Evolutionary models of phylogenetic trees
Evolutionary models of phylogenetic trees
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DOI：
10.1098/rspb.2003.2374
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发表时间：
2003-07-07
影响因子：
4.7
通讯作者：
Pinelis, I
中科院分区：
文献类型：
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作者：
Pinelis, I
最广泛使用的进化树模型是等速率马尔可夫(ERM)模型。一个问题是，ERM模型预测的树木失衡程度低于从实际数据推断的树木的观测结果；事实上，观测到的失衡往往落在ERM模型预测的值和比例可区分排列(PDA)模型预测的值之间。在这里，提出了一个连续多速率(MR)演化模型族，它包含与PDA和ERM模型相对应的整个子族。此外，这一MR系列涵盖了从“完全平衡”到“完全不平衡”的各种型号。特别是，MR家族包含了其他已知的进化模式。MR家族非常多才多艺，几乎没有关于进化特征的假设；但它非常容易受到严格分析的影响。特别是，这种分析有助于揭示适应性、准稳定和长期停滞是造成失衡的主要可能原因。然而，MR模型在功能上很简单，只需要三个参数就可以再现观察到的不平衡。
The most widely used evolutionary model for phylogenetic trees is the equal-rates Markov (ERM) model. A problem is that the ERM model predicts less imbalance than observed for trees inferred from real data; in fact, the observed imbalance tends to fall between the values predicted by the ERM model and those predicted by the proportional-to-distinguishable-arrangements (PDA) model. Here, a continuous multirate (MR) family of evolutionary models is presented which contains entire subfamilies corresponding to both the PDA and ERM models. Furthermore, this MR family covers an entire range from 'completely balanced' to 'completely unbalanced' models. In particular, the MR family contains other known evolutionary models. The MR family is very versatile and virtually free of assumptions on the character of evolution; yet it is highly susceptible to rigorous analyses. In particular, such analyses help to uncover adaptability, quasi-stabilization and prolonged stasis as major possible causes of the imbalance. However, the MR model is functionally simple and requires only three parameters to reproduce the observed imbalance.