Sharma Prashant P, Vahtera Varpu, Kawauchi Gisele Y, Giribet Gonzalo
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
Cladistics. 2011 Oct;27(5):538-549. doi: 10.1111/j.1096-0031.2010.00345.x. Epub 2010 Dec 15.
The robustness of clades to parameter variation may be a desirable quality or even a goal in phylogenetic analyses. Sensitivity analyses used to assess clade stability have invoked the incongruence length difference (ILD or ILD) metric, a measure of congruence among datasets, to compare a series of most-parsimonious results from re-running analyses under different analytical conditions. It is also common practice to select a single "optimal" parameter set that minimizes ILD across all parameter sets. However, the divergent molecular evolution of ribosomal genes and protein-encoding genes-specifically the bias against transversion events in coding genes of conserved function-suggests that deployment of multiple parameter sets could outperform the use of a single parameter set applied to all molecules. We explored congruence in five published datasets by including mixed parameter sets in our sensitivity analysis. In four cases, mixed parameter sets outperformed the previously reported, single optimal parameter set. Conversely, multiple parameter sets did not outperform a single optimal parameter set in a case in which actual strong topological conflict exists between data partitions. Exploration of mixed parameter sets may prove useful when combining ribosomal and protein-encoding genes, due to the relatively higher frequency of single- and double-base pair indel events in the former, and the relatively lower frequency of transversions in the latter. © The Willi Hennig Society 2010.
进化枝对参数变化的稳健性在系统发育分析中可能是一种理想的特性甚至是一个目标。用于评估进化枝稳定性的敏感性分析采用了不一致长度差异（ILD）指标，这是一种数据集间一致性的度量，用于比较在不同分析条件下重新运行分析得到的一系列最简约结果。选择一个能使所有参数集中的ILD最小化的单一“最优”参数集也是常见做法。然而，核糖体基因和蛋白质编码基因的分子进化存在差异——特别是在具有保守功能的编码基因中对颠换事件存在偏向性——这表明使用多个参数集可能比将单个参数集应用于所有分子的效果更好。我们在敏感性分析中纳入混合参数集，探究了五个已发表数据集中的一致性。在四个案例中，混合参数集的表现优于先前报道的单一最优参数集。相反，在数据分区之间实际存在强烈拓扑冲突的一个案例中，多个参数集的表现不如单一最优参数集。由于核糖体基因中单碱基对和双碱基对插入缺失事件的频率相对较高，而蛋白质编码基因中颠换的频率相对较低，因此在合并核糖体基因和蛋白质编码基因时，探究混合参数集可能会被证明是有用的。© 威利·亨尼希协会 2010 年。
