Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case.
Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case.
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DOI：
10.1093/sysbio/syy001
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发表时间：
2018-07-01
影响因子：
6.5
通讯作者：
Yoder AD
中科院分区：
文献类型：
--
作者：
Reis MD;Gunnell GF;Barba-Montoya J;Wilkins A;Yang Z;Yoder AD
灵长类动物长期以来一直是一个测试的情况下发展的系统发育方法的分歧时间估计。尽管有大量的研究，但是，冠灵长类动物相对于古近纪（K-Pg）边界的起源时间和主要冠群的多样化时间仍然存在争议。在这里，我们分析了372个分类群（367个灵长类和5个外群，340万个对齐碱基对）的数据集，其中包括9个灵长类基因组。我们系统地探讨了化石校准和分子钟模型的不同解释对灵长类动物分歧时间估计的影响。我们发现，即使是很小的差异，在建设化石校准可以有一个显着的影响，估计发散时间，特别是最古老的节点在树中。值得注意的是，分子速率模型（自相关或独立分布速率）的选择对估计的时间有特别强的影响，独立速率模型产生了更古老的年龄估计，为更深的节点在演化史。我们实现热力学积分，结合高斯积分，在程序MCMCMCTree中，并使用它来计算时钟模型的贝叶斯因子。贝叶斯模型的选择表明，自相关率模型更好地拟合灵长类动物的数据，我们的结论是，在此模型下的时间估计应该是首选。我们发现，对于八个核心节点的演化史，时间估计的不确定性接近化石不确定性所施加的理论极限。因此，这些估计不太可能通过收集额外的分子序列数据来改善。所有的分析都把灵长类的起源放在K-Pg界线附近，要么在白垩纪，要么跨越界线进入古近纪。
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous–Paleogene (K–Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K–Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.
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DOI：
10.1016/0031-0182(94)00104-g
发表时间：
1995-05-01
影响因子：
3
作者：
BADGLEY, C;BEHRENSMEYER, AK
通讯作者：
BEHRENSMEYER, AK
影响因子：
64.8
作者：
Bloch, Jonathan I.;Woodruff, Emily D.;MacFadden, Bruce J.
通讯作者：
MacFadden, Bruce J.
影响因子：
2.8
作者：
BENEFIT, BR;PICKFORD, M
通讯作者：
PICKFORD, M
影响因子：
1.4
作者：
Buckley, GA
通讯作者：
Buckley, GA
影响因子：
10.7
作者：
Burgess, Ralph;Yang, Ziheng
通讯作者：
Yang, Ziheng