Measures of divergence between populations and the effect of forces that reduce variability

Wright's F-ST and related statistics are often used to measure the extent of divergence among populations of the same species relative to the net genetic diversity within the species. This paper compares several definitions of F-ST which are relevant to DNA sequence data, and shows that these must be used with care when estimating migration parameters. It is also pointed out that F-ST is strongly influenced by the level of within-population diversity. In situations where factors such as selection on closely linked sites are expected to have stronger effects on within population diversity at some loci than at others, differences among loci can result entirely from differences in within-population diversities. It is shown that several published cases of differences in F-ST among regions of high and low recombination in Drosophila may be caused in this way. For the purpose of comparisons of levels of between-population differences among loci or species which are subject to different intensities of forces that reduce variability within local populations, absolute measures of divergence between populations should be used in preference to relative measures such as F-ST.