In this analysis we have assumed there is Hardy-Weinberg equilibrium (HWE) and linkage equilibrium among the loci. As departures from HWE are transient with random mating, they can be ignored, but LD can persist, and hence the estimated effects at locus C depend on those fitted at B and vice versa. The effect of LD is to reduce the number of haplotypes that segregate in the population so what would be epistatic variance becomes additive or dominance variance. For example, consider the A × A model and complete LD, i.e. equal frequencies at B and C loci and both loci segregating but with only two haplotypes present. Then only Bc and bC haplotypes are present, and genotypic values are 0 for homozygous classes and a for heterozygotes (‘pure’ overdominance), or only BC and bc haplotypes, with genotypic values 2a for homozygotes and a for heterozygotes (‘pure’ underdominance). In either case variances are the same as for the dominance case with a = 0. Thus LD would lead to attribution of real epistatic variance to additive or dominance variance, and would exacerbate the results obtained from discussions of gene frequency distribution.
