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In the beginning of the section, the effective population size was defined by how genetic variation in a population behaves over time. In ideal populations that are not changing much in census size over time, the different effective sizes are usually equivalent. In some situations, however, the different types of effective population size are not equivalent since they measure different aspects of genetic variation (Ewens 1982; Crow & Denniston 1988; Crandall et al. 1999).

A good way to understand the variance and inbreeding effective population sizes is to employ them with genetic data taken from a finite population experiencing genetic drift. Figure 3.20 shows the allele frequencies, change in allele frequencies, and change in heterozygosity in 10 simulated populations over four generations. The effective population sizes fluctuated from 100 to 10 to 50 and then back to 100 over four generations. Using equation 3.42, we would expect the genetic variation in this simulated population to exhibit the same amount of genetic drift over four generations as a population with a constant size of about 28 or 29 individuals.

The heterozygosities and allele frequencies in the 10 simulated populations are given in Tables 3.4 and 3.5. The change in heterozygosity can be used to estimate the inbreeding effective population, since the heterozygosity can be thought of as one minus the autozygosity. The decline in heterozygosity with time (equation 3.52) can be approximated by:

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