School of Natural Sciences & Psychology, Liverpool John Moores University, Liverpool L3 3AF, UK.
BMC Evol Biol. 2011 Sep 26;11:271. doi: 10.1186/1471-2148-11-271.
Understanding causes of biological diversity may be greatly enhanced by knowledge of divergence times. Strict and relaxed clock models are used in Bayesian estimation of divergence times. We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times. Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation. Published shallow phylogenies (Black bass, Primate-sucking lice, Podarcis lizards, Gallotiinae lizards, and Caprinae mammals) were also analysed to determine natural levels of rate variation relative to the performance of the different models.
Strict clock analyses performed well on data simulated under the independent rates model when the standard deviation of log rate on branches, σ, was low (≤ 0.1), but were inappropriate when σ>0.1 (95% of rates fall within 0.0082-0.0121 subs/site/Ma when σ = 0.1, for a mean rate of 0.01). The independent rates relaxed clock model performed well at all levels of rate variation, although posterior intervals on times were significantly wider than for the strict clock. The strict clock is therefore superior when rate variation is low. The performance of a correlated rates relaxed clock model was similar to the strict clock. Increased numbers of independent loci led to slightly narrower posteriors under the relaxed clock while older root ages provided proportionately narrower posteriors. The LRT had low power for σ = 0.01-0.1, but high power for σ = 0.5-2.0. Posterior means of σ2 were useful for assessing rate variation in published datasets. Estimates of natural levels of rate variation ranged from 0.05-3.38 for different partitions. Differences in divergence times between relaxed and strict clock analyses were greater in two datasets with higher σ2 for one or more partitions, supporting the simulation results.
The strict clock can be superior for trees with shallow roots because of low levels of rate variation between branches. The LRT allows robust assessment of suitability of the clock model as does examination of posteriors on σ2.
了解生物多样性的原因可以通过对分歧时间的了解得到极大的提高。贝叶斯估计分歧时间时使用严格时钟模型和宽松时钟模型。我们研究了以下问题：i）严格时钟模型是否普遍适用于分支之间的速率变化预计较低的浅层系统发育；ii）钟的似然比检验（LRT）是否可靠地告知哪种模型适用于约会分歧时间。使用严格和宽松的模型分析了在不同速率变化水平下模拟的序列。还分析了已发表的浅层系统发育（黑鲈，灵长类虱子，Podarcis 蜥蜴，Gallotiinae 蜥蜴和 Caprinae 哺乳动物），以确定相对于不同模型的性能，自然速率变化水平。
当分支上的对数速率的标准偏差（σ）较低（≤0.1）时，严格时钟分析在独立速率模型下模拟的数据表现良好，但当 σ>0.1 时则不合适（当 σ = 0.1 时，95％的速率落在 0.0082-0.0121 个分支/位点/ Ma 内，平均速率为 0.01）。独立速率宽松时钟模型在所有速率变化水平下均表现良好，尽管严格时钟的后验间隔明显更宽。因此，当速率变化较小时，严格时钟更优越。相关速率宽松时钟模型的性能与严格时钟相似。随着独立基因座数量的增加，在宽松时钟下，后验间隔略有变窄，而较旧的根年龄则提供了相应较窄的后验间隔。对于 σ = 0.01-0.1，LRT 的功效较低，但对于 σ = 0.5-2.0，功效较高。在已发表的数据集评估中，σ2的后验均值可用于评估速率变化。不同分区的速率变化范围从 0.05-3.38 不等。对于一个或多个分区的 σ2较高的两个数据集，宽松和严格时钟分析之间的分歧时间差异更大，这支持了模拟结果。
由于分支之间的速率变化较低，严格时钟可以在根部较浅的树中表现更好。LRT 允许对时钟模型的适用性进行稳健评估，对 σ2的后验分析也是如此。
