Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
复制标题
DOI：
10.1093/oxfordjournals.molbev.a026334
复制
发表时间：
2000-04-01
影响因子：
10.7
通讯作者：
Castresana, J
中科院分区：
文献类型：
--
作者：
Castresana, J
在系统发育分析中使用一些多序列比对，特别是那些不是很保守的序列比对，需要消除比对不好的位置和分歧区，因为它们可能不是同源的，或者可能已经被多个替换饱和。这里提出了一种计算机化的方法，它消除了这类位置，同时试图将信息站点的损失降至最低。该方法的基础是选择满足一组简单要求的位置块，这些位置块满足关于连续保守位置的数量、没有间隙和侧翼位置高度保守的要求，从而使最终的比对更适合于系统发育分析。为了说明这种方法的有效性，我们以来自不同真核生物线粒体基因组的10个线粒体蛋白质的比对为例。在最具分歧的比对中，移除位置的百分比较高。去除分歧片段后，不同序列的氨基酸组成更加均匀，成对距离变小。系统发育树表明，移除保守的块后，尤其是当有几个解析不佳的节点时，拓扑可能会不同。动物和真菌的分类得到了强有力的支持，但更基本的真核生物的地位却没有得到支持。使用计算机化的方法，如本文提出的方法，在一定程度上减少了手动编辑多个比对的必要性，使大数据集的系统发育分析自动化成为可能，并便于其他研究人员复制最终比对。
The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not he homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.