Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference
Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference
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DOI：
10.3389/fevo.2020.00183
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发表时间：
2020-06-26
影响因子：
3
通讯作者：
Warnock, Rachel C. M.
中科院分区：
文献类型：
--
作者：
Barido-Sottani, Joelle;van Tiel, Nina M. A.;Warnock, Rachel C. M.
由于岩石和化石记录的不完整性，时间校准树对许多灭绝的物种群体进行估计具有挑战性。此外，样本的精确年龄通常是未知的，因为它可能发生在岩石层跨越的时间间隔期间的任何时间。贝叶斯系统发育方法提供了一个连贯的框架，将多个来源的证据和不确定性。在这项研究中，我们模拟的数据集具有典型的古生代海洋无脊椎动物的特征，在字符和分类抽样。我们使用这些数据集来研究不同的年龄处理方法对估计的拓扑结构和发散时间的影响。我们的研究结果重申了建模化石年龄的不确定性的重要性，虽然我们发现，化石年龄的不确定性的相对影响取决于化石类群采样和字符采样。作为推断的一部分，对化石年龄进行采样，得到的拓扑和发散时间估计与将年龄固定在真实值上得到的估计一样好，而将化石年龄固定在不正确的值上会导致更高的误差和更低的覆盖率。随着化石和字符采样的增加，相对效果增加。因此，模拟化石年龄的不确定性是至关重要的，因为固定不正确的化石年龄将否定改进化石和特征采样的好处。
Time calibrated trees are challenging to estimate for many extinct groups of species due to the incompleteness of the rock and fossil records. Additionally, the precise age of a sample is typically not known as it may have occurred at any time during the time interval spanned by the rock layer. Bayesian phylogenetic approaches provide a coherent framework for incorporating multiple sources of evidence and uncertainty. In this study, we simulate datasets with characteristics typical of Palaeozoic marine invertebrates, in terms of character and taxon sampling. We use these datasets to examine the impact of different age handling methods on estimated topologies and divergence times obtained using the fossilized birth-death process. Our results reiterate the importance of modeling fossil age uncertainty, although we find that the relative impact of fossil age uncertainty depends on both fossil taxon sampling and character sampling. Sampling the fossil ages as part of the inference gives topology and divergence time estimates that are as good as those obtained by fixing ages to the truth, whereas fixing fossil ages to incorrect values results in higher error and lower coverage. The relative effect increases with increased fossil and character sampling. Modeling fossil age uncertainty is thus critical, as fixing incorrect fossil ages will negate the benefits of improved fossil and character sampling.