Natural selection or chance can both cause linkage equilibrium. When a disease mutation occurs on a founder chromosome, the disease mutation will be in linkage equilibrium with alleles from loci near to the gene.
The genotype of an organism is the combination of alleles that it possesses. If the paired alleles are the same, the organism is said to be homozygous for that characteristic; if they are different, the organism is said to be heterozygous for that trait.
Many variables impact linkage disequilibrium, including selection, the rate of genetic recombination, mutation rate, genetic drift, mating system, population structure, and genetic linkage.
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