Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
Syst Biol. 2010 Jan;59(1):1-8. doi: 10.1093/sysbio/syp072. Epub 2009 Oct 13.
Because a constant rate of DNA sequence evolution cannot be assumed to be ubiquitous, relaxed molecular clock inference models have proven useful when estimating rates and divergence dates. Furthermore, it has been recently suggested that using relaxed molecular clocks may provide superior accuracy and precision in phylogenetic inference compared with traditional time-free methods that do not incorporate a molecular clock. We perform a simulation study to determine if assuming a relaxed molecular clock does indeed improve the quality of phylogenetic inference. We analyze sequence data simulated under various rate distributions using relaxed-clocks, strict-clocks, and time-free Bayesian phylogenetic inference models. Our results indicate that no difference exists in the quality of phylogenetic inference between assuming a relaxed molecular clock and making no assumption about the clock-likeness of sequence evolution. This pattern is likely due to the bias-variance trade-off inherent in this type of phylogenetic inference. We also compared the quality of inference between Bayesian and maximum likelihood time-free inference models and found them to be qualitatively similar.
由于不能假定 DNA 序列进化的恒定速率无处不在，因此在估计速率和分歧日期时，放松的分子钟推断模型已被证明非常有用。此外，最近有人提出，与不包含分子钟的传统无时间方法相比，使用放松的分子钟可能会提供更准确和精确的系统发育推断。我们进行了一项模拟研究，以确定假设放松分子钟是否确实可以提高系统发育推断的质量。我们使用放松时钟、严格时钟和无时间贝叶斯系统发育推断模型分析了在各种速率分布下模拟的序列数据。我们的结果表明，在假设放松分子钟和不假设序列进化的时钟相似性之间，系统发育推断的质量没有差异。这种模式可能是由于这种系统发育推断中固有的偏差-方差权衡。我们还比较了贝叶斯和最大似然无时间推断模型之间的推断质量，发现它们在性质上相似。
