Estimating effective population size from linkage disequilibrium: severe bias in small samples
- 677 Downloads
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.
- Balloux F (1999) EASYPOP, a software for population genetics simulation. (http://www.unil.ch/izea/softwares/easypop.html) Institute of Ecology, University of Lausanne, Switzerland
- England PR (1998) The conservation genetics of population bottlenecks. Ph.D. thesis, Macquarie University, SydneyGoogle Scholar
- Frankham R (1996) Effective population size/adult population size ratios in wildlife: A review. Genet. Res., Camb. 66: 95–107Google Scholar
- Hill WG (1981) Estimation of effective population size from data on linkage disequilibrium. Genet. Res., Camb. 38: 209–216Google Scholar
- Raymond M, Rousset F (1995) GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism. J. Hered. 86: 248–249Google Scholar
- Waples RS (1991) Genetic methods for estimating effective population size of Cetacean populations. In Genetic Ecology of Whales and Dolphins (ed. Hoelzel AR), pp. 279–300. International Whaling Commission, Special Issue 13, CambridgeGoogle Scholar