Evolution is often described in terms of traits: a population becomes darker, faster, more resistant to disease, or better adapted to its environment. But those visible changes are not the most fundamental way biologists measure evolution.
At the population level, evolution can be defined much more precisely: evolution is a change in allele frequencies across generations.
An allele is one of the different versions of a gene. Allele frequency is the proportion of copies of a particular allele in a population. Tracking those proportions gives scientists a quantitative way to describe how populations change genetically over time—and to distinguish evolutionary change from changes that affect individuals but do not alter the population’s genetic makeup.
What is an allele frequency?
Consider a gene with two alleles, which we can call A and a. If a population contains 100 copies of that gene and 30 are A while 70 are a, the frequency of A is 0.30, or 30%, and the frequency of a is 0.70, or 70%.
The calculation is straightforward:
Allele frequency = number of copies of an allele ÷ total number of copies of the gene
In a diploid organism such as a human, each individual normally carries two copies of each autosomal gene—one inherited from each parent. So a population of 50 individuals has 100 copies of a particular autosomal gene. If 40 of those copies are allele A, the frequency of A is 40/100, or 0.40.
Allele frequency is therefore different from the frequency of a genotype. Genotype frequency describes how common particular combinations of alleles are, such as AA, Aa, and aa. Allele frequency describes how common the individual alleles are.
That distinction matters because evolution ultimately concerns changes in the population’s genetic composition. A population can have the same allele frequencies even if the proportions of particular genotypes change, and genotype frequencies can sometimes change without allele frequencies changing.
Why allele frequencies are central to evolution
Suppose allele A makes up 20% of the gene copies in one generation and 35% in the next. Something has changed in the population’s genetic composition. If that increase continues across generations, A is becoming more common in the population.
The change itself is what matters. An allele does not need to become the majority allele for evolution to occur. Increasing from 20% to 21% is an evolutionary change just as a shift from 20% to 80% is; the magnitude and biological significance are different, but both represent a change in allele frequency.
This definition also clarifies an important misconception: individual organisms do not evolve genetically during their lifetimes in the evolutionary sense. An individual can grow, learn, acclimate to temperature, or undergo other biological changes. But those changes do not by themselves constitute evolution. Evolutionary change occurs when the genetic composition of a population changes across generations.
How allele frequencies change
Several evolutionary processes can alter allele frequencies. The major ones are natural selection, genetic drift, gene flow, and mutation.
Natural selection
Natural selection occurs when individuals with heritable differences leave different numbers of surviving, reproducing offspring. If an allele contributes to a trait that improves reproductive success under particular environmental conditions, copies of that allele may become more common over generations.
For example, imagine a population in which an allele contributes to resistance against a disease. If resistant individuals tend to survive and reproduce more successfully than susceptible individuals, the resistance-associated allele can increase in frequency.
Selection does not necessarily make a population “better” in an absolute sense. Its effects depend on the environment and on what contributes to reproductive success. An allele that is advantageous in one setting can be neutral or disadvantageous in another.
Selection can also maintain multiple alleles rather than driving one to fixation. In some circumstances, different genetic variants are favored under different conditions, or individuals carrying different variants have advantages that prevent any one allele from completely replacing the others.
Genetic drift
Genetic drift is evolutionary change caused by random sampling of alleles from one generation to the next.
Chance can matter even when alleles have identical effects on survival and reproduction. Imagine a small population in which A and a are equally successful. If, simply by chance, individuals carrying more copies of A happen to leave more descendants in one generation, A may become more common in the next.
Drift is particularly powerful in small populations. It can cause alleles to become fixed, meaning that an allele reaches a frequency of 1, or lost, meaning its frequency falls to 0.
Two situations illustrate especially strong forms of drift. A population bottleneck occurs when a population undergoes a sharp reduction in size, leaving the surviving individuals with a chance-based sample of the original genetic variation. A founder effect occurs when a new population is established by a relatively small number of individuals. The alleles carried by those founders can become unusually common or rare in the new population simply because of the founding sample.
Unlike natural selection, genetic drift does not require an allele to provide an advantage or disadvantage.
Gene flow
Gene flow occurs when alleles move between populations through the movement and reproduction of individuals or through the movement of reproductive cells, such as pollen.
Suppose two populations of the same species have different frequencies of an allele. If individuals regularly migrate between them and reproduce, the allele frequencies of the populations can become more similar.
Gene flow can introduce genetic variants into populations where they were previously absent. It can also reduce genetic differences between populations when movement is substantial.
The evolutionary effect depends on the direction and amount of movement and on what happens to the incoming alleles after they enter the population.
Mutation
Mutation is the ultimate source of new genetic variants. A mutation is a change in DNA sequence. Most mutations do not automatically spread through a population; many have little effect on reproductive success, while others can be harmful or beneficial under particular conditions.
For an inherited mutation to contribute to evolutionary change, it generally must occur in a cell lineage that can contribute genetic material to offspring. In humans and other sexually reproducing organisms, changes in germline cells can be inherited, whereas most mutations that arise only in somatic cells are not passed to offspring.
Mutation introduces new variation, while processes such as selection and drift determine what happens to that variation within populations.
