A comparison of two indirect methods for estimating average levels of gene flow using microsatellite data

We compare the performance of Nm estimates based on F-ST and R-ST obtained from microsatellite data using simulations of the stepwise mutation model with range constraints in allele size classes. The results of the simulations suggest that the use of microsatellite loci can lead to serious overestimations of Nm, particularly when population sizes are large (N > 5000) and range constraints are high (K <20). The simulations also indicate that, when population sizes are small (N less than or equal to 500) and migration rates are moderate (Nm approximate to 2), violations to the assumption used to derive the Nm estimators lead to biased results. Under ideal conditions, i.e. large sample sizes (n(s) greater than or equal to 50) and many loci (n(l) greater than or equal to 20), R-ST performs better than Fs, for most of the parameter space. However, F-ST-based estimates are always better than R-ST when sample sizes are moderate or small (n(s) less than or equal to 10) and the number of loci scored is low (n(l) <20). These are the conditions under which many real investigations are carried out and therefore we conclude that in many cases the most conservative approach is to use F-ST.