Allele frequency

Allele frequency, or gene frequency, is the relative frequency of an allele (variant of a gene) at a particular
locus in a population, expressed as a fraction or percentage.[1] Specifically, it is the fraction of all
chromosomes in the population that carry that allele. Microevolution is the change in allele frequencies that
occurs over time within a population.

Given the following:

1. A particular locus on a chromosome and a given allele at that locus

2. A population of N individuals with ploidy n, i.e. an individual carries n copies of each
chromosome in their somatic cells (e.g. two chromosomes in the cells of diploid species)
3. The allele exists in i chromosomes in the population

then the allele frequency is the fraction of all the occurrences i of that allele and the total number of
chromosome copies across the population, i/(nN).

The allele frequency is distinct from the genotype frequency, although they are related, and allele frequencies
can be calculated from genotype frequencies.[1]

In population genetics, allele frequencies are used to describe the amount of variation at a particular locus or
across multiple loci. When considering the ensemble of allele frequencies for many distinct loci, their
distribution is called the allele frequency spectrum.

Contents
Calculation of allele frequencies from genotype frequencies
Monoploids
Diploids
Example
Dynamics
See also
References
External links

Calculation of allele frequencies from genotype frequencies

The actual frequency calculations depend on the ploidy of the species for autosomal genes.

Monoploids

The frequency (p) of an allele A is the fraction of the number of copies (i) of the A allele and the population or
sample size (N), so
Diploids

If , , and are the frequencies of the three genotypes at a locus with two alleles, then
the frequency p of the A-allele and the frequency q of the B-allele in the population are obtained by counting
alleles.[2]

Because p and q are the frequencies of the only two alleles present at that locus, they must sum to 1. To check
this:

and

If there are more than two different allelic forms, the frequency for each allele is simply the frequency of its
homozygote plus half the sum of the frequencies for all the heterozygotes in which it appears.

(For 3 alleles see Allele § Allele and genotype frequencies)

Allele frequency can always be calculated from genotype frequency, whereas the reverse requires that the
Hardy–Weinberg conditions of random mating apply.

Example

Consider a locus that carries two alleles, A and B. In a diploid population there are three possible genotypes,
two homozygous genotypes (AA and BB), and one heterozygous genotype (AB). If we sample 10 individuals
from the population, and we observe the genotype frequencies

1. freq (AA) = 6
2. freq (AB) = 3
3. freq (BB) = 1

then there are observed copies of the A allele and of the B allele, out of 20
total chromosome copies. The frequency p of the A allele is p = 15/20 = 0.75, and the frequency q of the B
allele is q = 5/20 = 0.25.

Dynamics
Population genetics describes the genetic composition of a population, including allele frequencies, and how
allele frequencies are expected to change over time. The Hardy–Weinberg law describes the expected
equilibrium genotype frequencies in a diploid population after random mating. Random mating alone does not
change allele frequencies, and the Hardy–Weinberg equilibrium assumes an infinite population size and a
selectively neutral locus.[1]
In natural populations natural selection (adaptation mechanism), gene flow, and mutation combine to change
allele frequencies across generations. Genetic drift causes changes in allele frequency from random sampling
due to offspring number variance in a finite population size, with small populations experiencing larger per
generation fluctuations in frequency than large populations. There is also a theory that second adaptation
mechanism exists – niche construction[3] According to extended evolutionary synthesis adaptation occur due
to natural selection, environmental induction, non-genetic inheritance, learning and cultural transmission.[4] An
allele at a particular locus may also confer some fitness effect for an individual carrying that allele, on which
natural selection acts. Beneficial alleles tend to increase in frequency, while deleterious alleles tend to decrease
in frequency. Even when an allele is selectively neutral, selection acting on nearby genes may also change its
allele frequency through hitchhiking or background selection.

While heterozygosity at a given locus decreases over time as alleles become fixed or lost in the population,
variation is maintained in the population through new mutations and gene flow due to migration between
populations. For details, see population genetics.

See also
Allele frequency net database
Allele frequency spectrum
Single-nucleotide polymorphism

References
1. Gillespie, John H. (2004). Population genetics : a concise guide (2. ed.). Baltimore, Md.: The
Johns Hopkins University Press. ISBN 978-0801880087.
2. "Population and Evolutionary Genetics" (https://www.ndsu.edu/pubweb/~mcclean/plsc431/pop
gen/popgen2.htm). ndsu.edu.
3. Scott-Phillips, T. C.; Laland, K. N.; Shuker, D. M.; Dickins, T. E.; West, S. A. (2014). "The Niche
Construction Perspective: A Critical Appraisal" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC
4261998). Evolution. 68 (5): 1231–1243. doi:10.1111/evo.12332 (https://doi.org/10.1111%2Fev
o.12332). PMC 4261998 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4261998).
PMID 24325256 (https://pubmed.ncbi.nlm.nih.gov/24325256).
4. Laland, K. N.; Uller, T.; Feldman, M. W.; Sterelny, K.; Müller, G. B.; Moczek, A.; Jablonka, E.;
Odling-Smee, J. (Aug 2015). "The extended evolutionary synthesis: its structure, assumptions
and predictions" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632619). Proc Biol Sci. 282
(1813): 20151019. doi:10.1098/rspb.2015.1019 (https://doi.org/10.1098%2Frspb.2015.1019).
PMC 4632619 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632619). PMID 26246559 (http
s://pubmed.ncbi.nlm.nih.gov/26246559).

External links
ALFRED database (http://alfred.med.yale.edu/alfred/)
EHSTRAFD.org – Earth Human STR Allele Frequencies Database (https://web.archive.org/we
b/20090713043812/http://www.ehstrafd.org/)
VWA 17 Allele Frequency in Human Population (Poster) (https://web.archive.org/web/2011072
6020415/http://www.ehstrafd.org/download/vWA_17_A1.rar)
Allele Frequencies in Worldwide Populations (http://www.allelefrequencies.net)
Cheung, KH; Osier MV; Kidd JR; Pakstis AJ; Miller PL; Kidd KK (2000). "ALFRED: an allele frequency
database for diverse populations and DNA polymorphisms" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC
102486). Nucleic Acids Research. 28 (1): 361–3. doi:10.1093/nar/28.1.361 (https://doi.org/10.1093%2Fnar%2
F28.1.361). PMC 102486 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102486). PMID 10592274 (http
s://pubmed.ncbi.nlm.nih.gov/10592274).

Middleton, D; Menchaca L; Rood H; Komerofsky R (2002). "New allele frequency database:

www.allelefrequencies.net". Tissue Antigens. 61 (5): 403–7. doi:10.1034/j.1399-0039.2003.00062.x (https://d
oi.org/10.1034%2Fj.1399-0039.2003.00062.x). PMID 12753660 (https://pubmed.ncbi.nlm.nih.gov/1275366
0).

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