Abstract
The effect of natural selection on the m MEP‐2 * locus on measures of genetic divergence among Atlantic salmon populations was investigated by examining the pattern of change in the level of genetic differentiation (F ST ) averaged over loci when data on the m MEP‐2 * locus were either included or excluded. The level of F ST among populations at various geographic scales was estimated from allele frequencies at up to four loci ( s AAT‐4 *, IDDH‐1 *, IDHP‐3 *, and m MEP‐2 *). At smaller geographic scales (within river systems or limited geographic regions) levels of variance in m MEP‐2 * allele frequencies were reduced relative to mean levels. At larger geographic scales (across continents or the species range) variation in m MEP‐2 * allele frequencies was greater than mean levels. These results suggest an a priori hypothesis for the effect of selection on the m MEP‐2 * locus which may be applied in future studies on variation in protein coding or other (e.g. mini‐ and microsatellite) loci in the Atlantic salmon. It is recommended that estimates of gene flow among populations of the Atlantic salmon based on mean F ST estimates which include data on the m MEP‐2 * locus should be viewed with caution.