Using the variance of pairwise differences to estimate the recombination rate

Abstract

A new estimator is proposed for the parameter C = 4Nc, where N is the population size and c is the recombination rate in a finite population model without selection. The estimator is an improved version of Hudson's estimator, which takes advantage of some recent theoretical developments. The improvement is slight, but the smaller bias and standard error of the new estimator support its use. The variance of the average number of pairwise differences is also derived, and is important in the formulation of the new estimator.