Estimating speciation and extinction rates is essential for understanding past and present biodiversity, but is challenging given the incompleteness of the rock and fossil records. Interest in this topic has led to a divergent suite of independent methods—paleontological estimates based on sampled stratigraphic ranges and phylogenetic estimates based on the observed branching times in a given phylogeny of living species. The fossilized birth–death (FBD) process is a model that explicitly recognizes that the branching events in a phylogenetic tree and sampled fossils were generated by the same underlying diversification process. A crucial advantage of this model is that it incorporates the possibility that some species may never be sampled. Here, we present an FBD model that estimates tree-wide diversification rates from stratigraphic range data when the underlying phylogeny of the fossil taxa may be unknown. The model can be applied when only occurrence data for taxonomically identified fossils are available, but still accounts for the incomplete phylogenetic structure of the data. We tested this new model using simulations and focused on how inferences are impacted by incomplete fossil recovery. We compared our approach with a phylogenetic model that does not incorporate incomplete species sampling and to three fossil-based alternatives for estimating diversification rates, including the widely implemented boundary-crosser and three-timer methods. The results of our simulations demonstrate that estimates under the FBD model are robust and more accurate than the alternative methods, particularly when fossil data are sparse, as the FBD model incorporates incomplete species sampling explicitly.

中文翻译：

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评估不完整的物种抽样对物种形成和灭绝率估计的影响

估计物种形成和灭绝率对于了解过去和现在的生物多样性至关重要，但鉴于岩石和化石记录的不完整性，这具有挑战性。对这个主题的兴趣导致了一套不同的独立方法——基于采样地层范围的古生物学估计和基于在给定的活物种系统发育中观察到的分支时间的系统发育估计。化石出生-死亡 (FBD) 过程是一个模型，它明确认识到系统发育树和样本化石中的分支事件是由相同的潜在多样化过程产生的。该模型的一个关键优势是它包含了某些物种可能永远不会被采样的可能性。这里，我们提出了一个 FBD 模型，当化石类群的潜在系统发育可能未知时，该模型从地层范围数据估计树范围内的多样化率。当只有分类学鉴定的化石的出现数据可用时，可以应用该模型，但仍然可以解释数据的系统发育结构不完整。我们使用模拟测试了这个新模型，并专注于不完整的化石恢复如何影响推断。我们将我们的方法与不包含不完整物种采样的系统发育模型和用于估计多样化率的三种基于化石的替代方法进行了比较，包括广泛实施的边界交叉法和三计时器方法。我们的模拟结果表明，FBD 模型下的估计比其他方法更稳健、更准确，