Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta).

A comparative study between microsatellite and allozyme markers was conducted on natural populations of resident brown trout (Salmo trutta) sampled over a reduced geographical scale and on hatchery strains. The higher level of polymorphism observed at microsatellite loci resulted in higher power of statistical tests for differentiation among population samples and for genotypic linkage disequilibrium. Genetic distances of Cavalli-Sforza and Edwards were on average two times larger for microsatellites than for allozymes but multilocus FST estimates computed over the entire set of populations were not significantly different for both categories of markers. Assignment tests of individual fish to the set of sampled populations demonstrated a much higher efficiency of microsatellites compared to allozymes. Pairwise multilocus FST estimates were significantly correlated to waterway distances and there was a significant tendency for the incorrectly classified individuals to be assigned to one of the nearest populations, indicating that isolation-by-distance acted significantly on brown trout populations. This increase of differentiation with distance was higher for allozymes than for microsatellites. Traditional measures of genetic differentiation (Cavalli-Sforza and Edwards' chord distance and FST) were compared for microsatellites to recently proposed statistics taking into account allele size differences (Goldstein's distance and PST). Using Goldstein's distance for neighbour-joining analysis did not improve the tree structure resolution. Multilocus estimates of PST and FST were not significantly different when computed over the entire set of populations but no significant correlation was detected between matrices of pairwise multilocus PST estimates and waterway distances.