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 ...
, the four-gamete test (FGT) is a method for detecting historical
recombination events.
Description
The four gamete-test detects pairs of
segregating sites that have arisen either by recombination or by 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, ...
. The test is based on an infinite-sites assumption (i.e. repeat mutations have zero probability). Under this hypothesis, 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 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 ...
data, then the following configuration could be generated ''without'' recombination. Indeed, for instance, from genotype 0, 0, one mutation can give rise to genotype 0, 1, and another mutation can give rise to genotype 1, 0.
However, the following configuration cannot be generated without recombination. Indeed, the assumption of the infinite site model supposes that mutation at site 1 in genotype 2 to produce genotype 4 is impossible (and so is mutation at site 2 in genotype 3).
Hence, in this example, the existence of genotype 4 is the hallmark of recombination. The FGT detects recombination events by identifying the type of configuration presented above in the data. FGT can be performed using R.
[{{cite web , url=https://search.r-project.org/CRAN/refmans/FourgameteP/html/FourgameteP.html , title=R: FourGamete Test ]
The FGT has low
statistical power
In frequentist statistics, power is the probability of detecting a given effect (if that effect actually exists) using a given test in a given context. In typical use, it is a function of the specific test that is used (including the choice of tes ...
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, nucleotide sequence, 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 mu ...
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
*
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 eukaryot ...
*
Coalescent theory
Coalescent theory is a Scientific modelling, model of how alleles sampled from a population may have originated from a most recent common ancestor, common ancestor. In the simplest case, coalescent theory assumes no genetic recombination, recombina ...
References
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