Biallelic markers such as single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms have become increasingly popular markers for various population genetics applications. However, the effort required to develop biallelic markers in nonmodel organisms is still substantial. In this study, we compared the estimation of various population genetic parameters (genetic divergence and structuring, isolation-by-distance, genetic diversity) using a limited number of biallelic markers (in total 7 loci) to those estimated with 14 microsatellite loci in 21 Atlantic salmon (Salmo salar) populations from northern Europe. Pairwise F ST values were significantly correlated between biallelic loci and microsatellite datasets, as was overall heterozygosity when both anadromous and nonanadromous populations were analyzed together. However, when the anadromous and nonanadromous samples were analyzed separately, only genetic divergence correlations remained significant. Biallelic markers alone were not sufficient for reliable neighbor-joining clustering of populations but gave highly similar isolation-by-distance signals when compared with microsatellites. Finally, although several population prioritization measures for conservation exhibited significant correlation between different marker types, the specific populations highlighted as being most valuable for conservation purposes varied depending on the marker type and conservation criteria applied. This study demonstrates that a relatively small set of biallelic markers can be sufficient for obtaining concordant results in most of the analyses compared with microsatellites, although estimates of genetic distance are generally more concordant than estimates of genetic diversity. This suggests that a relatively small number of biallelic markers can provide useful information for various population genetic applications. However, we emphasize that the use of much higher number of loci is preferable, especially when the genetic differences between populations are subtle or individual multilocus genotype-based analyses are to be performed.

Background: Single nucleotide polymorphisms (SNPs) represent the most abundant type of DNA variation in the vertebrate genome, and their applications as genetic markers in numerous studies of molecular ecology and conservation of natural populations are emerging. Recent large-scale sequencing projects in several fish species have provided a vast amount of data in public databases, which can be utilized in novel SNP discovery in salmonids. However, the suggested duplicated nature of the salmonid genome may hamper SNP characterization if the primers designed in conserved gene regions amplify multiple loci.

The level and hierarchical distribution of genetic variation in complete sequences of the Atlantic salmon (Salmo salar) growth hormone (GH1) gene were investigated in populations from Europe and North America with a view to inferring the major evolutionary forces affecting genetic variation at this locus. Seventeen polymorphic sites were identified in complete sequences from nine populations, with levels of noncoding (intron and untranslated region sequences) nucleotide diversity being similar to those observed in other species. No variation, however, was observed in exonic sequences, indicating that nucleotide diversity in the Atlantic salmon GH1 gene is three and 25 times less than that estimated for human and Drosophila coding sequences, respectively. This suggests that purifying selection is the predominant contemporary force controlling the molecular evolution of GH1 coding sequences. Comparison of haplotype relationships within and between populations indicated that differentiation between populations from Europe and North America was greater than within-continent comparisons. However, several haplotypes observed in the northernmost European populations were more similar to those observed in North American than to any other haplotypes observed in Europe. This is most likely to be a result of historical, rather than contemporary, gene flow. Neutrality test statistics, such as Tajima's D, were significantly positive in the European populations in which North American-like haplotypes were observed. Although a positive Tajima's D is commonly interpreted as the signal of balancing selection, a more likely explanation in this case is that either historical migration or ascertainment bias, rather than within population local adaptation, has given rise to an excess of intermediate frequency alleles.

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We report the identification of intraspecific sequence variation in the Atlantic salmon (Salmo salar) growth hormone 1 gene. Rapid and inexpensive assays for polymorphism detection were developed for 10 sites. Five of the assays detected single nucleotide polymorphisms (SNPs) using polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analyses, and five were indel polymorphisms, detected using fragment length analyses. The average within population frequency of the most common allele varied from 0.52 to 0.90, and the average within population heterozygosity varied from 0.02 to 0.37 in seven European salmon populations.