Estimating effective population size from linkage disequilibrium: severe bias in small samples
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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.
Keywordseffective population size linkage disequilibrium sampling bias
PRE was supported by an Australian Postdoctoral Fellowship, a Région Bourgogne Fellowship and the European Union Econogene project. Andrea Taylor kindly provided northern hairy-nosed wombat microsatellite genotypes. PRE, JMC and GL were supported by the Bureau des Ressources Génétiques. GL also received support from the Division of Biological Sciences at University of Montana.
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