The Effect of Recurrent Mutation on the Linkage Disequilibrium under a Selective Sweep

TL;DR

This paper provides analytical expressions for linkage disequilibrium patterns under soft and hard selective sweeps, highlighting how recurrent beneficial mutations influence genetic variation and haplotype structure.

Contribution

It introduces new analytical formulas for LD under recurrent mutation scenarios, differentiating soft sweeps from hard sweeps in genetic data analysis.

Findings

LD patterns differ significantly between soft and hard sweeps

Recurrent beneficial mutations alter haplotype structures

Analytical results align with simulation data

Abstract

A selective sweep describes the reduction of diversity due to strong positive selection. If the mutation rate to a selectively beneficial allele is sufficiently high, Pennings and Hermisson (2006a) have shown, that it becomes likely, that a selective sweep is caused by several individuals. Such an event is called a soft sweep and the complementary event of a single origin of the beneficial allele, the classical case, a hard sweep. We give analytical expressions for the linkage disequilibrium (LD) between two neutral loci linked to the selected locus, depending on the recurrent mutation to the beneficial allele, measured by $D$ and $\hat{\sigma_D^2}$, a quantity introduced by Ohta and Kimura (1969), and conclude that the LD-pattern of a soft sweep differs substantially from that of a hard sweep due to haplotype structure. We compare our results with simulations.