Fig. 5. Origins of linkage disequilibrium. In this example, there are two linked genes, A and B, one of which (A) has a bi-allelic polymorphism (A and A₁). A germline mutation occurs in gene B, creating allele B₁ (bold) in an individual who is heterozygous at gene A. The offspring of this individual have to inherit the haplotypes AB or A₁B₁ from this parent unless the two alleles are separated by a crossover, the chance of which is approximately 1% for every million bases separating the two genes. If no crossover ever occurs, then the descendant population (DP1) will consist of only three of the possible four allele combinations, and B₁ would always be associated with A₁ (A₁B having come from a different ancestor). The reciprocal, however, would not be the case (i.e. A₁ would not always be associated with B₁). In DP1, alleles at A and B would be observed to be in linkage disequilibrium because the frequencies of allele combinations would not equal the product of their frequencies, as would be expected if the four alleles were assorting independently. If there has been some recombination, a new haplotype AB₁ would appear in the population (DP2). If this was a rare and/or recent event, the new haplotype would still be less common than predicted and the alleles would still be in linkage disequilibrium. The rate at which linkage disequilibrium will decay depends on the recombination fraction

Return to article