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 (biology), adaptation, ...

, 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 sites 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 replication, DNA or viral repl ...

. 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 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.

Description

See also

References