The genotypic values (see Theory section) for the simple AA model for double homozygotes BBCC and bbcc are +2a and for bbCC and BBcc are 0, and all single or double heterozygotes are intermediate (+a). With linkage equilibrium, V A/V G = 1−HpHq/[Hp+Hq−3HpHq], where the heterozygosities are Hp and Hq at loci B and C. Thus V A/V G → 1 if either locus is at extreme frequency (i.e. p or q → 0 or 1), and equals 0 when p = q = 0.5. If p = q, for gene frequencies 0.1, 0.2, 0.3 and 0.4, V A/V G = 0.88, 0.69, 0.43 and 0.14. For the uniform distribution η 2 = 2/3, and for the ‘U’ distribution, the variances are a function of the population size, because more extreme frequencies are possible at larger population sizes. Thus η 2 = (2−4/K)/(2−3/K), where K = ln(2N), so η 2 → 1 for large K. Any residue is V AA.
