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

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 (< 100) and below the true N-e. This is probably due to the linkage disequilibrium generated by the sampling process itself and the inadequate correction for this phenomenon in the method. Results suggest that N-e estimates derived using this method should be regarded with caution in many cases. To improve the method's reliability and usefulness we propose a way to determine whether a given sample size exceeds the population N-e and can therefore be used for the computation of an unbiased estimate.