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Evolutionary Genetics: Linkage Equilibrium

Two loci are in linkage equilibrium if genotype frequencies at one locus are independent of genotype frequencies at the second locus, otherwise the two loci are in linkage disequilibrium. Linkage disequilibrium can arise from physical linkage, genetic drift, and selection on multilocus genotypes.

One can test whether or not two loci are in linkage equilibrium by comparing known two-locus genotype frequencies with two-locus genotype frequencies calculated from one-locus genotype frequencies. A chi-square test can be performed to determine if the known and expected differ significantly.

D, the coefficient of disequilibrium measures the amount of disequilibrium between two loci. The coefficient of disequilibrium is calculated as:


where ru is one half of the coupling heterozygote frequency (AB/ab), and st is one half of the repulsion heterozygote (Ab/aB).

Evolutionary Genetics: Linkage Equilibrium

Adjust the initial allelic frequencies and the two-locus fitness values to the right:

For best results, begin by setting the fitness values to 1.0, and initial allelic frequencies to 0.5. Then, decrease one or more of the fitness values by a small amount.

Both the observed and expected genotype frequencies are presented above the graph.

The two loci may be in linkage equilibrium or disequilibrium, depending on the fitness values chosen. During the simulation the current state is displayed above the graph.

The population represented to the right consists of 5000 randomly mating individuals.