Allele Frequency
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Allele frequency, or gene frequency, is the relative frequency of an
allele An allele is a variant of the sequence of nucleotides at a particular location, or Locus (genetics), locus, on a DNA molecule. Alleles can differ at a single position through Single-nucleotide polymorphism, single nucleotide polymorphisms (SNP), ...
(variant of a
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
) at a particular locus in a
population Population is a set of humans or other organisms in a given region or area. Governments conduct a census to quantify the resident population size within a given jurisdiction. The term is also applied to non-human animals, microorganisms, and pl ...
, 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 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 is a variant of the sequence of nucleotides at a particular location, or Locus (genetics), locus, on a DNA molecule. Alleles can differ at a single position through Single-nucleotide polymorphism, single nucleotide polymorphisms (SNP), ...
at that locus # 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 Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Here ''sets of chromosomes'' refers to the number of maternal and paternal chromosome copies, ...
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 among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, s ...
, 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.


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 :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. Mos ...
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. Mos ...
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. It is a key mechanism of evolution, the change in the Heredity, heritable traits characteristic of a population over generation ...
(
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 p ...
mechanism),
gene flow In population genetics, gene flow (also known as migration and allele flow) is the transfer of genetic variation, genetic material from one population to another. If the rate of gene flow is high enough, then two populations will have equivalent ...
, 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, ...
combine to change allele frequencies across generations.
Genetic drift Genetic drift, also known as random genetic drift, allelic drift or the Wright effect, is the change in the Allele frequency, frequency of an existing gene variant (allele) in a population due to random chance. Genetic drift may cause gene va ...
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 According to extended evolutionary synthesis 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 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 Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, s ...
.


See also

*
Allele frequency net database The Allele Frequency Net Database (abbreviated AlFreD) is a database containing the allele frequencies of immune genes and their corresponding alleles in different population Population is a set of humans or other organisms in a given regio ...
* Allele frequency spectrum * Minor allele frequency (MAF) *
Single-nucleotide polymorphism In genetics and bioinformatics, 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 ...


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