Linkage disequilibrium between loci with unknown phase.
Linkage disequilibrium is often measured by two statistics, D and r, which can be interpreted as the covariance and the correlation between loci and across gametes. When data consist of diploid genotypes, however, gametes cannot be identified. A variety of iterative statistical methods are used in such cases, all of which assume random mating. Previous work has shown that D and r can be expressed as covariances and correlations across diploid genotypes, provided that mating is random. We show here that this result also holds approximately when mating is nonrandom. This provides a means of estimating these parameters without iteration and without assuming random mating. This estimator is nearly as accurate as the widely used EM estimator and is many times faster.
Rogers
Alan R
AR
Department of Anthropology, University of Utah, Salt Lake City, Utah 84112, USA.
Huff
Chad
C
D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D004171:Diploidy; D005260:Female; D005828:Genetics, Population; D005838:Genotype; D005854:Germ Cells / Q000378:metabolism*; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D008957:Models, Genetic; D011995:Recombination, Genetic