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 chro ...
(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 ba ...
) 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 using a ...
, 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 a r ...
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 chro ...
at that locus
# A population of ''N'' individuals with
ploidy
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 mat ...
''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 compo ...
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, respectively ...
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
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 nu ...
, 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 pop ...
, 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 ...
.
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 (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 mat ...
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.
:
:
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 frequency can always be calculated from
genotype frequency
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 nu ...
, 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.
Mo ...
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
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
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 nu ...
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. Charle ...
(
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, mi ...
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 was ...
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 pop ...
.
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 ...
*
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 lar ...
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