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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 ...
, the four-gamete test is a method for detecting historical recombination events.


Description

Given a set of four or more sampled haploid
chromosomes A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
, the four-gamete test (FGT) detects recombination events by locating pairs of
segregating site Segregating sites are positions which show differences (polymorphisms) between related genes in a sequence alignment (are not conserved). Segregating sites include conservative, semi-conservative and non-conservative mutations. The proportion of s ...
s that cannot have arisen without either recombination or a repeat
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, m ...
. Under the infinite-sites assumption (i.e. repeat mutations have zero probability), the probability of a repeat mutation is zero, and hence a recombination event is inferred. For example, if the data being studied consists of bi-allelic
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 ...
data, then the following configuration could be generated ''without'' recombination. However, the following configuration cannot be generated without recombination. {, class="wikitable" ! Chromosome !! Site 1 !! Site 2 , - , 1 , , 0 , , 0 , - , 2 , , 1 , , 0 , - , 3 , , 0 , , 1 , - , 4 , , 1 , , 1 The FGT detects a recombination event if the above configuration occurs in the data. The data in the above configuration is considered to be ''incompatible'' with any non-recombining ancestral history. The FGT has low
statistical power In statistics, the power of a binary hypothesis test is the probability that the test correctly rejects the null hypothesis (H_0) when a specific alternative hypothesis (H_1) is true. It is commonly denoted by 1-\beta, and represents the chances ...
to detect recombination. Furthermore, the FGT is suitable only when the
mutation rate In genetics, the mutation rate is the frequency of new mutations in a single gene or organism over time. Mutation rates are not constant and are not limited to a single type of mutation; there are many different types of mutations. Mutation rates ...
is significantly smaller than the recombination rate. If the mutation rate is high, then the infinite-sites assumption is violated. For example, the FGT is generally suitable for human datasets, but is unsuitable for bacterial datasets.


See also

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Genetic recombination Genetic recombination (also known as genetic reshuffling) is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukary ...
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Coalescent theory Coalescent theory is a model of how alleles sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structu ...


References

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