Best-fit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies
Best-fit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies
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DOI：
10.1111/j.1558-5646.1998.tb01827.x
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发表时间：
1998-08-01
期刊：
影响因子：
3.3
通讯作者：
Hillis, DM
中科院分区：
文献类型：
--
作者：
Cunningham, CW;Zhu, H;Hillis, DM
尽管越来越复杂的DNA序列进化模型不断涌现，但在模型之间的选择仍然是系统发育重建中的一个主要问题。当树枝长度之间存在较大差异时，选择合适的模型被认为特别重要。当我们改变末端分支长度时，我们评估了嵌套模型重建实验生成的已知噬菌体T7系统发育的能力。然后，对于每个系统发展史，我们通过逐步向更简单的模型添加参数来确定最适合的模型。我们发现，在某些情况下，最佳拟合模型的选择受到参数添加顺序的影响。在系统发育方面，当短枝与长枝的比例为1：3或更小时，不同模式间的系统发育差异不大。然而，在极端末端枝长变异的条件下，模型之间不仅存在显著差异，而且最好的模型在克服长枝吸引方面总是最好的模型之一。即使使用最大似然方法来生成距离矩阵，最小进化距离方法的性能通常也低于离散最大似然方法。对立地间速率差异的校正对于克服长枝吸引尤为重要。我们结论的普遍性得到了早期模拟研究的支持，也得到了对得到良好支持的四分类羊膜动物系统发育的线粒体和核序列的初步分析的支持。
Despite the proliferation of increasingly sophisticated models of DNA sequence evolution, choosing among models remains a major problem in phylogenetic reconstruction. The choice of appropriate models is thought to be especially important when there is large variation among branch lengths. We evaluated the ability of nested models to reconstruct experimentally generated, known phylogenies of bacteriophage T7 as we varied the terminal branch lengths. Then, for each phylogeny we determined the best-fit model by progressively adding parameters to simpler models. We found that in several cases the choice of best-fit model was affected by the parameter addition sequence. In terms of phylogenetic performance, there was little difference between models when the ratio of short:long terminal branches was 1:3 or less. However, under conditions of extreme terminal branch-length variation, there were not only dramatic differences among models, but best-fit models were always among the best at overcoming long-branch attraction. The performance of minimum-evolution-distance methods was generally lower than that of discrete maximum-likelihood methods, even if maximum-likelihood methods were used to generate distance matrices. Correcting for among-site rate variation was especially important for overcoming long-branch attraction. The generality of our conclusions is supported by earlier simulation studies and by a preliminary analysis of mitochondrial and nuclear sequences from a well-supported four-taxon amniote phylogeny.