Natural selection, by favoring individuals with advantageous phenotypes, affects the composition of the population gene pool. Disadvantageous phenotypes, hence also the genotypes, are eliminated. Advantageous phenotypes, hence also the genotypes, are protected. Thus the number of disadvantageous alleles is reduced. They can even be completely eliminated. The number of advantageous alleles, on the other hand, increases, hence increasing the probability of their inheritance by progeny. Natural selection changes the composition of the gene pool in the direction consistent with the environmental requirements.

There are three types of selection: stabilizing, directional and disruptive. Selection affects the phenotypes, which mirror the genotypes, which, in turn, are determined by alleles. One can thus say, that selection affects alleles in a given gene pool.

• Stabilizing selection favors the most common allele (and traits). Frequency of rare alleles, hence of extremal traits, does not increase.
• Directional selection increases the number of one type of alleles at the sacrifice of the others, thus shifting the probability distributions in a given direction.
• Disruptive selection is a type of the directional one, which acts in several directions. A population is divided into subgroups that are still connected. They can still reproduce, but the flow of genes is reduced. Directional selection takes place within each of the subgroups.

Sometimes selection can be dependent on the allele frequency. Predators usually attack common individuals, making selection in the population of prey frequency dependent. An example of such selection can be found in the population of Sigara distincta. These water insects appear in three colors. If the number of individuals with each of these phenotypes is approximately equal (the allele frequency is similar), fish eat the ones that are more visible. However, when one of the colors starts dominating, individuals with this phenotype are eaten regardless of the better or worse camouflage. Because of that, less frequent alleles are not eliminated from the population. (11)

If a population is isolated, a change in allele frequency leads to creation of new species. This mechanism is called speciation.