Relationships between intrapopulational and interpopulational genetic diversity in man

The bottleneck effect (or extended period of reduced population size) is known to increase genetic distance (D) substantially, and this can be a serious factor that disturbs the phylogenetic relationships of populations inferred from genetic distance estimates. The bottleneck effect is also known to be a factor that disturbs the hierarchial relationships of the fixation indices (F_ST) or the coefficients of gene differentiation (G_ST) in subdivided populations. To examine the extent of the bottleneck effect on D and G_ST in human populations, the D and G_ST values were computed for various groups of populations from around the world, and their relationships with within-population heterozygosities were examined by using gene frequency data for protein and immunological loci. The results obtained indicate that the D value between a pair of populations is negatively correlated with the average within-population heterozygosity. This suggests that genetic distance estimates for small populations are seriously affected by the bottleneck effect, and that phylogenetic trees should be studied by taking into account this factor. The bottleneck effect on G_ST was also revealed from examination of the total gene diversity H_T and its components, interpopulational genetic variation (D_ST) and intrapopulational genetic variation (H_S). That is, a large value of G_ST in small populations was sometimes associated with the decrease of H_S rather than the increase of D_ST. Generally speaking, however, G_ST was larger when geographically distant populations were considered than when closely located populations were considered. When there is any trace of bottleneck effects, phylogenetic trees should be constructed by a method in which the rate of evolutionary change is allowed to vary from branch to branch.