PT - JOURNAL ARTICLE
AU - Hudson, Richard R.
TI - Two-Locus Sampling Distributions and Their Application
DP - 2001 Dec 01
TA - Genetics
PG - 1805--1817
VI - 159
IP - 4
4099 - http://www.genetics.org/content/159/4/1805.short
4100 - http://www.genetics.org/content/159/4/1805.full
SO - Genetics2001 Dec 01; 159
AB - Methods of estimating two-locus sample probabilities under a neutral model are extended in several ways. Estimation of sample probabilities is described when the ancestral or derived status of each allele is specified. In addition, probabilities for two-locus diploid samples are provided. A method for using these two-locus probabilities to test whether an observed level of linkage disequilibrium is unusually large or small is described. In addition, properties of a maximum-likelihood estimator of the recombination parameter based on independent linked pairs of sites are obtained. A composite-likelihood estimator, for more than two linked sites, is also examined and found to work as well, or better, than other available ad hoc estimators. Linkage disequilibrium in the Xq28 and Xq25 region of humans is analyzed in a sample of Europeans (CEPH). The estimated recombination parameter is about five times smaller than one would expect under an equilibrium neutral model.