The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support
The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support
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DOI：
10.1093/oxfordjournals.molbev.a004094
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发表时间：
2002-04-01
影响因子：
10.7
通讯作者：
Cunningham, CW
中科院分区：
文献类型：
--
作者：
Buckley, TR;Cunningham, CW
在分子遗传学中使用参数丰富的替代模型一直受到批评，因为这些模型可能会导致准确性和区分竞争拓扑结构的能力降低。我们已经探讨了核苷酸取代模型的复杂性和非参数自举支持下的最大似然（AIL）的真实关系是已知的具有高度的确定性的六个数据集之间的关系。我们还进行了等权最大简约分析，以评估忽略分支长度信息的影响，树的选择。我们观察到，对于除了一个数据集之外的每个数据集，相对于ML模型，最大简约性给出了正确节点集的Bootstrap支持的最低平均估计。对于几个数据集，我们建立了一个成功的系统发育分析的准确分布模型的网站率的变化是至关重要的。对于几个数据集，位点特异性速率模型的表现相对于伽马和不变位点模型非常差，最有可能是因为严重低估了分支长度。不变的网站模型也表现不佳的几个数据集，该模型有一个穷人的数据拟合。这表明添加伽马分布可能是至关重要的，相对于等速率模型，伽马和不变站点模型下正确节点的自举支持的估计通常会增加。我们的观察结果是相反的预测，这种模式会导致系统发育假说的信心降低。我们的研究结果提出了几个问题，模型选择的过程中，我们简要讨论了模型选择的不确定性和敏感性分析在分子遗传学中的作用。
The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relationship between nucleotide substitution model complexity and nonparametric bootstrap support under maximum likelihood (AIL) for six data sets for which the true relationships are known with a high degree of certainty. We also performed equally weighted maximum parsimony analyses in order to assess the effects of ignoring branch length information during, tree selection. We observed that maximum parsimony gave the lowest mean estimate of bootstrap support for the correct set of nodes relative to the ML models for every data set except one. For several data sets, we established that the exact distribution used to model among-site rate variation was critical for a successful phylogenetic analysis. Site-specific rate models were shown to perform very poorly relative to gamma and invariables sites models for several of the data sets most Likely because of the gross underestimation of branch lengths. The invariable sites model also performed poorly for several data sets where this model had a poor fit to the data. suggesting that addition of the gamma distribution can be critical, Estimates of bootstrap support for the correct nodes often increased under gamma and invariable sites models relative to equal rates models. Our observations are contrary to the prediction that such models cause reduced confidence in phylogenetic hypotheses. Our results raise several issues regarding the process of model selection, and we briefly discuss model selection uncertainty and the role of sensitivity analyses in molecular phylogenetics.