Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating.
Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating.
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DOI：
10.1016/j.ympev.2017.07.005
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发表时间：
2017-09
影响因子：
4.1
通讯作者：
Yang Z
中科院分区：
文献类型：
--
作者：
Barba-Montoya J;Dos Reis M;Yang Z
化石校准是分子时钟日期中最大的信息来源。
校准的质量对差异时间估计有重大影响。
通常，截断对校准有很大的影响。
产生有效先验的不同策略也产生了相当大的影响。
重要的是，在任何贝叶斯约会分析之前，都要检查约会计划之前使用的联合时间。
化石校准是将分子序列之间的距离分解为分子时钟年代分析中绝对时间和绝对速率的距离的最大信息来源。因此，即使有大量的分子数据可用，校准的质量也有望对差异时间估计产生重大影响。在贝叶斯分子时钟的日期中，化石校准信息通过先前的发散时间（先前的时间）纳入了分析中。在这里，我们评估了三种策略，用于将化石校准（以最小和最大年龄范围的形式）转换为先前的时间，这取决于它们是否从祖先节点的最大年龄借用信息以及下降节点的最小年龄以形成任何给定节点的临时节点的最低年龄。我们研究了一个简单的示例，可以在分析上进行处理，并使用三个贝叶斯约会程序分析了两个真实的数据集（一个灵长类动物物种之一，另一种48种种子植物物种）：McMctree，Mrbayes和Beast2。我们研究了不同的校准策略，出生死亡过程和自动截断是如何相互作用以确定先前时间的祖先节点年龄比后代节点更古老的约束。通常，截断对校准具有很大的影响，因此截断后校准节点年龄上的有效先验可能与用户指定的校准密度大不相同。产生有效先验的不同策略也产生了相当大的影响，导致边缘有效的先验截然不同。发现用于实施最小结合校准的任意参数对差异时间的先前和后部有很大的影响。我们的结果强调了在任何贝叶斯约会分析之前使用约会计划之前使用的联合时间的重要性。
Fossil calibrations are the utmost source of information in molecular clock dating. The quality of calibrations has a major impact on divergence time estimates. In general, truncation has a great impact on calibrations. The different strategies for generating the effective prior also had considerable impact. It is important to inspect the joint time prior used by the dating program before any Bayesian dating analysis. Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of calibrations is thus expected to have a major impact on divergence time estimates even if a huge amount of molecular data is available. In Bayesian molecular clock dating, fossil calibration information is incorporated in the analysis through the prior on divergence times (the time prior). Here, we evaluate three strategies for converting fossil calibrations (in the form of minimum- and maximum-age bounds) into the prior on times, which differ according to whether they borrow information from the maximum age of ancestral nodes and minimum age of descendent nodes to form constraints for any given node on the phylogeny. We study a simple example that is analytically tractable, and analyze two real datasets (one of 10 primate species and another of 48 seed plant species) using three Bayesian dating programs: MCMCTree, MrBayes and BEAST2. We examine how different calibration strategies, the birth-death process, and automatic truncation (to enforce the constraint that ancestral nodes are older than descendent nodes) interact to determine the time prior. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. Our results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis.
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影响因子：
6.5
作者：
Ronquist F;Klopfstein S;Vilhelmsen L;Schulmeister S;Murray DL;Rasnitsyn AP
通讯作者：
Rasnitsyn AP
影响因子：
9.4
作者：
Clarke, John T.;Warnock, Rachel C. M.;Donoghue, Philip C. J.
通讯作者：
Donoghue, Philip C. J.
影响因子：
2.9
作者：
Marshall, Charles R.
通讯作者：
Marshall, Charles R.
影响因子：
6.5
作者：
Bracken-Grissom, Heather D.;Ahyong, Shane T.;Crandall, Keith A.
通讯作者：
Crandall, Keith A.
影响因子：
10.7
作者：
Lepage, Thomas;Bryant, David;Lartillot, Nicolas
通讯作者：
Lartillot, Nicolas