Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision.

Unbiased estimates of theta = 4Nmicro in a random mating population can be based on either the number of alleles or the average number of nucleotide differences in a sample. However, if there is population structure and the sample is drawn from a single subpopulation, these two estimates of theta behave differently. The expected number of alleles in a sample is an increasing function of the migration rates, whereas the expected average number of nucleotide differences is shown to be independent of the migration rates and equal to 4N(T)micro for a general model of population structure which includes both the island model and the circular stepping-stone model. This contrast in the behavior of these two estimates of theta is used as the basis of a test for population subdivision. Using a Monte-Carlo simulation developed so that independent samples from a single subpopulation could be obtained quickly, this test is shown to be a useful method to determine if there is population subdivision.