Estimating effective population size from linkage disequilibrium: Severe bias in small samples

Abstract

Effective population size (N e) is a central concept in evolutionary biology and conservation genetics. It predicts rates of loss of neutral genetic variation, fixation of deleterious and favourable alleles, and the increase of inbreeding experienced by a population. A method exists for the estimation of N e from the observed linkage disequilibrium between unlinked loci in a population sample. While an increasing number of studies have applied this method in natural and managed populations, its reliability has not yet been evaluated. We developed a computer program to calculate this estimator of N e using the most widely used linkage disequilibrium algorithm and used simulations to show that this estimator is strongly biased when the sample size is small (