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Allele frequency, or gene frequency, is the relative frequency of an
allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chrom ...
(variant of a
gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
) at a particular
locus Locus (plural loci) is Latin for "place". It may refer to: Entertainment * Locus (comics), a Marvel Comics mutant villainess, a member of the Mutant Liberation Front * ''Locus'' (magazine), science fiction and fantasy magazine ** ''Locus Award' ...
in a
population Population typically refers to the number of people in a single area, whether it be a city or town, region, country, continent, or the world. Governments typically quantify the size of the resident population within their jurisdiction usi ...
, expressed as a fraction or percentage. Specifically, it is the fraction of all chromosomes in the population that carry that allele over the total population or sample size.
Microevolution Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection ( natural and artificial), gene flow and genetic drift. This change happens over ...
is the change in allele frequencies that occurs over time within a population. Given the following: # A particular locus on a chromosome and a given
allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chrom ...
at that locus # A population of ''N'' individuals with
ploidy Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Sets of chromosomes refer to the number of maternal and paternal chromosome copies, respectiv ...
''n'', i.e. an individual carries ''n'' copies of each chromosome in their
somatic cell A somatic cell (from Ancient Greek σῶμα ''sôma'', meaning "body"), or vegetal cell, is any biological cell forming the body of a multicellular organism other than a gamete, germ cell, gametocyte or undifferentiated stem cell. Such cells com ...
s (e.g. two chromosomes in the cells of
diploid Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Sets of chromosomes refer to the number of maternal and paternal chromosome copies, respectiv ...
species) # 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. In
population genetics Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and po ...
, 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 In population genetics, the allele frequency spectrum, sometimes called the site frequency spectrum, is the distribution of the allele frequencies of a given set of loci (often SNPs) in a population or sample. Because an allele frequency spectrum i ...
.


Calculation of allele frequencies from genotype frequencies

The actual frequency calculations depend on the
ploidy Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Sets of chromosomes refer to the number of maternal and paternal chromosome copies, respectiv ...
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 :p = i/N.


Diploids

If f(\mathbf), f(\mathbf), and f(\mathbf) 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. :p=f(\mathbf)+ \fracf(\mathbf)= \mbox :q=f(\mathbf)+ \fracf(\mathbf)= \mbox Because ''p'' and ''q'' are the frequencies of the only two alleles present at that locus, they must sum to 1. To check this: :p+q=f(\mathbf)+f(\mathbf)+f(\mathbf)=1 :q=1-p and p=1-q 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 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 Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. Mo ...
genotypes (AA and BB), and one
heterozygous Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. ...
genotype (AB). If we sample 10 individuals from the population, and we observe the genotype frequencies # freq (AA) = 6 # freq (AB) = 3 # freq (BB) = 1 then there are 6\times2 + 3 = 15 observed copies of the A allele and 1\times2 + 3 = 5 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 Genetic variation in populations can be analyzed and quantified by the frequency of alleles. Two fundamental calculations are central to population genetics: allele frequencies and genotype frequencies. Genotype frequency in a population is the n ...
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. In natural populations
natural selection Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Cha ...
(
adaptation In biology, adaptation has three related meanings. Firstly, it is the dynamic evolutionary process of natural selection that fits organisms to their environment, enhancing their evolutionary fitness. Secondly, it is a state reached by the po ...
mechanism),
gene flow In population genetics, gene flow (also known as gene migration or geneflow and allele flow) is the transfer of genetic material from one population to another. If the rate of gene flow is high enough, then two populations will have equivalent a ...
, and
mutation In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, m ...
combine to change allele frequencies across generations.
Genetic drift Genetic drift, also known as allelic drift or the Wright effect, is the change in the frequency of an existing gene variant (allele) in a population due to random chance. Genetic drift may cause gene variants to disappear completely and there ...
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 Niche construction is the process by which an organism alters its own (or another species') local environment. These alterations can be a physical change to the organism’s environment or encompass when an organism actively moves from one habita ...
According to
extended evolutionary synthesis The extended evolutionary synthesis consists of a set of theoretical concepts argued to be more comprehensive than the earlier modern synthesis of evolutionary biology that took place between 1918 and 1942. The extended evolutionary synthesis w ...
adaptation occur due to natural selection, environmental induction, non-genetic inheritance, learning and cultural transmission. 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 Hitchhiking (also known as thumbing, autostop or hitching) is a means of transportation that is gained by asking individuals, usually strangers, for a ride in their car or other vehicle. The ride is usually, but not always, free. Nomads hav ...
or
background selection Background may refer to: Performing arts and stagecraft * Background actor * Background artist * Background light * Background music * Background story * Background vocals * ''Background'' (play), a 1950 play by Warren Chetham-Strode Rec ...
. 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 Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and po ...
.


See also

*
Allele frequency net database The Allele Frequency Net Database is a database containing the allele frequencies of immune genes and their corresponding alleles in different population Population typically refers to the number of people in a single area, whether it be ...
*
Allele frequency spectrum In population genetics, the allele frequency spectrum, sometimes called the site frequency spectrum, is the distribution of the allele frequencies of a given set of loci (often SNPs) in a population or sample. Because an allele frequency spectrum i ...
*
Single-nucleotide polymorphism In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently ...


References


External links


ALFRED databaseEHSTRAFD.org – Earth Human STR Allele Frequencies DatabaseVWA 17 Allele Frequency in Human Population (Poster)Allele Frequencies in Worldwide Populations
{{MolecularEvolution Genetics concepts Population genetics Genetic genealogy