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Allele frequency

Allele frequency is a term of population genetics that is used in characterizing the genetic diversity of a species population, or equivalently the richness of its gene pool. Allele frequency is defined as follows:

Given a) a particular chromosome locus, b) a gene occupying that locus, c) a population of individuals carrying n chromosomes with that locus in each of their somatic cells (e.g. two chromosomes in the cells of diploid species) and finally d) a variant or allele of the gene, then the allele frequency of that allele is the fraction or percentage of loci that allele occupies. If the frequency of an allele is 10%, for example, then 90% of the given loci are occupied by other variants the gene, of which there may be one or many.

The frequencies of all the alleles of a given gene often are graphed together as an allele frequency distribution histogram-- or simply allele distribution. In the absence of selection and assuming other conditions, the frequency of allele conforms to the binomial distribution.

According to the Hardy-Weinberg principle, under ideal conditions the distribution and frequencies of alleles in a given population will remain the same from one generation to the next. Population genetics studies the different "forces" that might lead to changes in the distribution and frequencies of alleles -- in other words, evolution. Besides selection, these forces include genetic drift and migration.

In a diploid population, if an allele's frequency is 50%, half of loci will be occupied by the allele, but typically less than half of individuals will carry it. This is because not every individuals will be heterozygous, carrying only one copy of the allele in each of their somatic cells. Instead, many will be homozygous, carrying two copies, and a roughly equal number will carry zero copies (in the absence of selection).

Example

If there are four individuals in a population and at a given locus there are two possible alleles, A and a, then if the genotypes of the individuals are:

Individual 1: AA
Individual 2: aa
Individual 3: Aa
Individual 4: Aa

then the allele frequencies of allele A and allele a, respectively would be:

pA = (2 + 0 + 1 + 1)/8 = 0.5
pa = (0 + 2 + 1 + 1)/8 = 0.5



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