If HWE is assumed in a two-level population hierarchy, the data can be treated as haploid data where allele, not genotype, frequencies are used in the calculations. Because, in this scenario, Pop Theta (F_ST) and Overall F (F_IT) are equal and Within Pop f=0 (F_IS=0), only one parameter, Pop_Theta (F_ST), which represents the covariance of alleles from the same population relative to the covariance between alleles from different populations to estimate, must be estimated.
