Allele Frequency

Allele Frequency Definition

The allele frequency is the number of individual alleles of a certain type, divided by the total number of alleles of all types in a population. 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, scientist use the Hardy-Weinberg (HW) equation. The Hardy-Weinberg equation is written as follows:

1 = p2 + 2pq + q2

P and q each represent different alleles. P2 can represent the frequency of the homozygous dominant genotype, while q2 can represent 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.

In such 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. Since we already know what q2 is simply by observing the population, we can take the square root of q2 to find q. Once we know q, we can simply subtract q from 1 to find the frequency of p.

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.

  • Homozygous – Genotype containing one type of allele.
  • Heterozygous – Genotype containing two types of allele.
  • Recessive – Can be hidden by the effects of a dominant allele.
  • Dominant – Can mask the effects of a recessive allele.


1. In a population of flowers, a certain allele is lethal to the plant if the plant is homozygous recessive for the genotype. A single recessive allele with a dominant allele, a heterozygote, will produce a totally health plant, indistinguishable from a homozygous dominant plant. A scientist fertilizes 100 seeds, of which only 75 sprout. The scientist thinks the plants that didn’t sprout all had the lethal homozygous recessive genotype. What is the allele frequency of the recessive allele in the population?
A. 1.0
B. 0.5
C. 0.25

Answer to Question #1
B is correct. To find the allele frequency, count the number of homozygous recessive individuals. In this case, it was the number of individuals that did not sprout, or 25. Divide by the total number of offspring (100) to get 0.25. But wait! Remember that this value is q2, or the frequency of homozygous recessive individuals. To find the allele frequency, we must take the square root of q2. This leads us to the correct answer of 0.5. Therefore, while only .25 of the population suffered because of the allele, it is present in 50% of the entire population.

2. If 1 in 2,500 newborns is affected with the autosomal recessive disorder Cystic Fibrosis, how many babies are born of 2,500 that are carriers? Assume there are only two alleles and that the population is not evolving.
A. 1/25 babies
B. 1/50 babies
C. 98/2500 babies

Answer to Question #2
A is correct. As in the last problem, 1/2500 babies being born with cystic fibrosis represents q2, or the frequency of the homozygous recessive genotype. The question asks us about the carriers, or the heterozygous genotype. This is represented in the Hardy-Weinberg equation by the expression 2pq. To find 2pq, we must first find q and p. We know that 1/2500 is q2, so we can take the square root of 1/2500 to find q. In this case, q is equal to 1/50. Because p + q = 1, we know that p is equal to 49/50. To find 2pq, we simply multiply 2(1/50)(49/50) which equals 98/2500. This means 98 of the 2500 will be carriers, 1 will have cystic fibrosis, and the rest will be completely healthy.

3. A new mutation is introduced into a populations of flies that allows them to not get caught in a spider’s web. The mutated allele produces a protein that coats the fly’s body and dissolves spider-web. The allele frequency of this new trait is very low, as it only recently was introduced to the population and only a few generations have passed. What will happen to the allele frequency of the new allele over time?
A. It will get larger
B. It will get smaller
C. It will stay the same

Answer to Question #3
A is correct. Allele frequencies, though static in a population in a single generation, can change over time as selective pressures kill off unsuccessful allele types and allow successful alleles to reproduce. The new mutation created by the flies allows them to successfully escape the previously unescapable spider-web. Flies with this mutation will be given more opportunities to mate, and will be eaten less. As more and more of these flies reproduce, the allele frequency for this new mutation begins to increase. Eventually, the mutation might be so useful that organisms without the mutation go extinct, and the allele frequency is 100%. In this case, the trait is thought to be “fixed”, as the only changes that can undo it are new mutations.
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