Linkage Disequilibrium (LD)
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Linkage disequilibrium (LD) across chromosomal regions is manifested by non-random association of alleles at different loci in a given population or datasets. Alleles in different loci are said to be in LD when the frequency of association of their different alleles is higher or lower than what would be expected if the loci were fully independent and associated randomly.
In the figure below (adapted from here), a variant on the ancestral chromosome is represented by a red triangle. The alleles that are physically close tend to stick with the ancestral variant despite recombination limits for the region in which the variant is at (the yellow region).
Linkage disequilibrium is influenced by many factors:
Selection
Rate of genetic recombination
Mutation rate
Genetic drift
System of mating
Population structure
Genetic linkage.
As a result, the pattern of linkage disequilibrium in a genome is a powerful signal of the population genetic processes that are structuring it.
Read more detailed information about LD from Matti Pirinen's course slides and notes.
