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.

Read more about Linkage DisequilibriumDefinition, Role of Recombination, Example: Human Leukocyte Antigen (HLA) Alleles, Resources, Analysis Software, Simulation Software

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Genetic Basis of Natural Selection - Selection and Genetic Variation - Genetic Linkage
... Genetic linkage occurs when the loci of two alleles are linked, or in close proximity to each other on the chromosome ... a selective sweep has occurred or not can be investigated by measuring linkage disequilibrium, or whether a given haplotype is overrepresented in the population ... Therefore, the presence of a block of strong linkage disequilibrium might indicate that there has been a 'recent' selective sweep near the center of the block, and ...
Detecting Selective Sweeps
... One method is to measure linkage disequilibrium, i.e ... Therefore, the presence of strong linkage disequilibrium might indicate that there has been a recent selective sweep, and can be used to identify sites recently under ... evidence for a selective sweep in yellow germplasm reducing diversity at this locus and linkage disequilibrium in surrounding regions ...