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.

中文翻译：

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忽略化石年龄的不确定性会导致时间校准树推断中的拓扑和发散时间估计不准确

由于岩石和化石记录的不完整性，时间校准的树木很难估计许多已灭绝的物种群。此外，样本的精确年龄通常是未知的，因为它可能发生在岩层跨越的时间间隔内的任何时间。贝叶斯系统发育方法为整合多种证据来源和不确定性提供了一个连贯的框架。在这项研究中，我们模拟了具有典型古生代海洋无脊椎动物特征的数据集，包括特征和分类单元采样。我们使用这些数据集来检查不同年龄处理方法对使用化石生死过程获得的估计拓扑和发散时间的影响。我们的结果重申了对化石年龄不确定性建模的重要性，尽管我们发现化石年龄不确定性的相对影响取决于化石分类单元抽样和特征抽样。对化石年龄进行采样作为推理的一部分给出的拓扑和发散时间估计与通过将年龄固定为真相所获得的估计一样好，而将化石年龄固定为不正确的值会导致更高的错误和更低的覆盖率。相对影响随着化石和特征采样的增加而增加。因此，对化石年龄不确定性进行建模至关重要，因为修复不正确的化石年龄将抵消改进化石和特征采样的好处。而将化石年龄固定为不正确的值会导致更高的错误和更低的覆盖率。相对影响随着化石和特征采样的增加而增加。因此，对化石年龄不确定性进行建模至关重要，因为修复不正确的化石年龄将抵消改进化石和特征采样的好处。而将化石年龄固定为不正确的值会导致更高的错误和更低的覆盖率。相对影响随着化石和特征采样的增加而增加。因此，对化石年龄不确定性进行建模至关重要，因为修复不正确的化石年龄将抵消改进化石和特征采样的好处。