Linkage disequilibrium

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In population genetics, linkage disequilibrium (LD) is a measure of non-random association between segments of DNA (alleles) at different positions on the chromosome (loci) in a given population based on a comparison between the frequency at which two alleles are detected together at the same loci and the frequencies at which each allele is detected at that loci overall, whether it occurs with or without the other allele of interest. Loci are said to be in linkage disequilibrium when the frequency of being detected together (the frequency of association of their different alleles) is higher or lower than expected if the loci were independent and associated randomly.^[1]

While the pattern of linkage disequilibrium in a genome is a powerful signal of the population genetic processes that are structuring it, it does not indicate why the pattern emerges by itself. 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.

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).^[1] Furthermore, linkage disequilibrium is sometimes referred to as gametic phase disequilibrium;^[2] however, the concept also applies to asexual organisms and therefore does not depend on the presence of gametes.