The average difference between observed and Hardy-Weinberg expected heterozygosity within each subpopulation due to non-random mating. The correlation between the states of two alleles in a genotype sampled at random from any subpopulation. The reduction in heterozygosity due to subpopulation divergence in allele frequency. The difference between the average expected heterozygosity of subpopulations and the expected heterozygosity of the total population. Alternately, the probability that two alleles sampled at random from a single subpopulation are identical given the probability that two alleles sampled from the total population are identical.

The correlation between the states of two alleles in a genotype sampled at random from a single subpopulation given the possibility of non-random mating within populations and allele frequency divergence among populations.

uniform allele frequencies among subpopulations expected with panmixia.

Accounting for non-random mating and divergence of subpopulation allele frequency necessitates several new versions of the fixation index. The definitions of these new fixation indices are shown in Table 4.6. Let's employ and interpret each of these versions of the fixation index for the example in Fig. 4.6. FIS compares average observed heterozygosity of individuals in each subpopulation and the average Hardy-Weinberg expected heterozygosity for all subpopulations (the I stands for individuals and the S for subpopulations). FIS is identical to the single-population F used in section 2.5 except that it is now an average for all subpopulations. Using the heterozygosities determined above,

This is a result that makes biological sense since there are fewer heterozygotes in each subpopulation than would be expected under random mating given the subpopulation allele frequencies. Thus, there is more homozygosity or fixation within the two subpopulations than expected under random mating. The subpopulations on average have a deficit of heterozygosity as expected if there is consanguineous mating taking place.

The next level in the hierarchy is the average expected heterozygosity for subpopulations compared with expected heterozygosity for the total population or Fst (the S stands for subpopulations and the T for the total population). Based on the heterozygosities determined previously,

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