gene frequencies

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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, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meaning ''generation'' or ''birth'' ) is a basic unit of her ...

) 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 ...

, 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 molecule with part or all of the genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by ...
''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 genetics Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) Though heredity had been observed for millennia, Gregor Men ...
, 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 molecule with part or all of the genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by ...
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 $f\left(\mathbf\right)$, $f\left(\mathbf\right)$, and $f\left(\mathbf\right)$ 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. :$p=f\left(\mathbf\right)+ \fracf\left(\mathbf\right)= \mbox$ :$q=f\left(\mathbf\right)+ \fracf\left(\mathbf\right)= \mbox$ Because ''p'' and ''q'' are the frequencies of the only two alleles present at that locus, they must sum to 1. To check this: :$p+q=f\left(\mathbf\right)+f\left(\mathbf\right)+f\left(\mathbf\right)=1$ :$q=1-p$ 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 principle, 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 # 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 frequency, 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 (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 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 Genetic hitchhiking, 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 Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) Though heredity had been observed for millennia, Gregor Men ...
.