"Linkage disequilibrium is an interesting and important concept in population genetics. I think it is easiest to illustrate it by thinking of two genes, each with two alleles. If there is nothing particularly going on in the population we would expect the association between those alleles both within and between the loci to be random. They won't be any more likely to co-occur than we would expect from the basis of their respective frequencies in the population. That's known as linkage equilibrium. The opposite is linkage disequilibrium - when there is a non-random association between the alleles at different loci."

Linda Partridge