## Allele Frequency Definition

The** allele frequency**, or **gene frequency,** represents the incidence of a particular gene that occurs in a particular locus in the population, expressed as a fraction or percentage. Basically, alleles are the variant forms of a gene that are in the same position or genetic locus on a chromosome.

In particular, this means that **the allele frequency** is the proportion of all chromosomes in the population that carries this allele.

## What is Allele Frequency?

Allele frequency, or gene frequency, is the relative frequency of an allele (a variant of a gene) at a particular locus in a population, expressed as a fraction or percentage. Specifically, it is the fraction of all chromosomes in the population that carry that allele.

The allele frequency is different from the phenotypic ratio in that it accounts for all alleles, even if they are recessive and are “hidden” within carrier organisms. The phenotypic ratio only describes the phenotypes or actual physical features that are present within a population.

To find the allele frequency, scientists must consider heterozygous individuals, which may be hiding a recessive allele. Allele frequency is most commonly calculated using the Hardy-Weinberg equation, which describes the relationship between two alleles within a population.

When more than two alleles are present, scientists must use more complex methods to determine the actual allele frequency. Allele frequency can change over time as evolution acts upon a population and the population adapts by increasing or decreasing the frequency of certain alleles.

Calculating allele frequencies is a complex topic, which combines aspects of math and genetics. In general, all of the alleles in a population add up to 100%. So, we can use mathematical formulas to predict and determine the allele frequency of an allele in a population.

## How to Calculate Allele Frequency?

Allele frequency refers to how common an allele is in a population. It is determined by counting how many times the allele appears in the population then dividing by the total number of copies of the gene.

To find the number of alleles in a given population, you must look at all the phenotypes present. The phenotypes that represent the allele are often masked by dominant and recessive alleles working in conjunction. To analyze the allele frequency in a population, scientists use the Hardy-Weinberg (HW) equation. The Hardy-Weinberg equation is written as follows:

1 = p^{2} + 2pq + q^{2}

P and q each represent the allele frequency of different alleles. The term p^{2} represents the frequency of the homozygous dominant genotype. The other term, q^{2}, represents the frequency of the homozygous recessive genotype.

While it would be impossible to count all of the hidden alleles, it is easy to count the number of recessive phenotypes in a population. Recessive phenotypes are caused by two recessive alleles. Therefore, q^{2} can be easily observed by dividing the total number of recessive phenotypes by the total number of individuals. Let’s look at an example of how we can use this information to calculate the allele frequency of any given allele.

## Allele Frequency Example

Allele frequency refers to how frequently a particular allele appears in a population. For instance, if all the alleles in a population of pea plants were purple alleles, W, the allele frequency of W would be 100%, or 1.0.

In a simplified scenario, p and q are the only alleles in the population, and the population is not developing any mutations. If this is the case, the sum of the allele frequencies of p and q must equal 1 because with only two alleles the combined frequency must equal 100%.

### Finding q

In this example, consider a hypothetical population of rabbits. A certain recessive allele within rabbits causes the rabbits to be white, while all of the other rabbits are black. Only a rabbit with two recessive alleles for a particular gene will be white. When we observe the population, we find that there are 16 white rabbits and 84 black rabbits.

Since we already know what q^{2} is simply by observing the population, we can take the square root of q^{2} to find q. In this case, the white rabbits contain two recessive alleles. The white rabbits account for 16 of the 100 total rabbits. In a percentage, this is exactly 16%, or 0.16. This number is equivalent to q^{2}. Taking the square root, we find that the allele frequency of q (white) is 0.4, or 40%.

### Finding p

Once we know q, we can simply subtract q from 1 to find the frequency of p. This works only in a simplified scenario, where p and q are the only alleles and account for 100% of the total alleles. In this case, p will be equal to 60% of the alleles, or 0.6.

## Common Mistakes to Avoid in the calculation of Allele Frequency

### Trying to Find p First

One mistake that students commonly make is trying to calculate p by observing the population, then taking the square root. This does not work in typical recessive/dominant allele relationships, simply because a dominant allele can hide a recessive allele.

For instance, if we were to calculate the square root of .84 (proportion of black rabbits), we would get nearly 92%. This overestimates the p allele frequency because of the fact that heterozygous phenotypes are actually hiding a recessive allele and should not be counted towards p.

### Relating Allele Frequency to Fitness

A common misconception of allele frequency is that it is directly related to the evolutionary fitness of a particular allele. Just because an allele is frequent or infrequent has no bearing on the fitness of that allele.

For example, many recessive traits that are deleterious “hide” in a population. This can mean that while it appears to exist at really low levels, it is in fact just hiding in the hybrids of the population. Other times, a new beneficial mutation will have a very low allele frequency. A new allele must establish itself in a population by outcompeting other alleles.

To do this is must be continuously replicated across many generations. In this way, many beneficial alleles are still highly underrepresented in the population because the population has not had time to evolve.