Linkage disequilibrium

In population genetics, linkage disequilibrium 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 what would be expected if the loci were independent and associated randomly.

Linkage disequilibrium is influenced by many factors, including selection, the rate of recombination, the rate of mutation, 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 ${\displaystyle p_{A}}$ at one locus (i.e. ${\displaystyle p_{A}}$ is the proportion of gametes with A at that locus), while at a different locus allele B occurs with frequency ${\displaystyle p_{B}}$. Similarly, let ${\displaystyle p_{AB}}$ be the frequency with which both A and B occur together in the same gamete (i.e. ${\displaystyle p_{AB}}$ is the frequency of the AB haplotype).

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