Linkage Disequilibrium

In population genetics, linkage disequilibrium is the non-random association of alleles at two or more loci, that may or may not be on the same chromosome. It is also referred to as gametic phase disequilibrium, or simply gametic disequilibrium. In other words, linkage disequilibrium is the occurrence of some combinations of alleles or genetic markers in a population more often or less often than would be expected from a random formation of haplotypes from alleles based on their frequencies. It is not the same as linkage, which is the presence of two or more loci on a chromosome with limited recombination between them. The amount of linkage disequilibrium depends on the difference between observed and expected (assuming random distributions) allelic frequencies. Populations where combinations of alleles or genotypes can be found in the expected proportions are said to be in linkage equilibrium.

The level of linkage disequilibrium is influenced by a number of factors, including genetic linkage, selection, the rate of recombination, the rate of mutation, genetic drift, non-random mating, and population structure. A limiting example of the effect of rate of recombination may be seen in some organisms (such as bacteria) that reproduce asexually and hence exhibit no recombination to break down the linkage disequilibrium. An example of the effect of population structure is the phenomenon of Finnish disease heritage, which is attributed to a population bottleneck.