The phenomenon by which certain allele
s are found in combination
more often than would be expected given their frequency
in the population
. If we have two loci (A and B) and two alleles at each (A and a, and B and b) and each is present in 50% of the population, you would expect 25% to be AB, 25% to be Ab, 25% to be aB and 25% to be ab. Variation from this leads to linkage disequilibrium
. It's pretty easy to imagine why if we imagine a freak case. Imagine that Ab and aB are normal, healthy
animals. Imagine that AB and ab are dead
animals. If 50% of the population are Ab and 50% aB, we satisfy our original condition of each allele having a frequency of 50% within the population.
Most cases will not be this extreme, but linkage disequilibrium is inevitable if the fitness of each combination of alleles is not the same.