Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion.
Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion.
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DOI：
10.1093/oxfordjournals.molbev.a040371
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发表时间：
1985-11
影响因子：
10.7
通讯作者：
of Intragenic
中科院分区：
文献类型：
--
作者：
of Intragenic
简单但准确的统计测试检测集群相关的核苷酸变化的DNA提出。测试是基于一组s个位点在总共n个位点中的线性分布，其中s个位点可能是可变位点、插入/删除位点或以其他方式分类的位点。这些测试对于检测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和E-J）。每一次这样的分裂被称为一次系统发育分裂。将这些方法应用于人类γ -珠蛋白基因转换的一个有充分记录的案例表明，三个观察到的分区中的两个对应的位点显着聚集，而将这些方法应用于类人猿线粒体DNA序列-其中没有重组预期发生-没有证据表明这种聚集。这表明分裂特异性位点的聚类主要是由于基因内重组或基因转换。讨论了解释观察到的位点聚类的其他假设，如偏选择或突变。
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.