Molecular Biology and Evolution, Vol 15, 590-599, Copyright © 1998 by Society for Molecular Biology and Evolution
J Maynard Smith and NH Smith
In this article, a method is proposed for detecting recombination in the
sequences of a gene from a set of closely related organisms. The method,
the Homoplasy Test, is appropriate when the sequences are rather similar,
differing by 1%-5% of nucleotides. It is effective in detecting relatively
frequent recombination between a set of rather similar strains, in contrast
to previous methods which detect rare or unique transfers between more
distant strains. It is based on the fact that, if there is no recombination
and if no repeated mutations have occurred (homoplasy), then the number of
polymorphic sites, v, is equal to the number of steps, t, in a
most-parsimonious tree. If the number of "apparent homoplasies" in the
most-parsimonious tree, h = t-v, is greater than zero, then either
homoplasies have occurred by mutation or there has been recombination. An
estimate of the distribution of h expected on the null hypothesis of no
recombination depends on Se, the "effective site number," defined as
follows: if ps is the probability that two independent substitutions in the
gene occur at the same site, then Se = 1/ps. Se can be estimated if a
suitable outgroup is available. The Homoplasy Test is applied to three
bacterial genes and to simulated gene trees with varying amounts of
recombination. Methods of estimating the rate, as opposed to the
occurrence, of recombination are discussed.
ORIGINAL ARTICLE
Detecting recombination from gene trees
School of Biological Sciences, University of Sussex, Brighton, United Kingdom.
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