Abstract
Four tributaries of Lake St‐Jean (Québec, Canada) are used for spawning and juvenile habitat by land‐locked Atlantic salmon. Spawning runs have drastically declined since the mid‐1980s, and consequently, a supportive‐breeding programme was undertaken in 1990. In this study, we analysed seven microsatellite loci and mtDNA, and empirically estimated effective population sizes to test the hypotheses that (i) fish spawning in different tributaries form genetically distinct populations and (ii) the supportive breeding programme causes genetic perturbations on wild populations. Allele frequency distribution, molecular variance and genetic distance estimates all supported the hypothesis of genetic differentiation among salmon from different tributaries. Gene flow among some populations was much more restricted than previously reported for anadromous populations despite the small geographical scale (40 km) involved. Both mtDNA and microsatellites revealed a more pronounced differentiation between populations from two tributaries of a single river compared with their differentiation with a population from a neighbouring river. The comparison of wild and F 1 ‐hatchery fish (produced from breeders originating from the same river) indicated significant changes in allele frequencies and losses of low‐frequency alleles but no reduction in heterozygosity. Estimates of variance and inbreeding population size indicated that susceptibility to genetic drift and inbreeding in one population increased by twofold after only one generation of supplementation.