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The allele that encodes for the most common form of a phenotype in natural population is called a wild type allele and all the rest of the alleles encoding forms other than the wild type are called mutant alleles. Do they result from mutations of the wild type allele?

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    $\begingroup$ Hey there, is there any particular reason you keep reverting the changes to the question's tags? $\endgroup$ – YviDe Dec 30 '15 at 15:18
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The determination of whether an allele is wild-type or mutant has to do with the frequency that it is observed within a population.

In genetics, a wild-type allele can be defined as

  1. an allele, or DNA variant, whose frequency is more than 1% in a population.
  2. an allele that dictates the most frequently observed phenotype in a population.

Genetics; From Genes to Genomes, Fifth Edition, Hartwell, et. al.

A mutant allele is then defined as

  1. an allele, or DNA variant, whose frequency is less than 1% in a population.
  2. an allele that dictates a phenotype seen only rarely in a population.

Genetics; From Genes to Genomes, Fifth Edition, Hartwell, et. al.

So mutant in this respect only means that the phenotype is seen less frequently in the population.

There is a sequence difference in the alleles, which leads to a phenotypic difference, but if the mutant allele provides an evolutionary advantage that ends up being selected form then it will eventually become the most representative allele in the population and will then be the wild-type.

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No, not necessarily!

The terms might be confusing I agree. The most common allele (the wild type allele) might be a mutant of one other type of allele (one mutant allele) present in the population.

The reason we call the least common alleles the mutant alleles is that beneficial mutations are rare compared to neutral or deleterious mutations. If at a given locus most mutations are deleterious, then the mutant alleles will never reach a high frequency. However, if at a given locus a beneficial mutation occurs, then this beneficial mutation will likely rise quick quickly in frequency and therefore there is only a limited time frame under which the most common allele is actually a mutant of a least common allele. In consequence, we tend to call the least common alleles "mutant alleles". This name is often a good fit to the reality but not necessarily.

Note by the way that there are other sorts of selection regime occurring at a given locus that may maintain polymorphism at relatively high heterozygosity such as any form of balancing selection.

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