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Allele frequency

 

 
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Allele frequency
 
 
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Allele frequency is the number of copies of a particular allele
Allele

An allele is one member of a pair or series of different forms of a gene. Usually alleles are coding region, but sometimes the term is used to refer to a junk DNA....
 divided by the number of copies of all alleles at the genetic place (locus) in a population
Population

File:Population density.pngIn biology, a population is the collection of inter-breeding organisms of a particular species; in sociology, a collection of human beings....
. It can be expressed for example as a percentage
Percentage

In mathematics, a percentage is a way of expressing a number as a fraction of 100 . It is often denoted using the percent sign, "%". For example, 45% is equal to 45 / 100, or 0.45....
. In population genetics
Population genetics

Population genetics is the study of the allele frequency distribution and change under the influence of the four evolutionary processes: natural selection, genetic drift, mutation and gene flow....
, allele frequencies are used to depict the amount of genetic
Genetics

Genetics , a discipline of biology, is the science of heredity and Genetic variation in living organisms. The fact that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals through selective breeding....
 diversity at the individual, population, and species
Species

In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring....
 level.

Given the following:
  1. a particular locus
    Locus (genetics)

    In the fields of genetics and evolutionary computation, a locus is a fixed position on a chromosome such as the position of a genetic marker that may be occupied by one or more genes....
     on a chromosome
    Chromosome

    A chromosome is an organized structure of DNA and protein that is found in Cell . A chromosome is a single piece of DNA that contains many genes, regulatory sequence and other genetic sequence....
     and the gene
    Gene

    A gene is the basic unit of heredity in a living organism. All living things depend on genes. Genes hold the information to build and maintain their cell and pass genetic trait to offspring....
     occupying that locus
  2. a population of individuals carrying n loci in each of their somatic cell
    Somatic cell

    Somatic cells are any cell s forming the body of an organism, as opposed to germline cells. In mammals, germline cells are the spermatozoa and ova which fuse during fertilization to produce a cell called a zygote, from which the entire mammalian embryo develops....
    s (e.g.






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    Allele frequency is the number of copies of a particular allele
    Allele

    An allele is one member of a pair or series of different forms of a gene. Usually alleles are coding region, but sometimes the term is used to refer to a junk DNA....
     divided by the number of copies of all alleles at the genetic place (locus) in a population
    Population

    File:Population density.pngIn biology, a population is the collection of inter-breeding organisms of a particular species; in sociology, a collection of human beings....
    . It can be expressed for example as a percentage
    Percentage

    In mathematics, a percentage is a way of expressing a number as a fraction of 100 . It is often denoted using the percent sign, "%". For example, 45% is equal to 45 / 100, or 0.45....
    . In population genetics
    Population genetics

    Population genetics is the study of the allele frequency distribution and change under the influence of the four evolutionary processes: natural selection, genetic drift, mutation and gene flow....
    , allele frequencies are used to depict the amount of genetic
    Genetics

    Genetics , a discipline of biology, is the science of heredity and Genetic variation in living organisms. The fact that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals through selective breeding....
     diversity at the individual, population, and species
    Species

    In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring....
     level.

    Given the following:
    1. a particular locus
      Locus (genetics)

      In the fields of genetics and evolutionary computation, a locus is a fixed position on a chromosome such as the position of a genetic marker that may be occupied by one or more genes....
       on a chromosome
      Chromosome

      A chromosome is an organized structure of DNA and protein that is found in Cell . A chromosome is a single piece of DNA that contains many genes, regulatory sequence and other genetic sequence....
       and the gene
      Gene

      A gene is the basic unit of heredity in a living organism. All living things depend on genes. Genes hold the information to build and maintain their cell and pass genetic trait to offspring....
       occupying that locus
    2. a population of individuals carrying n loci in each of their somatic cell
      Somatic cell

      Somatic cells are any cell s forming the body of an organism, as opposed to germline cells. In mammals, germline cells are the spermatozoa and ova which fuse during fertilization to produce a cell called a zygote, from which the entire mammalian embryo develops....
      s (e.g. two loci in the cells of diploid species, which contain two sets of chromosomes)
    3. variants or allele
      Allele

      An allele is one member of a pair or series of different forms of a gene. Usually alleles are coding region, but sometimes the term is used to refer to a junk DNA....
      s of the gene exist,
    then the allele frequency is the fraction or percentage of times that a given allele is present at a locus within the population.

