We describe genetic variation at three microsatellite single loci and six allozyme loci of seven natural Atlantic salmon populations from Ireland and Spain. A comparison of genetic variability detected at both types of loci is performed. Also, the relative value of microsatellite single locus variability with regard to the identification of individual salmon populations is assessed. Microsatellite loci are shown to display higher levels of variation than allozyme loci.Mean number of alleles (6 1.53) and heterozygosity (0.46 0.04) at microsatellite loci are greater than those found for allozymes (1.85±0.05 and 0.21±0.03, respectively), and some microsatellite alleles appear to be specific for a location or geographical area. Allozyme and microsatellite variation show the same pattern of differentiation between populations with Irish and Spanish populations grouped into different clusters. However, greater values of genetic distance were found among microsatellite (D = 0.0747±0.011) rather than among allozyme loci (D = 0.0449 0.008). These results provide evidence that microsatellite-based analysis of genetic variation will be useful in the identification of individual populations of Atlantic salmon.

Electrophoretic studies of proteins remain a primary source of insight into genetic diversity in many species including the Atlantic salmon Salmo salar, one of the most culturally and economically important fish species of the North Atlantic region. Since 1966, >350 scientific papers on protein variation have been published encompassing 25 000þ salmon from over 400 locations in >200 river systems across the species' distribution. Variation has been detected at 30% of the 110 protein loci screened, though most studies examine <40. The method has been applied largely to the investigation of population structure and differentiation, but work has also led to the systematic revision of the genus Salmo and remains the primary source of insight into hybridization in the wild with brown trout Salmo trutta. Spatial patterns of differentiation show temporal stability, both within and among river systems, and strongly support structuring of the species into river and tributary specific populations and the designation of European and North American populations as distinct sub-species. They also show widespread regional differentiation within both continents, beyond the marked subcontinental differences between Baltic Sea and Atlantic Ocean populations in Europe. Most of the differentiation probably reflects gene flow and founder events associated with colonization following the retreat of the glaciers from much of the species' modern range. However, variation at MEP-2* shows strong correlations with environmental temperature, both within and among rivers, and associations with phenotypic performance. This suggests selection is acting on the locus and provides †Author to whom correspondence should be addressed. Tel.: þ44 (0) 796 472060; fax: þ44 (0) 1796 473523; # 2005 Crown copyright compelling evidence for the local adaptation of populations. Protein studies have led to more population centred management of the species and have been exploited in the discrimination of regional stocks in mixed stock analysis in high seas fisheries, particularly in the Baltic Sea, and as markers for the assessment of stocking success. They have also advanced insight into how the genetic character of populations can be changed in cultivation and the potential impact of salmon aquaculture and stocking on wild populations. The method has been largely superseded by DNA based analyses, but the results remain highly relevant to Atlantic salmon management and conservation and are an irreplaceable data set for studying genetic stability of populations over time. # 2005 Crown copyright

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The relationship between heterozygosity at genetic markers (six allozyme and eight microsatellite loci), and fluctuating asymmetry (FA), length and weight was investigated in two samples of Atlantic salmon (Salmo salar L.) with different timings of first active feeding (early (EA) and late (LA) salmon). This trait had previously been related to fitness. EA fish show smaller values of FA, are longer, heavier and are more heterozygous at allozyme loci than are conspecific LA fish. Also within both samples, heterozygosity at allozyme loci was inversely related to FA and was positively related to weight and length. However, no significant differences in microsatellite diversity (heterozygosity and mean d 2 measurements) were observed between samples (EA vs LA). Furthermore, no association was observed between the variability at microsatellite loci and FA, weight or length within each sample. These results suggest that allozyme loci, in themselves, influence fitness components, rather than associations arising from associative overdominance.

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