In summary, linkage disequilibrium reflects the difference between the expected haplotype frequencies under the assumption of independence, and observed haplotype frequencies.
For example, populations that represent recent mixtures of separated ancestral groups can exhibit longer-range linkage disequilibrium between susceptibility alleles and genetic markers than is the case for other populations.
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 selection.
On a population level, processes that influence linkage disequilibrium include genetic linkage, epistatic natural selection, rate of recombination, mutation, genetic drift, random mating, genetic hitchhiking and gene flow.
Linkage disequilibrium describes a situation in which some combinations of genes or genetic markers occur more or less frequently in a population than would be expected from their distances apart.
The amount of linkage disequilibrium depends on the difference between observed allelic frequencies and those expected from a homogenous, randomly distributed model.