Population genetics · BEGINNER LESSON
Linkage disequilibrium
Linkage disequilibrium (LD) is the non-random association of alleles or markers at two loci, meaning the combination seen together in a population differs from what random pairing would predict. It is measured with statistics such as D and r^2, which can change with allele frequency and distance between loci.
What LD is and what is measured
Linkage disequilibrium (LD) describes association between alleles at two loci, or more generally between genomic markers. The measured quantity is not the physical chromosome itself, but the degree of non-random association in a population. Common summaries include D and r^2, and the sources note that LD can also be considered across many loci as a genomic pattern.
[1] An equal-tempered measure of linkage disequilibrium - PubMed [2] Estimating Linkage Disequilibrium and Effective Population Size ... [3] X-LDR: an atlas of linkage disequilibrium across species - PMC
Why LD changes
LD changes because of recombination, which breaks up allele combinations over generations. The excerpts describe LD as decaying over generations and often being maintained only over short distances, while long-range LD can still exist. In practice, LD across increasing physical distance often shows a nonlinear decrease, and that pattern can differ between populations or species.
[2] Estimating Linkage Disequilibrium and Effective Population Size ... [3] X-LDR: an atlas of linkage disequilibrium across species - PMC
What LD can reveal
Because LD reflects how alleles are associated in a population, it can provide insight into population history, selection intensity, recombination dynamics, and effective population size (Ne), which means the size of an idealized breeding population that would show the same amount of random genetic drift. Short- and long-distance LD can reflect different generations in the past, so LD patterns can be used to study recent and older population events.
[2] Estimating Linkage Disequilibrium and Effective Population Size ... [3] X-LDR: an atlas of linkage disequilibrium across species - PMC
Limits and interpretation
LD values depend on allele frequencies, so values from different populations or loci are not always directly comparable. The sources also note that different LD measures can behave differently, and that population structure, selection, genotyping strategy, and related methods can change observed LD patterns. In other words, an LD value is a summary of association, not a direct measure of one single cause.
[1] An equal-tempered measure of linkage disequilibrium - PubMed [2] Estimating Linkage Disequilibrium and Effective Population Size ... [3] X-LDR: an atlas of linkage disequilibrium across species - PMC
SEE THE IDEA
How linkage disequilibrium behaves in a population
Two genetic positions are considered together.
Some allele combinations occur more or less often than chance predicts.
Recombination breaks associations, so LD usually decays.
The remaining association can inform history, structure, and effective population size.
Allele associations are created, altered, and gradually reduced by recombination, leaving measurable LD patterns.
A simple view of LD: association between loci is measured, then shaped over time by recombination and population history.
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Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.