We have developed a method for the analysis of microsatellite data that is useful in the elucidation of the demographic history of populations. This method, the P(K) distribution method of pairwise comparisons, is analogous to the mismatch distribution of sequence comparisons developed for the analysis of mitochondrial sequence data by Rodgers and Harpending and is defined as the distribution of the number of repeat unit differences between alleles when each allele in a sample is compared with every other allele in the sample. Using computer simulations of microsatellite loci, we show that the shape of the distribution of P(K) changes in a distinctive manner as a function either of time since population expansion or effective population size. Increases in both of these affect the P(K) distribution in a similar fashion leading to a change from a steep distribution with a P(O) peak to one with a nonzero peak. Analysis of three data sets from surveys of microsatellite loci in ethnographically defined populations reveals that most (9/12) of the African populations analyzed, but none of the 30 non-African populations showed P(K) distributions with nonzero peaks. These P(K) distributions indicate either an earlier expansion or a larger effective population size for African populations. This observation is consistent with the hypothesized African origin of modern human.
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