Linkage Equilibrium - Background
Two loci are in linkage equilibrium if genotype frequencies at one locus are independent of genotype frequencies at the second locus, otherwise the two loci are in linkage disequilibrium. Linkage disequilibrium can arise from physical linkage, genetic drift, and selection on multilocus genotypes.
One can test whether or not two loci are in linkage equilibrium by comparing known two-locus genotype frequencies with two-locus genotype frequencies calculated from one-locus genotype frequencies. A chi-square test can be performed to determine if the known and expected differ significantly.