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where pi and qi are the allele frequencies in subpopulation i and there are n subpopulations. We could use the notation 2pq since the expected heterozygosity is determined for each subpopulation and then averaged. Here the observed allele frequency is used to estimate the Hardy-Weinberg expected heterozygos-ity for each subpopulation.

At the most inclusive level in a subdivided population, we can calculate the expected heterozygosity of the total population:

where p and q are average allele frequencies for all the subpopulations. The average allele frequency for all subpopulations is equivalent to combining all alleles for all subpopulations into a single population and then simply estimating allele frequencies. In other words, it is the allele frequency for the total population without any divergence among subpopulations taken into account. HT is therefore the Hardy-Weinberg expected frequency of heterozygotes in the entire population if there were no population structure of allele frequencies.

These different levels of observed and expected heterozygosity are diagrammed in Fig. 4.6 for the case of a total population composed of two subpopulations that each contain 10 diploid individuals. In both subpopulations, three of the 10 individuals are heterozygotes giving observed heterozygote

Total population (HT)

Subpopulation 1

Subpopulation 2

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