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.
