The likelihood node density effect and consequences for evolutionary studies of molecular rates
The likelihood node density effect and consequences for evolutionary studies of molecular rates
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DOI：
10.1111/j.1558-5646.2007.00188.x
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发表时间：
2007-10-01
期刊：
影响因子：
3.3
通讯作者：
Lee, Michael S. Y.
中科院分区：
文献类型：
--
作者：
Hugall, Andrew F.;Lee, Michael S. Y.
在物种丰富的群体中，许多分子进化表现出较长的根到顶端的路径长度，这鼓励了将分支发生与加速的分子进化联系起来的假设。然而，这种模式也可能是由一种称为节点密度效应（NDE）的人为因素造成的：当用于重建树的方法低估了额外节点所揭示的多个命中时，就会发生这种效应，从而导致具有更多终端分类群的分支中的根到顶端路径长度更长。在这里，我们使用一个双重的方法来证明，最大似然和贝叶斯方法也遭受NDE已知影响简约。首先，故意使模拟和重建模型不匹配的模拟表明，模型差异越大，实际树长度和重建树长度之间的差距越大，NDE越大。其次，分类单元抽样操作与经验数据表明，NDE仍然可以存在时，使用优化的模型：在12个数据集，70出109姐妹路径比较显示显着的证据NDE。除非模型相当精确地重建真实的树长度，并且考虑到真实的序列进化的复杂性，这可能是不常见的，否则它将始终产生节点密度伪影。在通常遇到的发散水平，10%的树木长度低估的结果在>= 80%的模拟的非破坏性显示出积极的NDE。贝叶斯树有一个轻微的，但一贯更强的效果。这种普遍存在的方法的人工制品增加了明显的速率异质性，并可以妥协的影响分子进化率的因素，使用路径长度在拓扑不对称树的调查。
Many molecular phylogenies show longer root-to-tip path lengths in species-rich groups, encouraging hypotheses linking cladogenesis with accelerated molecular evolution. However, the pattern can also be caused by an artifact called the node density effect (NDE): this effect occurs when the method used to reconstruct a tree underestimates multiple hits that would have been revealed by extra nodes, leading to longer root-to-tip path lengths in clades with more terminal taxa. Here we use a twofold approach to demonstrate that maximum likelihood and Bayesian methods also suffer from the NDE known to affect parsimony. First, simulations deliberately mismatching the simulation and reconstruction models show that the greater the model disparity, the greater the gap between actual and reconstructed tree lengths, and the greater the NDE. Second, taxon sampling manipulation with empirical data shows that NDE can still be present when using optimized models: across 12 datasets, 70 out of 109 sister path comparisons showed significant evidence of NDE. Unless the model fairly accurately reconstructs the real tree length-and given the complexity of real sequence evolution this may be uncommon-it will consistently produce a node density artifact. At commonly encountered divergence levels, a 10% underestimation of tree length results in >= 80% of simulated phylogenies showing a positive NDE. Bayesian trees have a slight but consistently stronger effect. This pervasive methodological artifact increases apparent rate heterogeneity, and can compromise investigations of factors influencing molecular evolutionary rate that use path lengths in topologically asymmetric trees.