Allele frequency is not the same as a trait’s frequency
It is tempting to equate a genetic allele with a visible trait, but the relationship is often more complicated.
A single gene can have multiple alleles, and a person’s phenotype—the observable characteristics of an organism—can be influenced by several genes as well as the environment. Some alleles have effects that depend on which other alleles are present. Dominance relationships can also make the connection between genotype and phenotype less direct.
For example, in a simple gene with alleles A and a, individuals with genotypes AA and Aa might have the same observable phenotype even though their genotypes differ. Counting that phenotype would therefore not tell you directly how common A is.
This is one reason population geneticists distinguish carefully between genotype frequencies, allele frequencies, and phenotype frequencies.
How allele frequencies are calculated in diploid populations
For a gene with two alleles, A and a, suppose a population contains:
- 36 individuals with genotype AA
- 48 individuals with genotype Aa
- 16 individuals with genotype aa
There are 100 individuals and therefore 200 copies of the gene.
The number of A copies is:
- 2 × 36 from AA individuals
- 1 × 48 from Aa individuals
That gives 120 A copies. The frequency of A is therefore 120/200 = 0.60, or 60%.
The remaining 80 copies are a, so the frequency of a is 0.40.
The same calculation can be expressed using genotype frequencies. If the frequencies of AA, Aa, and aa are represented by , , and , then:
frequency of A = f(AA) + ½f(Aa)
The heterozygotes contribute half their gene copies to each allele.
For genes on sex chromosomes, the calculation requires additional care because males and females can carry different numbers of copies of particular chromosomes. Population geneticists therefore specify the genetic system and population being measured rather than assuming that every gene follows the simple two-copies-per-individual calculation.
The Hardy-Weinberg principle provides a useful baseline
Population genetics often begins with the Hardy-Weinberg principle, which describes what genotype frequencies are expected to be when allele frequencies remain constant under a specified set of idealized conditions.
For two alleles, with allele frequencies and , where , the expected genotype frequencies are:
AA: p2p^2
Aa: 2pq2pq
aa: q2q^2
These expectations apply when a population meets assumptions including random mating and the absence of evolutionary forces such as selection, mutation, migration, and genetic drift, along with a sufficiently large population for random sampling effects to be negligible.
The Hardy-Weinberg model is not a claim that real populations are perfectly static. Instead, it provides a null model: a mathematical baseline against which population geneticists can compare observed data.
If observed genotype frequencies differ from Hardy-Weinberg expectations, that difference can prompt questions about mating patterns, population structure, selection, sampling, or other factors. Importantly, a deviation from Hardy-Weinberg expectations does not automatically prove that natural selection is occurring.
What it means when an allele becomes common
An allele that reaches a frequency of 1 in a population is described as fixed in that population. An allele at frequency 0 is absent from the population at that point in time.
But high frequency does not necessarily mean an allele is advantageous, and low frequency does not necessarily mean it is harmful.
Natural selection can increase a beneficial allele, but genetic drift can also raise an allele’s frequency by chance. In a small population, a neutral allele can become fixed without providing any reproductive advantage.
Similarly, a harmful allele can sometimes persist because selection may be weak, the allele may have effects that depend on genetic background or environment, or new copies may continually arise through mutation. The evolutionary history of an allele cannot be inferred from its frequency alone.
Why populations can evolve without gaining new mutations
Evolution does not require the appearance of a brand-new mutation in every generation.
A population already contains genetic variation. If the relative frequencies of existing alleles change—for example, because of natural selection or genetic drift—the population has evolved even though no new allele was created.
Mutation matters because it generates new genetic variants, but it is only one of several processes that change the frequencies of variants already present.
This distinction is especially important when thinking about natural selection. Selection does not create a useful allele because an organism needs it. Instead, existing heritable variation can be sorted by differences in survival and reproduction, causing some variants to become more common.
Measuring evolution in real populations
In practice, estimating allele frequencies is more complicated than counting obvious physical traits. Researchers may obtain genetic data from individuals, identify particular variants, and determine how frequently those variants occur in the population being studied.
The definition of the population matters. An allele can be common in one population and uncommon in another. Frequencies can also differ across geographic regions, age groups, or other defined samples. A reported frequency is therefore meaningful only when the population and sampling method are understood.
Modern genetic studies may examine large numbers of variants across the genome. These data allow researchers to investigate patterns consistent with natural selection, population history, migration, demographic changes, and genetic drift.
But observing that an allele’s frequency differs between populations does not, by itself, reveal why. Differences can arise through selection, drift, migration, mutation, historical population structure, or combinations of these processes.
Allele frequencies connect genetics to evolutionary history
Allele frequencies provide a numerical language for evolutionary change. They let biologists move from statements such as “this variant became more common” to measurable questions: How common was it? How quickly did its frequency change? Did the change occur independently in different populations? Could random drift explain it, or is there evidence for selection?
The numbers do not replace the biological story. They make the story testable.
Evolution can involve enormous changes in organisms over geological time, but the underlying process can often be tracked through comparatively simple shifts in the proportions of genetic variants. When allele frequencies change from one generation to another, the genetic composition of the population has changed—and that is evolution in measurable form.
