For codominant markers, the presence of all four possible two-locus gametes in a sample is often used as evidence for recombination between the loci in question (Hudson and Kaplan 1984). For dominant genotypic data (like AFLPs or transposon displat (TD)), the underlying gametes can only be discerned for the homozygote recessive, and the four-gamete test is not possible.

However, an analogous comparison can be made using the presence of 3-locus genotypes: all eight three-locus genotypes provide similar evidence for recombination. While the four-gamete test is used to identify the product of meiotic crossovers, gene conversion or conversion-like processes could create the same pattern if the conversion tract included one of the typed markers. Because multiple mutations can lead to the loss of a dominant display band, an important caveat of these tests is that observed genotypic patterns may be explained in part by recurrent mutation rather than recombination or gene conversion.

For a given dataset, tabulating a list of the 3-locus combinations that fail the eight-zygote test allows us to establish the minimum number of marker-events required to explain the observed data. Note that this is NOT the same as the number of recombination events needed to explain the data, which may be much smaller. Instead, this is the number of markers that must be involved in at least one event in order to explain the data. A single crossover, for example, could explain multiple marker-events.

Here is an R function to calculate the minimum number of “marker-events” required to explain the observed data.

eight.zygote.R

Also, an example dataset. Each column is a different locus, and each row an individual. For this dataset, 1 marker-event is required to explain the data (i.e. one 3-locus combination shows all 8 possible genotypes).

csome.txt

Tags: analysis