The phenomenon by which certain alleles 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.

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