Maynard Smith J, Smith N H
School of Biological Sciences, University of Sussex, Brighton, United Kingdom.
Mol Biol Evol. 1998 May;15(5):590-9. doi: 10.1093/oxfordjournals.molbev.a025960.
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.
本文提出了一种用于检测一组亲缘关系密切的生物体中某个基因序列重组情况的方法。该方法即同塑性检验，适用于序列相似度较高、核苷酸差异为1% - 5%的情况。与之前检测更遥远菌株间罕见或独特转移的方法不同，它在检测一组相似度较高的菌株间相对频繁的重组方面很有效。它基于这样一个事实：如果不存在重组且没有发生重复突变（同塑性），那么多态性位点的数量v等于最简约树中的步长t。如果最简约树中“表观同塑性”的数量h = t - v大于零，那么要么是通过突变发生了同塑性，要么发生了重组。在无重组的零假设下，h的预期分布估计值取决于“有效位点数量”Se，其定义如下：如果ps是基因中两个独立替换发生在同一位点的概率，那么Se = 1/ps。如果有合适的外类群，就可以估计Se。同塑性检验应用于三个细菌基因以及具有不同重组量的模拟基因树。文中还讨论了估计重组率而非重组发生率的方法。
