Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively, fossil calibrations can be used a posteriori, to transform previously estimated relative divergence times that were inferred without considering fossil information, into absolute divergence times. However, as branch length is the product of the rate of evolution and the duration in time of the considered branch, the extent to which a posteriori-calibrated, relative divergence time methods can disambiguate time and rate, is unclear. Here, we use forward evolutionary simulations and compare a priori and a posteriori calibration strategies using different molecular clock methods and models. Specifically, we compare three Bayesian methods, the strict clock, uncorrelated clock and autocorrelated clock, and the non-Bayesian algorithm implemented in RelTime. We simulate phylogenies with multiple, independent substitution rate changes and show that correct timescales cannot be inferred without the use of calibrations. Under our simulation conditions, a posteriori calibration strategies almost invariably inferred incorrect rate changes and divergence times. The a priori integration of fossil calibrations is fundamental in these cases to improve the accuracy of the estimated divergence times. Relative divergence times and absolute timescales derived by calibrating relative timescales to geological time a posteriori, appear to be less reliable than a priori calibrated, timescales.

中文翻译：

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先验和后验校准策略在发散时间估计中的表现。

宽松的分子钟方法允许使用基因组数据来估计整个生命树的分歧时间。这在贝叶斯分析中最常见，其中分子钟通过化石信息的整合进行先验校准。或者，可以事后使用化石校准，将先前估计的相对发散时间（在不考虑化石信息的情况下推断出）转换为绝对发散时间。然而，由于分支长度是进化速率和所考虑分支的持续时间的乘积，因此后验校准的相对分歧时间方法可以在多大程度上消除时间和速率的歧义尚不清楚。在这里，我们使用前向进化模拟，并使用不同的分子钟方法和模型比较先验和后验校准策略。具体来说，我们比较了三种贝叶斯方法：严格时钟、不相关时钟和自相关时钟，以及 RelTime 中实现的非贝叶斯算法。我们模拟了具有多个独立替代率变化的系统发育，并表明如果不使用校准就无法推断出正确的时间尺度。在我们的模拟条件下，后验校准策略几乎总是推断出不正确的速率变化和发散时间。在这些情况下，化石校准的先验整合对于提高估计分歧时间的准确性至关重要。通过将相对时间尺度事后校准到地质时间而得出的相对分歧时间和绝对时间尺度似乎不如先验校准的时间尺度可靠。