The number of nuclear small subunit (SSU) ribosomal RNA (rRNA) sequences for Nematoda has increased dramatically in recent years, and although their use in constructing phylogenies has also increased, relatively little attention has been given to their alignment. Here we examined the sensitivity of the nematode SSU data set to different alignment parameters and to the removal of alignment ambiguous regions. Ten alignments were created with CLUSTAL W using different sets of alignment parameters (10 full alignments), and each alignment was examined by eye and alignment ambiguous regions were removed (creating 10 reduced alignments). These alignment ambiguous regions were analyzed as a third type of data set, culled alignments. Maximum parsimony, neighbor-joining, and parsimony bootstrap analyses were performed. The resulting phylogenies were compared to each other by the symmetric difference distance tree comparison metric (SymD). The correlation of the phylogenies with the alignment parameters was tested by comparing matrices from SymD with corresponding matrices of Manhattan distances representing the alignment parameters. Differences among individual parsimony trees from the full alignments were frequently correlated with the differences among alignment parameters (580/1000 tests), as were trees from the culled alignments (403/1000 tests). Differences among individual parsimony trees from the reduced alignments were less frequently correlated with the differences among alignment parameters (230/1000 tests). Differences among majority-rule consensus trees (50%) from the parsimony analysis of the full alignments were significantly correlated with the differences among alignment parameters, whereas consensus trees from the reduced and culled analyses were not correlated with the alignment parameters. These patterns of correlation confirm that choice of alignment parameters has the potential to bias the resultant phylogenies for the nematode SSU data set, and suggest that the removal of alignment ambiguous regions reduces this effect. Finally, we discuss the implications of conservative phylogenetic hypotheses for Nematoda produced by exploring alignment space and removing alignment ambiguous regions for SSU rDNA.

中文翻译：

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线虫小亚基系统发育与比对参数相关

近年来，线虫的核小亚基 (SSU) 核糖体 RNA (rRNA) 序列的数量急剧增加，尽管它们在构建系统发育中的使用也有所增加，但对它们的比对关注相对较少。在这里，我们检查了线虫 SSU 数据集对不同对齐参数和去除对齐模糊区域的敏感性。使用 CLUSTAL W 使用不同的对齐参数集（10 个完整对齐）创建 10 个对齐，并通过眼睛检查每个对齐并​​删除对齐模糊区域（创建 10 个减少的对齐）。这些比对模糊区域被分析为第三种类型的数据集，剔除比对。进行了最大简约、相邻连接和简约自举分析。通过对称差异距离树比较度量（SymD）将产生的系统发育相互进行比较。通过将来自 SymD 的矩阵与代表比对参数的曼哈顿距离的相应矩阵进行比较，来测试系统发育与比对参数的相关性。来自完整对齐的单个简约树之间的差异经常与对齐参数之间的差异（580/1000 测试）相关，来自剔除对齐的树（403/1000 测试）也是如此。来自简化对齐的单个简约树之间的差异与对齐参数之间的差异（230/1000 测试）之间的相关性较低。来自完整比对的简约分析的多数规则共识树 (50%) 之间的差异与比对参数之间的差异显着相关，而来自减少和剔除分析的共识树与比对参数无关。这些相关性模式证实，比对参数的选择有可能使线虫 SSU 数据集的系统发育产生偏差，并表明去除比对模糊区域会减少这种影响。最后，我们讨论了通过探索比对空间和去除 SSU rDNA 的比对模糊区域而产生的线虫保守系统发育假设的影响。而来自减少和剔除分析的共识树与对齐参数无关。这些相关性模式证实，比对参数的选择有可能使线虫 SSU 数据集的系统发育产生偏差，并表明去除比对模糊区域会减少这种影响。最后，我们讨论了通过探索比对空间和去除 SSU rDNA 的比对模糊区域而产生的线虫保守系统发育假设的影响。而来自减少和剔除分析的共识树与对齐参数无关。这些相关性模式证实，比对参数的选择有可能使线虫 SSU 数据集的系统发育产生偏差，并表明去除比对模糊区域会减少这种影响。最后，我们讨论了通过探索比对空间和去除 SSU rDNA 的比对模糊区域而产生的线虫保守系统发育假设的影响。