Table 2.

Expected Genotype Frequencies under Random Mating.

	BB	Bb	bb	Exp. Freq.
AA	g 1	g 2	g 3	p 2
Aa	g 4	g 5	g 6	$2p(1-p)$
aa	g 7	g 8	g 9	${(1-p)}^2$
Exp. freq.	q 2	$2q(1-q)$	${(1-q)}^2$	1

Note.—For a given pair or loci, the nine possible two-locus genotypes have frequencies which sum to 1. We assume random mating, so expected marginal genotype frequencies follow expected Hardy–Weinberg proportions. The g_i’s are shorthand for each of the possible observed two-locus genotypes. For example, a diploid sample where we observe the left locus heterozygous as Aa and the right locus homozygous bb contributes to frequency g₆.