What is Allele Frequency? – How to Calculate it!

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?

An allele frequency is calculated by dividing the number of times the allele of interest is observed in a population by the total number of copies of all the alleles at that particular genetic locus in the population. Allele frequencies can be represented as a decimal, a percentage, or a fraction.

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 = p2 + 2pq + q2

P and q each represent the allele frequency of different alleles. The term p2 represents the frequency of the homozygous dominant genotype. The other term, q2, 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, q2 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.

Let’s look at an example. Consider the very small population of nine pea plants shown below. Each pea plant has two copies of the flower color gene.

Allele Frequency Example

If we look at the two copies of the gene in each plant and count how many W copies there are, we find that there are 13. If we count how many W copies there are, we find that there are five. The total number of gene copies in the total population is 13 + 5 = 18

We can divide the number of copies of each allele by the total number of copies to get the allele frequency. If there are only two alleles for a gene in a population, their frequencies are given the symbols ppp and qqq:

The frequency of all alleles of a gene must be one or 100%.

The allele frequency is different from the genotype frequency or the phenotype frequency. Genotype and phenotype frequencies can also be calculated and are important in understanding population evolution, but they are not the same as allele frequency. The following diagram shows the difference:

Allele Frequency Example

Now let’s say we come back a generation later and check the genotypes of the new pea plants that now make up the population. To find the allele frequencies, we look again at the genotype of each individual, count the number of copies of each allele and divide by the total number of gene copies. Now we notice that the frequency has fallen from W to 8/18 = 0.44, or 44%, and the frequency has increased from w to 10/18, or 56%.

Allele Frequency Example

The allele frequencies in the population have changed over generations. So, according to the definition of microevolution, we can say that the population has evolved. When we actually do research, we may want to use a statistical test to confirm that these proportions are really different.

Later in this tutorial, we will examine the factors that lead to the evolution of a population, including natural selection, genetic drift – random change – and other factors.

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.

What is Allele Frequency?

An allele frequency is calculated by dividing the number of times the allele of interest is observed in a population by the total number of copies of all the alleles at that particular genetic locus in the population. Allele frequencies can be represented as a decimal, a percentage, or a fraction.

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.

What is an example of allele frequency?

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