Natural selection increases the frequency of advantageous mutations and decreases the frequency of deleterious mutations.

Natural selection increases the frequency of advantageous alleles, resulting in adaptation. In some cases, it can promote the fixation of advantageous alleles, meaning the allele has a frequency of 1. To start with, a new advantageous allele will exist as a single copy in a single individual (that is, as a heterozygote), but, under the influence of natural selection, the advantageous allele can eventually replace all the other alleles in the population. Natural selection that increases the frequency of a favorable allele is called positive selection.

As we have seen, most mutations to functional genes are deleterious. In extreme cases, they are lethal to the individuals carrying them and are thus eliminated from the population. Sometimes, however, natural selection is inefficient in getting rid of a deleterious allele. Consider a recessive lethal mutation, b (that is, one that is lethal only as a homozygote, bb, and has no effect as a heterozygote, Bb). When it first arises, all the other alleles in the population are B, which means that the first b allele that appears in the population must be paired with a B allele, resulting in a Bb heterozygote. Because natural selection does not act against heterozygotes in this case, the b allele may increase in frequency by chance alone (we discuss below how this happens). Only when two b alleles come together to form a bb homozygote does natural selection act to rid the population of the allele. Natural selection that decreases the frequency of a deleterious allele is called negative selection.

Many human genetic diseases show this pattern: The deleterious allele is rare and recessive. Because it is rare, homozygotes for it are formed only infrequently. Remember that the expected frequency of homozygotes in a population under the Hardy–Weinberg equilibrium is the square of the frequency of the allele in the population. Therefore, if the allele frequency is 0.01, we expect 0.01 × 0.01, or 1 in every 10,000 individuals, to be homozygous for it. Thus, the genetic disease occurs rarely, and the allele remains in the population because it is recessive and not expressed as a heterozygote.