What Is Linkage Disequilibrium?

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  • Written By: Victoria Blackburn
  • Edited By: Jessica Seminara
  • Last Modified Date: 14 September 2019
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In the field of genetics, population genetics studies how often specific copies of genes — or alleles — appear and how they interact with other alleles from other genes. It also looks at how processes of evolution such as natural selection and mutations affect alleles. The distribution of alleles can be either independent of other alleles at a different location, or it may be affected by other alleles. When the distribution of an allele, or alleles, is not independent of other alleles, it is called linkage disequilibrium.

Evolution of an organism occurs through genetic variation. Different combinations of genes, and different combinations of alleles of different genes, lead to different phenotypes of organisms. This means that genetic variation produces organisms of a species that are similar but can look different and function differently. Genetic variation can make an organism more or less successful in terms of survival and reproduction. The theory of natural selection states that evolution occurs through survival of the fittest, or survival of those that are more successful at passing on their genes.


Genes are not independent units that are passed on by themselves to offspring. Instead, genes are affected by the environment as well as by other genes. Genetic coadaption is the term used to refer to how well genes interact with other genes. Natural selection favors those alleles that interact well with alleles of other genes at different locations within the DNA. Genetic coadaption can exist between the alleles of some genes but not others.

For example, gene A and gene B each have two alleles, which are A1 and A2 and B1 and B2, respectively. If an organism inherits A1 and B1 or A2 and B2, it can be presumed in this example to be better adapted to survive than if it inherits A1 and B2 or A2 and B1. This means that through natural selection, the genetic combinations of A1B1 and A2B2 would be favored as the organism with these alleles is more likely to survive and reproduce. As such, these alleles are said to be in linkage disequilibrium as they would not be passed on randomly to offspring, but instead, certain pairs are favored.

Linkage disequilibrium is measured by comparing the frequencies of alleles within a population, but it is not permanent. Random mating between organisms can lead to a decrease in the occurrence of the linked alleles. Permanent linkage disequilibrium can occur if one combination results in a higher fitness level of an organism, such as when the other combination results in a lethal mutation in a zygote. The further apart the locations of the alleles, the more difficult it is to maintain linkage disequilibrium.


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