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Samples were collected from broodstocks of five major domesticated strains and from four Norwegian major wild stocks. The individuals were screened for genetic variability at eight enzyme coding loci. The domesticated strain which is based mainly on R. Namsen and R. Surna differed significantly from both of its source populations at most of the loci studied. In the DOM‐2 strain a slow allele at MDH‐2*, not found in any of the other samples, was found at a comparatively high frequency (0·127). At MEP‐2*, allelic frequencies varied much, with two domesticated strains close to fixation for alternative alleles. In the samples from wild stocks, the frequencies of MEP‐2* lay around 0·5. These changes are likely caused by founder effects, genetic drift and the ongoing selection programmes. The amount of genetic variability differed among the domesticated strains. Also, mean number of alleles were about 12% lower in farmed strains than in wild stocks, and percentage polymorphic loci were 14% lower in farmed strains. Mean heterozygosity was about 17% lower in farmed strains than in wild stocks. FST, varied strongly among loci and was particularly high for MEP‐2* and ESTD*, with a mean of 0·119, compared to 0·021 for the wild stocks separately. The genetic distance between DOM‐1 and its source populations in River Namsen and River Surna was several times higher than that observed between the wild populations. This demonstrates that a rapid and significant change has taken place over seven generations. The ESTD*94 allele, typical for North American salmon, and absent in all other samples in the present study, was found in fairly high frequency in the northern River Neiden wild sample. This suggests the existence of a barrier to gene flow between salmon from North Norway and more southern populations, and reflects that northern salmon are slightly or not at all represented in the domesticated strains.