The dynamics of interlocus associations in the three-locus hitchhiking model. 2. The pairwise linkage disequilibrium between two neutral loci (Q1087841)

[For part I see ibid. 23, 285-304 (1986; Zbl 0595.92006).] This paper is concerned with a hitchhiking model for three diallelic autosomal loci in a large randomly mating diploid population with discrete nonoverlapping generations. The assumption is that only one of the three loci is under selection (s), and the other two are neutral (n). Both the nsn and snn case are considered. The pairwise association \(D_{nn}\) between the two neutral loci is studied, where at least one of these is in linkage equilibrium with the selected locus. It is shown that whenever the pairwise associations between the selected and each neutral locus are negligible with respect to the three-way linkage disequilibrium, four different classes of trajectories are possible. Thus, there is no simple relation between the linkage disequilibium and the linkage between two neutral markers. The position effect within nsn and snn systems is discussed, and the hitchhiking effects within them contrasted. Some technical details are given in the Appendix.