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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 one of two, or more, forms of a given gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance ...
(variant of a
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

gene
) 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), ''Locus'' (magazine), science fiction and fantasy magazine ...
in a
population Population typically refers the number of people in a single area whether it be a city or town, region, country, or the world. Governments typically quantify the size of the resident population within their jurisdiction by a process called a ...

population
, expressed as a fraction or percentage. Specifically, it is the fraction of all chromosomes in the population that carry that allele.
Microevolution Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation Image:Darwin Hybrid Tulip Mutation 2014-05-01.jpg, A tulip flower exhibiting a partially y ...
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 one of two, or more, forms of a given gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance ...
at that locus # A population of ''N'' individuals with
ploidy Ploidy () is the number of complete sets of chromosome A chromosome is a long DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, wh ...
''n'', i.e. an individual carries ''n'' copies of each chromosome in their
somatic cell A somatic cell (from Ancient Greek Ancient Greek includes the forms of the Greek language used in ancient Greece and the classical antiquity, ancient world from around 1500 BC to 300 BC. It is often roughly divided into the following period ...
s (e.g. two chromosomes in the cells of
diploid Ploidy () is the number of complete sets of chromosomes in a cell (biology), cell, and hence the number of possible alleles for Autosome, autosomal and Pseudoautosomal region, pseudoautosomal genes. Sets of chromosomes refer to the number of mate ...
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 that deals with genetic differences within and between s, and is a part of . Studies in this branch of examine such phenomena as , , and . Population genetics was a vital ingredient in the of the . Its pri ...
, 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 spectrumIn population genetics, the allele frequency spectrum, sometimes called the site frequency spectrum, is the distributionDistribution may refer to: Mathematics *Distribution (mathematics) Distributions, also known as Schwartz distributions ...
.


Calculation of allele frequencies from genotype frequencies

The actual frequency calculations depend on the
ploidy Ploidy () is the number of complete sets of chromosome A chromosome is a long DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, wh ...
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 A zygote (from Greek ζυγωτός ''zygōtos'' "joined" or "yoked", from ζυγοῦν ''zygoun'' "to join" or "to yoke") is a eukaryotic cell formed by a fertilization event between two gamete A gamete ( /ˈ ...
genotypes (AA and BB), and one
heterozygous Zygosity (the noun, zygote, is from the Greek zygotos "yoked," from zygon "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 or ...

heterozygous
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 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 right , Here the relation between genotype and phenotype is illustrated, using a Punnett square, for the character of peta ...
(
adaptation In , adaptation has three related meanings. Firstly, it is the dynamic evolutionary process that fits s to their environment, enhancing their . Secondly, it is a state reached by the population during that process. Thirdly, it is a or adapti ...

adaptation
mechanism),
gene flow In , gene flow (also known as gene migration or geneflow and flow) is the transfer of material from one to another. If the rate of gene flow is high enough, then two populations will have equivalent allele frequencies and therefore can be cons ...

gene flow
, and
mutation In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechan ...
combine to change allele frequencies across generations.
Genetic drift Genetic drift (allelic drift or the Sewall Wright effect) is the change in the frequency of an existing gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, M ...

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 Niche construction is the process by which an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the Life#Biology, properties of life. It is ...
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 Evolutionary biology is the subfield of biology Biology is the natu ...
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 that is gained by asking individuals, usually strangers, for a ride in their or other vehicle. The ride is usually, but not always, free. s have also used hitchhiki ...
or
background selection{{Short description, A phenomenon inducing a loss of genetic diversity Background selection describes the loss of genetic diversity Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species, it ranges widel ...
. 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 that deals with genetic differences within and between s, and is a part of . Studies in this branch of examine such phenomena as , , and . Population genetics was a vital ingredient in the of the . Its pri ...
.


See also

*
Allele frequency net databaseThe allele frequency net database is a database containing the allele frequencies of immune In biology, immunity is the capability of multicellular organisms to resist harmful microorganism A microorganism, or microbe,, ''mikros'', "small") an ...
*
Allele frequency spectrumIn population genetics, the allele frequency spectrum, sometimes called the site frequency spectrum, is the distributionDistribution may refer to: Mathematics *Distribution (mathematics) Distributions, also known as Schwartz distributions ...
*
Single-nucleotide polymorphism In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interacti ...


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 Population genetics Genetic genealogy