PT - JOURNAL ARTICLE
AU - Hudson, Richard R.
TI - THE SAMPLING DISTRIBUTION OF LINKAGE DISEQUILIBRIUM UNDER AN INFINITE ALLELE MODEL WITHOUT SELECTION
DP - 1985 Mar 01
TA - Genetics
PG - 611--631
VI - 109
IP - 3
4099 - http://www.genetics.org/content/109/3/611.short
4100 - http://www.genetics.org/content/109/3/611.full
SO - Genetics1985 Mar 01; 109
AB - The sampling distributions of several statistics that measure the association of alleles on gametes (linkage disequilibrium) are estimated under a two-locus neutral infinite allele model using an efficient Monte Carlo method. An often used approximation for the mean squared linkage disequilibrium is shown to be inaccurate unless the proper statistical conditioning is used. The joint distribution of linkage disequilibrium and the allele frequencies in the sample is studied. This estimated joint distribution is sufficient for obtaining an approximate maximum likelihood estimate of C = 4Nc, where N is the population size and c is the recombination rate. It has been suggested that observations of high linkage disequilibrium might be a good basis for rejecting a neutral model in favor of a model in which natural selection maintains genetic variation. It is found that a single sample of chromosomes, examined at two loci cannot provide sufficient information for such a test if C < 10, because with C this small, very high levels of linkage disequilibrium are not unexpected under the neutral model. In samples of size 50, it is found that, even when C is as large as 50, the distribution of linkage disequilibrium conditional on the allele frequencies is substantially different from the distribution when there is no linkage between the loci. When conditioned on the number of alleles at each locus in the sample, all of the sample statistics examined are nearly independent of λ = 4Nμ, where μ is the neutral mutation rate.