    For example, if the frequency of an allele is 20% in a given population, then among population members, one in five chromosomes will carry that allele. Four out of five will be occupied by other variant(s) of the gene. Note that for diploid genes the fraction of individuals that carry this allele may be nearly two in five. If the allele distributes randomly, then the binomial theorem
    Binomial theorem

    In mathematics, the binomial theorem is an important formula giving the expansion of exponentiation of sums. Its simplest version states that...
     will apply: 32% of the population will be heterozygous for the allele (i.e. carry one copy of that allele and one copy of another in each somatic cell) and 4% will be homozygous (carrying two copies of the allele). Together, this means that 36% of diploid individuals would be expected to carry an allele that has a frequency of 20%. However, alleles distribute randomly only under certain assumptions, including the absence of selection
    Selection

    In the context of evolution, certain traits or alleles of a species may be subject to selection depending on the Pragmatics the user has with the word....
    . When these conditions apply, a population is said to be in Hardy-Weinberg equilibrium
    Hardy-Weinberg principle

    The Hardy?Weinberg principle states that both allele and genotype frequencies in a population remain constant—that is, they are in equilibrium—from generation to generation unless specific disturbing influences are introduced....
    .

    The frequencies of all the alleles of a given gene often are graphed together as an allele frequency distribution
    Frequency distribution

    In statistics, a frequency statistical distribution is a tabulation of the values that one or more variables take in a Sampling ....
     histogram
    Histogram

    In statistics, a histogram is a graphical display of tabulated frequency , shown as bars. It shows what proportion of cases fall into each of several Categorization....
    , or allele frequency spectrum. Population genetics studies the different "forces" that might lead to changes in the distribution and frequencies of alleles -- in other words, to evolution
    Evolution

    In biology, evolution is change in the heritability trait of a population of organisms from one generation to the next. These changes are caused by a combination of three main processes: variation, reproduction, and selection....
    . Besides selection, these forces include genetic drift
    Genetic drift

    Genetic drift or allelic drift is the change in the relative frequency with which a gene variant occurs in a population that results from the fact that alleles in offspring are a Sampling of those in the parents, and because of the role of chance in determining whether a given individual survives and reproduces....
    , mutation
    Mutation

    In biology, mutations are changes to the nucleotide sequence of the genetic material of an organism. Mutations can be caused by copying errors in the genetic material during cell division, by exposure to ultraviolet or ionizing radiation, chemical mutagens, or virus , or can be induced by the organism, itself, by cellular processes such as s...
     and migration.

    Calculation of allele frequencies from genotype frequencies


    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 a-allele are obtained by counting alleles. Because each homozygote AA consists only of A-alleles, and because half of the alleles of each heterozygote Aa are A-alleles, the total frequency p of A-alleles in the population is calculated as

    frequency of A

    Similarly, the frequency q of the a allele is given by

    frequency of a

    It would be expected that p and q sum to 1, since they are the frequencies of the only two alleles present. Indeed they do:

    and from this we get:

    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. Allele frequency can always be calculated from genotype frequency
    Genotype frequency

    In population genetics, the genotype frequency is the frequency or proportion of genotypes in a population.It may be denoted thus:Compare allele frequency....
    , whereas the reverse requires that the Hardy-Weinberg conditions of random mating apply. This is partly due to the three genotype frequencies and the two allele frequencies. It is easier to reduce from three to two.

    An example population

    Consider a population of ten individuals and a given locus with two possible alleles, A and a. Suppose that the genotype
    Genotype

    The genotype is the trait we can't see. The genotype is the Genetics constitution of a cell, an organism, or an individual usually with reference to a specific character under consideration....
    s of the individuals are as follows:
    AA, Aa, AA, aa, Aa, AA, AA, Aa, Aa, and AA
    Then the allele frequencies of allele A and allele a are: so if an individual is chosen at random there is a 70% chance it will carry that allele and there is a 30% chance that an individual chosen at random will have the a-allele

    The effect of mutation


    Let ù be the mutation rate
    Mutation rate

    In genetics, the mutation rate is the chance of a mutation occurring in an organism or gene in each generation . The mutation frequency is the number of individuals in a population with a particular mutation, and tends to be reported more often as it is easier to measure ....
     from allele A to some other allele a ( the probability that a copy of gene A will become a during the DNA replication preceding meiosis). If is the frequency of the A allele in generation t, if is the frequency of the a allele in generation t, and if there are no other causes of gene frequency change (no natural selection, for example), then the change in allele frequency in one generation is

    where is the frequency of the preceding generation. This tells us that the frequency of A decreases (and the frequency of a increases) by an amount that is proportional to the mutation rate ú and to the proportion p of all the genes that are still available to mutate. Thus gets smaller as the frequency of p itself decreases, because there are fewer and fewer A alleles to mutate into a alleles. We can make an approximation that, after n generations of mutation,

    See also

    • Genotype frequency
      Genotype frequency

      In population genetics, the genotype frequency is the frequency or proportion of genotypes in a population.It may be denoted thus:Compare allele frequency....
    • Hardy-Weinberg principle
      Hardy-Weinberg principle

      The Hardy?Weinberg principle states that both allele and genotype frequencies in a population remain constant—that is, they are in equilibrium—from generation to generation unless specific disturbing influences are introduced....

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