fish over the following 14 days, after which all fishwere removed and measured. Primaries and secondaries were initiallythe same size and body condition and exhibited the same degreeof site fidelity. However, primaries darted higher into thewater column to intercept prey items, fed at a higher rate,and subsequently grew faster. Larger fish (in terms of body length)tended to be more dominant, and dominants grew faster than subordinates.However, there was no difference in dominance between primaries andsecondaries. These results suggest that the well-documentedadvantage of early-emerging salmon fry over late-emerging frycannot be completely attributed to intrinsic differences andthat the advantage is partly mediated via a prior residenceeffect. Furthermore, prior residents gain foraging advantageswithout necessarily becoming more dominant.     

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.     

Spawning-strategy-dependent diets in two North American populations of Atlantic salmon Salmo salar

The diet of repeat-spawner Atlantic salmon Salmo salar was investigated using carbon and nitrogen stable-isotope values from the outer growth band of scales, which reflect the fish's consumption and growth during their most recent marine phase. Isotope values for S. salar displaying different spawning strategies were compared between and within the Miramichi and Nashwaak Rivers, New Brunswick, Canada and a Bayesian mixing model was used to infer dietary contributions from potential prey items. Significant differences in the stable-isotope values were found among spawning strategies and between rivers, indicating differences in diet and feeding area, consistent with hypotheses. Bayesian mixing model results inferred the main prey items consumed during marine feeding by S. salar to consist of hyperiid amphipods and capelin Mallotus villosus for repeat alternate spawners from both rivers, sandlance Ammodytes sp. for repeat consecutive spawners from the Miramichi River and amphipods for repeat consecutive spawners from the Nashwaak River. These results demonstrate the diversity of feeding tactics among S. salar spawning strategies from the same river and between populations from different rivers. Accounting for differences in prey availability and the subsequent impact on S. salar diet and spawner return rates (i.e., marine survival) will facilitate the application of ecosystem-based management practices, such as ensuring that fisheries for forage species do not indirectly adversely affect S. salar return rates.     

Atlantic salmon (Salmo salar) of the Pigou and Bouleau Rivers,Quebec

Synopsis Juvenile Atlantic salmon of the Pigou and Bouleau Rivers, Quebec, were studied during the summer of 1972 and 1973. Growth increments for Pigou salmon averaged 36–50 mm yr^–1 and smolts averaged 2.9 yrs old. Bouleau salmon grew slower (26–41 mm yr^–1) and became smolts at a slightly older mean age (3.1 yrs). Mature male parr were more abundant in all age-groups from the Plgou River, possibly because of the faster growth. In terms of management, the Pigou River has little potential for increased salmon production because of limited habitat. On the other hand, the Bouleau River has considerable potential, and salmon production could be increased if the upper reaches were made accessible to migrating salmon.Contribution number 36 of the Matamek Research Station, Woods Hole Oceanographic Institute.