An allele that does not affect the fitness of an organism—that is, an allele that is no better or worse than alternative alleles at the same locus—is called a neutral allele. Neutral alleles are added to a population over time through mutation, providing the population with considerable genetic variation. The frequencies of neutral alleles are not affected directly by natural selection. Even in large populations, neutral alleles may be lost, or may increase in frequency, purely by random genetic drift.

Much of the phenotypic variation we are able to observe is not neutral. However, modern techniques enable us to measure *neutral variation at the molecular level and provide the means to distinguish it from adaptive variation.