Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity
Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity
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DOI：
10.1093/sysbio/syac049
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发表时间：
2022-07-21
影响因子：
6.5
通讯作者：
O'Meara, Brian C.
中科院分区：
文献类型：
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作者：
Beaulieu, Jeremy M.;O'Meara, Brian C.
化石出生-死亡（FBD）模型是一种在估计多样化率时直接结合化石信息的自然吸引人的方法。然而，原始FBD推导的一个重要但经常被忽视的特性是，它区分了两种类型的采样谱系。在这里，我们首先讨论并展示了严重采样不足的影响，甚至不包括代表谱系样本的化石，这些样本也有采样的后代。然后，我们通常通过实施和测试两种类型的FBD模型来探索包括化石的好处，其中一种是将化石集转换为地层范围，在更复杂的基于可能性的模型中，假设整个树的多个速率类别。在各种模拟情景下，包括存在于我们评估的模型集之外的情景，包括化石很少比完全排除它们的分析表现更好。在最好的情况下，包含化石可以提高精度，但不会影响偏差。同样，我们发现，将化石集转换为地层范围，这是弥补k型化石数量低估影响的一种方法，导致周转率和灭绝分数估计值通常被低估。尽管化石对于理解时间上的多样性仍然是必不可少的，但在理解一种现存的、主要是现代的树木的多样性的具体情况下，它们并不是特别有益。
The fossilized birth-death (FBD) model is a naturally appealing way of directly incorporating fossil information when estimating diversification rates. However, an important yet often overlooked property of the original FBD derivation is that it distinguishes between two types of sampled lineages. Here, we first discuss and demonstrate the impact of severely undersampling, and even not including fossils that represent samples of lineages that also had sampled descendants. We then explore the benefits of including fossils, generally, by implementing and then testing two types of FBD models, including one that converts a fossil set into stratigraphic ranges, in more complex likelihood-based models that assume multiple rate classes across the tree. Under various simulation scenarios, including a scenario that exists far outside the set of models we evaluated, including fossils rarely outperform analyses that exclude them altogether. At best, the inclusion of fossils improves precision but does not influence bias. Similarly, we found that converting the fossil set to stratigraphic ranges, which is one way to remedy the effects of undercounting the number of k-type fossils, results in turnover rates and extinction fraction estimates that are generally underestimated. Although fossils remain essential for understanding diversification through time, in the specific case of understanding diversification given an existing, largely modern tree, they are not especially beneficial.