Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites
Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites
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DOI：
10.1093/molbev/msn098
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发表时间：
2008-07-01
影响因子：
10.7
通讯作者：
Martin, William
中科院分区：
文献类型：
--
作者：
Gruenheit, Nicole;Lockhart, Peter J.;Martin, William
序列的协变（COV）样特性描述甚少，其对系统发育分析的影响也知之甚少。我们通过模拟证明，在非相邻谱系中可变位点比例发生变化的进化模型下，跨位点速率 (RAS) 和 COV 模型的对数似然值变得相似，使得模型难以区分。此外，尽管 COV 和 RAS 模型比使用这些模拟数据的同质模型提供了极大的似然评分改进，但树构建的重建精度较低，这表明当怀疑不同进化谱系中可变位点的比例不同时要谨慎。我们研究了最近开发的应急测试的性能，该测试可检测针对蛋白质数据修改的 COV 型进化的存在。我们报告说，如果可变位点的比例（p（var））以谱系特定的方式变化，使得它们在不同谱系中的分布变得足够不重叠，那么列联检验可能会错误地建议同质模型。同样令人担忧的是，所研究的群体之间可变位点的比例可能不同。在叶绿体蛋白质的研究中，发现测试的解释容易受到分类群的不同划分的影响，使得测试在实施中非常主观。差异程度和可变位点比例差异的极端组间差异可能导致了这种效应。
The covarion (COV)-like properties of sequences are poorly described and their impact on phylogenetic analyses poorly understood. We demonstrate using simulations that, under an evolutionary model where the proportion of variable sites changes in nonadjacent lineages, log likelihood values for rates across site (RAS) and COV models become similar, making models difficult to distinguish. Further, although COV and RAS models provide a great improvement in likelihood scores over a homogeneous model with these simulated data, reconstruction accuracy of tree building is low, suggesting caution when it is suspected that proportions of variable sites differ in different evolutionary lineages. We study the performance of a recently developed contingency test that detects the presence of COV-type evolution modified for protein data. We report that if proportions of variable sites (p(var)) change in a lineage-specific manner such that their distributions in different lineages become sufficiently nonoverlapping, then the contingency test can incorrectly suggest a homogeneous model. Also of concern is the possibility of different proportions of variable sites between the groups being studied. In a study of chloroplast proteins, interpretation of the test is found to be susceptible to different partitioning of taxon groups, making the test very subjective in its implementation. Extreme intergroup differences in the extent of divergence and difference in proportions of variable sites could be contributing to this effect.