Positive association between alleles at selectively neutral loci

Abstract

Linkage disequilibrium (LD) is a non-independent distribution of alleles at different loci and might be defined using directional and directionless approaches. While analytical theory is available for directionless LD, analytical theory for directional LD is less developed. In this study we investigated directional LD generated by random drift between two selectively neutral loci. When the sign of LD is determined by the ancestral-derived status of these alleles, its expected value is zero. In contrast, computer simulations show that random drift leads to a tendency of rare, as well as of common, alleles to occur together. This observation is supported by a straightforward analytical argument. If only those generations where both loci are polymorphic are taken into account, the magnitude of the resulting directional LD depends only on Ne. These observations might give an opportunity to directly estimate Ne from the data on genetic variation within a single generation.