Stephens J C
Center for Demographic and Population Genetics, University of Texas, Houston 77225.
Mol Biol Evol. 1985 Nov;2(6):539-56. doi: 10.1093/oxfordjournals.molbev.a040371.
Simple but exact statistical tests for detecting a cluster of associated nucleotide changes in DNA are presented. The tests are based on the linear distribution of a set of s sites among a total of n sites, where the s sites may be the variable sites, sites of insertion/deletion, or categorized in some other way. These tests are especially useful for detecting gene conversion and intragenic recombination in a sample of DNA sequences. In this case, the sites of interest are those that correspond to particular ways of splitting the sequences into two groups (e.g., sequences A and D vs. sequences B, C, and E-J). Each such split is termed a phylogenetic partition. Application of these methods to a well-documented case of gene conversion in human gamma-globin genes shows that sites corresponding to two of the three observed partitions are significantly clustered, whereas application to hominoid mitochondrial DNA sequences--among which no recombination is expected to occur--shows no evidence of such clustering. This indicates that clustering of partition-specific sites is largely due to intragenic recombination or gene conversion. Alternative hypotheses explaining the observed clustering of sites, such as biased selection or mutation, are discussed.
本文提出了用于检测DNA中相关核苷酸变化簇的简单而精确的统计检验方法。这些检验基于一组s个位点在总共n个位点中的线性分布，其中s个位点可以是可变位点、插入/缺失位点或以其他方式分类的位点。这些检验对于检测DNA序列样本中的基因转换和基因内重组特别有用。在这种情况下，感兴趣的位点是那些对应于将序列分成两组的特定方式的位点（例如，序列A和D与序列B、C以及E-J）。每一种这样的划分都称为系统发育划分。将这些方法应用于人类γ-珠蛋白基因中一个有充分记录的基因转换案例表明，与三个观察到的划分中的两个相对应的位点显著聚集，而应用于类人猿线粒体DNA序列（预计其中不会发生重组）则没有显示出这种聚集的证据。这表明特定划分位点的聚集主要是由于基因内重组或基因转换。文中还讨论了解释观察到的位点聚集的其他假设，如偏向性选择或突变。
