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Linkage disequilibrium occurs when alleles at two loci are not inherited independently causaing a deviation of the expected frequency. In the contrary, linkage equilibrium occurs when the alleles of two loci are completely independent, and the expected frequency of alleles and the actual inherited frequency is the same.

Linkage equilibrium is part of the principles of Hardy-Weinberg, which describes the random association of alleles. Under linkage equilibrium the frequency of a gamete carrying any combination of alleles equals the product of the frequency of those alles (Hartl and Clark, 2007). Disequilibrium is, therefore, a result of gamet preference (selection), the result of an ancentral introduction of a mutation, or the effect of a small population size with prevalent alleles and reduced recombination rates.

In nature, linkage disequilibrium is a common phenomenon, where often two or more loci are over-represented. If random association is achieved by an increase of effective population size and recombination rates, then equilibrium can be slowly obtained over generations.

Linkage disequilibrium is a population genetics term than can be associated to chromosomal linkage, but does not describe the same phenomenon. For instance, non-random associations of alleles at two loci can occur even if the two genes are genetically unlinked by their distance on the chromosomes. This is mostly true when the founding population is small and interbreeds mostly among itself. The opposite event can also be true, where two alleles at a linked loci are randomly associated due to crossing over.

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