Population History and Linkage Disequilibrium


Population history and demographic structure influence the evolution of linkage disequilibrium between loci. Besides recombination and mutation, processes like selection, genetic drift, bottlenecks, admixture, population substructure and population expansion fundamentally influence the association of linked loci.

Keywords: association; bottleneck; constant population; population expansion; selection; population substructure

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.



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Zöllner, Sebastian(Apr 2008) Population History and Linkage Disequilibrium. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005428.pub2]