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

Abstract

We compare the performance of Nm estimates based on FST and RST 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 </= 500) and migration rates are moderate (Nm approximately 2), violations to the assumption used to derive the Nm estimators lead to biased results. Under ideal conditions, i.e. large sample sizes (ns >/= 50) and many loci (nl >/= 20), RST performs better than FST for most of the parameter space. However, FST-based estimates are always better than RST when sample sizes are moderate or small (ns </= 10) and the number of loci scored is low (nl < 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 FST.

Detecting loci under selection in a hierarchically structured population

“…Note that this interpretation problem does not occur when one computes r ST instead of F ST because highly mutable loci can show both large heterozygosity and large r ST (see Figure 2a). Thus, although it has been advocated that the use of F ST should be preferred over that of r ST for estimating migration rates (for example, Gaggiotti et al, 1999), we find here that the use of r ST seems more appropriate than F ST when detecting STR loci under selection because r ST is essentially unbiased (Slatkin, 1995, and Figure 2), and because the testing procedure based on coalescent simulations adequately handles r ST variability across loci.…”

Mito-nuclear discordance in the degree of population differentiation in a marine goby

“…Moreover, R ST can be less accurate in reflecting population differentiation because of its higher associated variances (Balloux and Lugon-Moulin, 2002). Therefore, the number of loci screened has to increase before a consistent pattern is reached (Gaggiotti et al, 1999;Balloux and Goudet, 2002). This has already been empirically observed with European grayling Thymallus thymallus (Koskinen et al, 2004).…”

“…This suggests that, although both measures are correlated, F ST correlates better with mtDNA than R ST . In theory, F ST is more sensitive than R ST for recent intraspecific divergence (Gaggiotti et al, 1999;Balloux and Lugon-Moulin, 2002). Moreover, R ST can be less accurate in reflecting population differentiation because of its higher associated variances (Balloux and Lugon-Moulin, 2002).…”

Microsatellite DNA variation indicates low levels of genetic differentiation among cuttlefish (Sepia officinalis L.) populations in the English Channel and the Bay of Biscay

“…As it is still a matter of debate which is the most suitable statistic model to describe genetic variation among samples (see Goodman, 1997;Valsecchi et al, 1997;Gaggiotti et al, 1999;Hardy et al, 2003), both models were used to analyse the data of this study: The IAM-based F ST (Wright, 1969), which can also be estimated by θ (Cockerham and Weir, 1984), and the SMMbased R ST (Slatkin, 1995) were calculated pairwise for all four populations using the Arlequin software v.2.000. F ST and R ST values were tested for significant departure from zero using permutation procedures implemented in Arlequin v.2.000.…”