Use of differential expression data for identification of novel immune relevant expressed sequence tag-linked microsatellite markers in Atlantic salmon (Salmo salar L.)

Despite the large number of genes contributing to the immune response, wildlife immunogenetic studies have tended to focus mostly on the major histocompatibility complex-related genes. Here, we utilized previously published microarray and competitive RNA hybridization information to identify 3750 immune relevant Atlantic salmon (Salmo salar) expressed sequence tags. We then identified those expressed sequence tags containing microsatellites and subsequently designed 48 primer pairs and tested them for polymorphism in Atlantic salmon. Altogether, 16 polymorphic markers were characterized, with allele numbers ranging from two to 18, and these 16 loci were further tested in five other salmonid species.     

Effects of long-term exercise on survival, homing and straying of released Atlantic salmon smolts

Atlantic salmon 1+ pre-smolts were exercised under low (LE) or moderate (ME) water current velocities prior to release. The flow regimes had a minor effect on freshwater growth and did not affect total Carlin-tag recaptures significantly, but the LE adults strayed more frequently and the ME salmon homed more successfully to the release site.     

Isolation and characterization of variable (GT)n repetitive sequences from Atlantic salmon, Salmo salar L.

Microsatellites are islands of long repeats of mono-, di- or trinucleotides evenly distributed in the eukaryotic genome with an average distance of 50–100 kb. They display a high degree of length polymorphism and heterozygosity at individual loci, making them highly useful as markers in the development of genomic maps of eukaryotes. In the present work, we examined the dinucleotide repeat motif (dG-dT)_n in the Atlantic salmon, Salmo salar L., genome. The frequency of (dG-dT)_n microsatellites in salmon correlates well with earlier published estimations. Cloning and sequencing of 45 salmon microsatellites revealed perfect and imperfect repeats, but no compound microsatellites. The distribution of number of repeat units in salmon microsatellites differ significantly from that of higher vertebrates. Salmon tends to have more long repeat stretches and less intermediate length repeats.     

Wild adult hybrids of Salmo salar L. and Salmo trutta L.

Ovarian development was impaired in three adult Salmo salar L. × S. trutta L. hybrids identified among adult salmonids in Scottish fisheries. Species-specific variation at enzyme loci indicated that the fish were F1 hybrids and mitochondrial DNA analysis showed them to be the progeny of S. salar females.     

Assessing introgression of foreign strains in wild Atlantic salmon populations: variation in microsatellites assessed in historic scale collections

1. Genetic variation at five microsatellite loci was analysed in a collection of scales (1970–97) sampled from Atlantic salmon adults returning to the Nivelle River (South France).
2. Native and foreign fish (from an allochthonous Scottish stock introduced into the river to increase population size) were clearly identified as all foreign individuals released in the river were physically marked.
3. Introgression of foreign genes into the native gene pool has occurred, although the reproductive success of foreign Atlantic salmon in the wild was lower than that of native individuals.
4. The utility of old scale samples for investigating the impact of foreign stocking on wild fish populations is demonstrated in this work.     

The relationship between smolt density and fry density in salmonids

If the Ricker stock–recruitment model describes the relationship between egg density and survivor density at different stages of the life cycle, then the relationship between smolt density and fry density is not simple. Using data from a long-term study (1966–1990) of a sea trout population Salmo trutta , the relationship between density of potential smolts and fry densities in late M ay/early June or late August/early September is shown to be a reflexed curve with zero origin, so that there are two smolt densities for each fry density. A linear relationship is obtained only when the exponential parameter in the Ricker model is constant for the different life Stages.     

Introgression in the genus Salmo via allotriploids

Hybridization between sympatric species is not uncommon in the wild. Wild allotriploids (individuals with two chromosome sets from a species + one chromosome set from another species) are generally the result of a backcross between interspecific hybrids that produce unreduced gametes and one of the parental species. In animals, allotriploids are commonly sterile, except for some vertebrate species complexes in which allotriploids reproduce by parthenogenesis, gynogenesis and/or hybridogenesis, producing generally clonal or hemiclonal gametes; nuclear DNA introgression between hybridizing species is considered to be extremely rare. Employing species-specific molecular markers, we show genetic introgression between the chromosomally well-differentiated salmonids Atlantic salmon (2n = 58) and brown trout (2n = 80) through spontaneous bisexual reproduction of allotriploids leading to salmon-like offspring bearing some brown trout genes. Although introgression between these Salmo species can occur via allotriploids, we hypothesize that extinction of parental species can be discarded based on very low survival of allotriploid offspring.     

Demographics and landscape features determine intrariver population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland

Contemporary genetic structure of Atlantic salmon (Salmo salar L.) in the River Moy in Ireland is shown here to be strongly related to landscape features and population demographics, with populations being defined largely by their degree of physical isolation and their size. Samples of juvenile salmon were collected from the 17 major spawning areas on the river Moy and from one spawning area in each of five smaller nearby rivers. No temporal allele frequency differences were observed within locations for 12 microsatellite loci, whereas nearly all spatial samples differed significantly, suggesting that each was a separate population. Bayesian clustering and landscape genetic analyses suggest that these populations can be combined hierarchically into five genetically informative larger groupings. Lakes were found to be the single most important determinant of the observed population structure. Spawning area size was also an important factor. The salmon population of the closest nearby river resembled genetically the largest Moy population grouping. In addition, we showed that anthropogenic influences on spawning habitats, in this case arterial drainage, can affect relationships between populations. Our results show that Atlantic salmon biodiversity can be largely defined by geography, and thus, knowledge of landscape features (for example, as characterized within Geographical Information Systems) has the potential to predict population structure in other rivers without an intensive genetic survey, or at least to help direct sampling. This approach of combining genetics and geography, for sampling and in subsequent statistical analyses, has wider application to the investigation of population structure in other freshwater/anadromous fish species and possibly in marine fish and other organisms.     

Genetic variation at the Me-2 locus in the Atlantic salmon within and between rivers: evidence for its selective maintenance

Spatial variation at the diallelic Me-2 locus in the Atlantic salmon, Salmo salar L., was analysed using data from 95 river basins. Gene diversity was apportioned as follows: 63% within samples, 20% between North America and Europe, 14% between regions within continents and 3% within and among rivers within regions. On both continents the variation between rivers was clinal with latitude and highly correlated with summer temperatures. The correlation was detectable within and between rivers. These correlations strongly suggest that variation at the locus is subject to the direct or indirect effects of natural selection, and that caution is required when interpreting between-location differentiation at the locus as evidence for distinct stocks.