Fu's $F_S$

Fu [3] proposes a different statistic based on the infinite sites model of mutation. He suggests estimating the probability of observing a random sample with a number of alleles equal to or smaller than the observed value under given the observed level of diversity and the assumption that all of the alleles are selectively neutral. If we call this probability $\hat S$, then

$$F_S = \ln\left(\frac{\hat S}{1 - \hat S}\right) \quad .$$

A negative value of $F_S$ is evidence for an excess number of alleles, as would be expected from a recent population expansion or from genetic hitchhiking. A positive value of $F_S$ is evidence for an deficiency of alleles, as would be expect from a recent population bottleneck or from overdominant selection. Fu's simulations suggest that $F_S$ is a more sensitive indicator of population expansion and genetic hitchhiking than Tajima’s $D$. Those simulations also suggest that the conventional P-value of 0.05 corresponds to a P-value from the coalescent simulation of 0.02. In other words, $F_S$ should be regarded as significant if $P < 0.02$.