Simmons Mark P, Müller Kai F, Webb Colleen T
Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
Nees-Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, Bonn, D-53115, Germany.
Cladistics. 2008 Dec;24(6):1039-1050. doi: 10.1111/j.1096-0031.2008.00230.x. Epub 2008 Aug 27.
Sensitivity analysis provides a way to measure robustness of clades in sequence-based phylogenetic analyses to variation in alignment parameters rather than measuring their branch support. We compared three different approaches to multiple sequence alignment in the context of sensitivity analysis: progressive pairwise alignment, as implemented in MUSCLE; simultaneous multiple alignment of sequence fragments, as implemented in DCA; and direct optimization followed by generation of the implied alignment(s), as implemented in POY. We set out to determine the relative sensitivity of these three alignment methods using rDNA sequences and randomly generated sequences. A total of 36 parameter sets were used to create the alignments, varying the transition, transversion, and gap costs. Tree searches were performed using four different character-coding and weighting approaches: the cost function used for alignment or equally weighted parsimony with gap positions treated as missing data, separate characters, or as fifth states. POY was found to be as sensitive, or more sensitive, to variation in alignment parameters than DCA and MUSCLE for the three empirical datasets, and POY was found to be more sensitive than MUSCLE, which in turn was found to be as sensitive, or more sensitive, than DCA when applied to the randomly generated sequences when sensitivity was measured using the averaged jackknife values. When significant differences in relative sensitivity were found between the different ways of weighting character-state changes, equally weighted parsimony, for all three ways of treating gapped positions, was less sensitive than applying the same cost function used in alignment for phylogenetic analysis. When branch support is incorporated into the sensitivity criterion, our results favour the use of simultaneous alignment and progressive pairwise alignment using the similarity criterion over direct optimization followed by using the implied alignment(s) to calculate branch support.
敏感性分析提供了一种方法，用于在基于序列的系统发育分析中衡量进化枝对比对参数变化的稳健性，而非衡量它们的分支支持度。在敏感性分析的背景下，我们比较了三种不同的多序列比对方法：如MUSCLE中实现的渐进成对比对；如DCA中实现的序列片段同时多比对；以及如POY中实现的直接优化，随后生成隐含比对。我们着手使用rDNA序列和随机生成的序列来确定这三种比对方法的相对敏感性。总共使用了36个参数集来创建比对，改变转换、颠换和空位成本。使用四种不同的字符编码和加权方法进行树搜索：用于比对的成本函数或同等加权简约法，将空位位置视为缺失数据、单独字符或第五种状态。对于三个经验数据集，发现POY比对参数变化的敏感性与DCA和MUSCLE相同，或比它们更敏感；当使用平均刀切值测量敏感性时，发现POY比对随机生成的序列比MUSCLE更敏感，而MUSCLE比对DCA更敏感，或与DCA一样敏感。当在加权字符状态变化的不同方式之间发现相对敏感性存在显著差异时，对于所有三种处理空位位置的方式，同等加权简约法比对系统发育分析中用于比对的相同成本函数的敏感性更低。当将分支支持纳入敏感性标准时，我们的结果支持使用基于相似性标准的同时比对和渐进成对比对，而不是先进行直接优化，然后使用隐含比对来计算分支支持。
