Linkage disequilibrium

In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than expected if the loci were independent and associated randomly. Linkage disequilibrium is influenced by many factors, including selection, the rate of genetic recombination, mutation rate, genetic drift, the system of mating, population structure, and genetic linkage. As a result, the pattern of linkage disequilibrium in a genome is a powerful signal of the population genetic processes that are structuring it. In spite of its name, linkage disequilibrium may exist between alleles at different loci without any genetic linkage between them and independently of whether or not allele frequencies are in equilibrium (not changing with time). Furthermore, linkage disequilibrium is sometimes referred to as gametic phase disequilibrium; however, the concept also applies to asexual organisms and therefore does not depend on the presence of gametes. Suppose that among the gametes that are formed in a sexually reproducing population, allele A occurs with frequency at one locus (i.e. is the proportion of gametes with A at that locus), while at a different locus allele B occurs with frequency . Similarly, let be the frequency with which both A and B occur together in the same gamete (i.e. is the frequency of the AB haplotype). The association between the alleles A and B can be regarded as completely random—which is known in statistics as independence—when the occurrence of one does not affect the occurrence of the other, in which case the probability that both A and B occur together is given by the product of the probabilities. There is said to be a linkage disequilibrium between the two alleles whenever differs from for any reason. The level of linkage disequilibrium between A and B can be quantified by the coefficient of linkage disequilibrium , which is defined as provided that both and are greater than zero.