The fossilized birth–death (FBD) process provides an ideal model for inferring phylogenies from both extant and fossil taxa. Using this approach, fossils are directly integrated into the tree, leading to a statistically coherent prior on divergence times. Since fossils are typically not associated with molecular sequences, additional information is required to place fossils in the tree. We use simulations to evaluate two different approaches to handling fossil placement in FBD analyses: using topological constraints, where the user specifies monophyletic clades based on established taxonomy, or using total-evidence analyses, which use a morphological data matrix in addition to the molecular alignment. We also explore how rate variation in fossil recovery or diversification rates impacts these approaches. We find that the extant topology is well recovered under all methods of fossil placement. Divergence times are similarly well recovered across all methods, with the exception of constraints which contain errors. We see similar patterns in datasets which include rate variation, however, relative errors in extant divergence times increase when more variation is included in the dataset, for all approaches using topological constraints, and particularly for constraints with errors. Finally, we show that trees recovered under the FBD model are more accurate than those estimated using non-time calibrated inference. Overall, we show that both fossil placement approaches are reliable even when including uncertainty. Our results underscore the importance of core taxonomic research, including morphological data collection and species descriptions, irrespective of the approach to handling phylogenetic uncertainty using the FBD process.

中文翻译：

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将 F 放入 FBD 分析：树约束还是形态数据？

化石出生-死亡（FBD）过程为从现存和化石类群推断系统发育提供了一个理想的模型。使用这种方法，化石被直接整合到树中，从而在分歧时间上产生统计上一致的先验。由于化石通常与分子序列无关，因此需要额外的信息才能将化石放置在树中。我们使用模拟来评估在 FBD 分析中处理化石放置的两种不同方法：使用拓扑约束，用户根据已建立的分类法指定单系进化枝，或使用总证据分析，除了分子排列之外还使用形态数据矩阵。我们还探讨了化石回收率或多样化率的变化如何影响这些方法。我们发现，在所有化石放置方法下，现存的拓扑结构都得到了很好的恢复。除了包含错误的约束之外，所有方法的发散时间都同样得到了很好的恢复。我们在包括速率变化的数据集中看到了类似的模式，但是，对于使用拓扑约束的所有方法，特别是对于有误差的约束，当数据集中包含更多变化时，现有发散时间的相对误差会增加。最后，我们表明，在 FBD 模型下恢复的树木比使用非时间校准推理估计的树木更准确。总的来说，我们表明即使包含不确定性，这两种化石放置方法也是可靠的。我们的结果强调了核心分类学研究的重要性，包括形态数据收集和物种描述，无论使用 FBD 过程处理系统发育不确定性的方法如何。