Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection
Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection
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DOI：
10.1098/rstb.2004.1523
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发表时间：
2004-10-29
影响因子：
6.3
通讯作者：
Sanderson, MJ
中科院分区：
文献类型：
--
作者：
Near, TJ;Sanderson, MJ
利用DNA序列数据估计物种分化时间在进化论、生态学和生物地理学研究中发挥着越来越重要的作用。大多数工作都集中在获得适当种类的数据和开发最佳估计程序上，而较少关注利用化石对分歧进行校准。具有多个化石校准点的案例研究为以新的方式检查发散时间估计问题提供了重要的机会。我们讨论了两个交叉验证程序，它们解决了分歧时间估计中推理的不同方面。“交叉验证”是一种用于确定不同个体校准对总体估计的影响的程序。这可以识别具有异常大的误差效应的化石，并可能需要进一步的检查。“基于Fossil的模型交叉验证”是一个完全不同的过程，它使用化石在速率平滑或其他推理方法的背景下识别分子进化的最佳模型。这两个程序都应用于最近的两项研究：一项是对单子叶被子植物的分析，有八个化石校准；另一项是对胎盘哺乳动物的分析，有九个化石校准。在每一种情况下，化石校准的影响都可以从大到小排序，在两项研究中的一项中，化石提供了关于最佳分子进化模式的决定性证据。
Estimates of species divergence times using DNA sequence data are playing an increasingly important role in studies of evolution, ecology and biogeography. Most work has centred on obtaining appropriate kinds of data and developing optimal estimation procedures, whereas somewhat less attention has focused on the calibration of divergences using fossils. Case studies with multiple fossil calibration points provide important opportunities to examine the divergence time estimation problem in new ways. We discuss two cross-validation procedures that address different aspects of inference in divergence time estimation. 'Fossil cross-validation' is a procedure used to identify the impact of different individual calibrations on overall estimation. This can identify fossils that have an exceptionally large error effect and may warrant further scrutiny. 'Fossil-based model cross-validation' is an entirely different procedure that uses fossils to identify the optimal model of molecular evolution in the context of rate smoothing or other inference methods. Both procedures were applied to two recent studies: an analysis of monocot angiosperms with eight fossil calibrations and an analysis of placental mammals with nine fossil calibrations. In each case, fossil calibrations could be ranked from most to least influential, and in one of the two studies, the fossils provided decisive evidence about the optimal molecular evolutionary model.