DETECTING RECOMBINATION FROM GENE TREES

In this article, a method is proposed for detecting recombination in t he sequences of a gene from a set of closely related organisms. The me thod, the Homoplasy Test, is appropriate when the sequences are rather similar, differing by 1%-5% of nucleotides. It is effective in detect ing relatively frequent recombination between a set of rather similar strains, in contrast to previous methods which detect rare or unique t ransfers between mon 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, nu, is equal to the number of steps, t, in a most-parsimonious tree. If the number of ''a pparent homoplasies'' in the most-parsimonious tree, h = t - nu, is gr eater than zero, then either homoplasies have occurred by mutation or then has been recombination. An estimate of the distribution of h expe cted on the null hypothesis of no recombination depends on S-e, the '' effective site number'' defined as follows: if p(s) is the probability that two independent substitutions in the gene occur at the same site , then S-e = 1/p(s). S-e can be estimated if a suitable outgroup is av ailable. The Homoplasy Test is applied to three bacterial genes and to simulated gene trees with varying amounts of recombination. Methods o f estimating the rate, as opposed to the occurrence, of recombination are discussed.