The partition matrix: Exploring variable phylogenetic signals along nucleotide sequence alignments
The partition matrix: Exploring variable phylogenetic signals along nucleotide sequence alignments
复制标题
DOI：
10.1093/oxfordjournals.molbev.a025784
复制
发表时间：
1997-05-01
影响因子：
10.7
通讯作者：
Easteal, S
中科院分区：
文献类型：
--
作者：
Jakobsen, IB;Wilson, SR;Easteal, S
分区矩阵是用于比对后的核苷酸序列的比较分析的图形工具。它对于研究经历网状进化的序列军团的发散性遗传是特别有用的。通过确定一组比对序列中的简约信息位点与从序列推断的二进制分区的一致性来生成分区矩阵。由于保持了位点的线性顺序，因此矩阵可用于评估支持或与特定分区冲突的位点的分布是否沿比对的长度沿着变化。矩阵的有用性，在允许视觉识别区域之间的进化历史的差异取决于分区显示的顺序，提出了几个合适的排序方案。我们演示了使用分区矩阵解释进化的卡他鼻灵长类动物的性染色体上的假常染色体边界区。它的常规使用应有助于避免试图从其进化已被网状化的序列中推导出单一的同源性，并有助于鉴定网状化背后的基因转换或重组事件。该方法相对较快。它是探索性的，它可以形成我们讨论的更正式的分析的基础。
The partition matrix is a graphical tool for comparative analysis of nucleotide sequences following alignment. It is particularly useful for investigating the divergent phylogenies of sequence legions undergoing reticulate evolution. A partition matrix is generated by determining the consistency of the parsimoniously informative sites in a set of aligned sequences with the binary partitions inferred from the sequences. Since the linear order of sites is maintained, the matrix can be used to assess whether the distribution of sites either supporting or conflicting with particular partitions changes along the length of the alignment. The usefulness of the matrix in allowing visual identification of differences in evolutionary history among regions depends on the order in which partitions are shown; several suitable ordering schemes are proposed. We demonstrate the use of the partition matrix in interpreting the evolution of the pseudoautosomal boundary region on the sex chromosome of catarrhine primates. Its routine use should help to avoid attempts to derive single phylogenies from sequences whose evolution has been reticulate and to identify the gene conversion or recombination events underlying the reticulation. The method is relatively fast. It is exploratory, and it can form the basis for more formal analysis, which we discuss.