Figure 1. Simple model for the generation of linkage disequilibrium (LD). The polymorphisms b/B and c/C already existed when the locus carrying allele A became polymorphic and allele a appeared on a B–C haplotype background. As time passed, recombination events reshuffled chromosomal fragments (indicated by a pair of scissors). Each recombination event affects only one individual. The segment that is identical by descent (IBD) with the founder is indicated by the identical colour as the founder, a change in shading indicates shuffled chromosomal fragments. In the present the fragment ‘a–B’ is IBD in all carriers of the a allele. The locus A/a is in absolute LD with the locus b/B.

Figure 2. Drift-induced linkage disequilibrium (LD) in a constant Wright–Fisher population. Each rectangle represents a haplotype consisting of the two biallelic loci A/a and B/b. The loci are in linkage equilibrium in generation 1. In each generation, each chromosome has a random number of descendants. After 10 generations, haplotype a–b is lost and locus a/A is in absolute LD with locus b/B.

Figure 3. Stratification and admixture-based linkage disequilibrium (LD). Originally the population consisted of two distinct subpopulations that are unknown to the investigator. We observe three loci, A/a, B/b and C/c. The loci B/b and C/c are linked but A/a is unlinked (indicated by //). If subpopulations 1 and 2 are considered to be one population, all polymorphisms that have a different allelic distribution in subpopulations 1 and 2 show association with the C allele, regardless of whether the locus is distant (a/A) or close (b/B). Recombination breaks up the association with distant loci. After several generations of random mating between the populations, only closely linked loci like B/b and C/c are still in LD.