Mutations alter an organisms genotype and occasionally this causes different phenotypes to appear. Most mutations have little effect on an organism's phenotype, health, or reproductive fitness. Mutations that do have an effect are usually deleterious, but occasionally some can be beneficial. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene, about 70 percent of these mutations will be harmful with the remainder being either neutral or weakly beneficial.^[60]

An evolutionary tree of eukaryotic organisms, constructed by comparison of several orthologous gene sequences

Population genetics studies the distribution of genetic differences within populations and how these distributions change over time.^[61] Changes in the frequency of an allele in a population is mainly influenced by natural selection, where a given allele provides a selective or reproductive advantage to the organism,^[62] as well as other factors such as genetic drift, artificial selection and migration.^[63]

Over many generations, the genomes of organisms can change significantly, resulting in the phenomenon of evolution. Selection for beneficial mutations can cause a species to evolve into forms better able to survive in their environment, a process called adaptation.^[64] New species are formed through the process of speciation, often caused by geographical separations that prevent populations from exchanging genes with each other.^[65] The application of genetic principles to the study of population biology and evolution is referred to as the modern synthesis.

By comparing the homology between different species genomes it is possible to calculate the evolutionary distance between them and when they may have diverged (called a molecular clock).^[66] Genetic comparisons are generally considered a more accurate method of characterizing the relatedness between species than the comparison of phenotypic characteristics.^{[citation needed]} The evolutionary distances between species can be used to form evolutionary trees – these trees represent the common descent and divergence of species over time, although they do not show the transfer of genetic material between unrelated species (known as horizontal gene transfer and most common in bacteria).