As we saw earlier, another way that a population can evolve is through non-random mating. In random mating, individuals select mates without regard for genotype. In non-random mating, by contrast, individuals preferentially choose mates according to their genotypes. The result is that certain phenotypes increase and others decrease. Because non-random mating just rearranges alleles already in the gene pool and, unlike migration or mutation, does not add new alleles to the population, the genotype frequencies change, whereas the allele frequencies do not.

Probably the most evolutionarily significant form of non-random mating is inbreeding, in which mating occurs between close relatives. Inbreeding increases the frequency of homozygotes and decreases the number of heterozygotes in a population without affecting allele frequencies.

Consider a rare allele b that is at frequency 0.001 in a population. According to the Hardy–Weinberg equilibrium, the expected frequency of bb homozygotes is 0.001² = 0.000001. Now let’s see what happens to the frequency of bb homozygotes when there is inbreeding. A father with one b allele has a son and daughter who mate and have offspring. We know that the probability that the brother inherited the allele from his father is 0.5, and the same is true for his sister. The probability that the siblings’ child is homozygous bb is the probability each sibling inherited a copy from their father (0.5 × 0.5) multiplied by the probability that their child inherited b from both of them (0.5 × 0.5), or (0.5)⁴ = 0.0625. Needless to say, 0.0625 is a considerably higher probability than 0.000001.

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If b is a deleterious recessive mutation, it may contribute to inbreeding depression in the child, a reduction in the child’s fitness caused by homozygosity of deleterious recessive mutations. Inbreeding depression is a major problem in conservation biology, especially when endangered species are bred in captivity in programs starting with a just a small number of individuals.