Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
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DOI：
10.1093/molbev/msi125
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发表时间：
2005-05-01
影响因子：
10.7
通讯作者：
Cooper, A
中科院分区：
文献类型：
--
作者：
Ho, SYW;Phillips, MJ;Cooper, A
近年来，已经开发了许多系统发育方法，用于在模型下估计分子速率和分歧日期，这些模型通过允许整个树的速率变化来放松分子钟约束。这些方法的使用频率越来越高，但对其准确性的研究却很少。我们使用九分类单元树上模拟的核苷酸序列测试了几种宽松时钟方法（惩罚似然和使用各种速率变化模型的贝叶斯推理）的准确性。当序列以恒定速率进化时，这些方法能够准确地推断速率，但当假设分子钟时，估计会更加精确。当序列在自相关速率变化模型下演化时，使用惩罚似然以及使用速率变化的对数正态和指数模型的贝叶斯推理可以准确地估计速率，而其他模型的表现则不佳。当序列在不相关的速率变化模型下演化时，只有使用指数速率模型的贝叶斯推理表现良好。总的来说，如果需要保守的发散时间估计方法，结果强烈建议使用速率变化的指数模型。提出了一个案例研究，其中我们使用基于模拟的方法来检验寒武纪时期速率升高的假设，发现这些高速率估计可能是速率估计方法的人为因素。如果存在这种偏差，那么后生动物分歧的年龄就会被系统性地低估。这项研究的结果对分子速率和分歧日期的研究具有重要意义。
In recent years, a number of phylogenetic methods have been developed for estimating molecular rates and divergence dates under models that relax the molecular clock constraint by allowing rate change throughout the tree. These methods are being used with increasing frequency, but there have been few studies into their accuracy. We tested the accuracy of several relaxed-clock methods (penalized likelihood and Bayesian inference using various models of rate change) using nucleotide sequences simulated on a nine-taxon tree. When the sequences evolved with a constant rate, the methods were able to infer rates accurately, but estimates were more precise when a molecular clock was assumed. When the sequences evolved under a model of autocorrelated rate change, rates were accurately estimated using penalized likelihood and by Bayesian inference using lognormal and exponential models of rate change, while other models did not perform as well. When the sequences evolved under a model of uncorrelated rate change, only Bayesian inference using an exponential rate model performed well. Collectively, the results provide a strong recommendation for using the exponential model of rate change if a conservative approach to divergence time estimation is required. A case study is presented in which we use a simulation-based approach to examine the hypothesis of elevated rates in the Cambrian period, and it is found that these high rate estimates might be an artifact of the rate estimation method. If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates.