Effects of Different Mutation Rates and Randomness on the Distribution of Linkage Disequilibrium

Abstract

Background Mutation has recently received much attention on its role in the evolution and genetics of complex trait. The linkage disequilibrium (LD) distribution can be affected by mutation as reported recently, in which the same mutation rates were adopted in the transition matrix. However, effects of different types, rates and randomness of mutation on LD distribution remain unexplored. Results Here, we considered in the transition matrix mutations at each locus to be of different types and rates (i.e. nucleotide transition or transversion treated differently), to examine how the LD distribution between two genetic loci was affected. After examining consecutively factors such as effective population size, recombination and selection, different mutation types and rates could further change the dynamics of LD distribution. However, at the current scale of mutation rate (weak at 10−9-10−8), mutation seemed to play only a minor role, compared to recombination and selection. A simple model further showed that mutation randomness increased the ruggedness of LD curves, which fluctuated around the steady state. Conclusions Taken together, different mutation rates and randomness could further disturb the dynamics of LD distribution. Our findings can help better understand the role of mutation in molecular evolution and complex trait genetics.