Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM, perform in this setting. We inferred the first tip-dated trees for ornithischian dinosaurs and combined them with fossil occurrence data to test whether the clade underwent an end-Cretaceous decline. We then simulated phylogenies and fossil records under empirical constraints to determine whether macroevolutionary and preservation rates can be teased apart under paleobiologically realistic conditions. We obtained discordant inferences about ornithischian macroevolution including a long-term speciation rate decline (BAMM), mostly flat rates with a steep diversification drop (PyRate) or without one (BAMM), and episodes of implausibly accelerated speciation and extinction (PyRate). Simulations revealed little to no conflation between speciation and preservation, but yielded spuriously correlated speciation and extinction estimates while time-smearing tree-wide shifts (BAMM) or overestimating their number (PyRate). Our results indicate that the small phylogenetic data sets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to yield potentially unreliable inferences about the diversification of extinct clades. We provide guidelines for interpreting the results of the existing approaches in light of their limitations and suggest how the latter may be mitigated. [BAMM; diversification; fossils; macroevolutionary rates; Ornithischia; PyRate.]

中文翻译：

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基于模型推断灭绝进化枝多样化率的经验和方法学挑战

物种形成和灭绝率的变化是进化枝多样化动态的关键，但试图从现存物种的系统发育中推断它们面临挑战。能够从现存和化石物种中合成信息的方法已经对随时间变化的多样化率变化产生了新的见解，但在分析完全灭绝的进化枝时，人们对它们的行为知之甚少。在这里，我们使用经验和模拟数据来评估两种流行的方法 PyRate 和 Fossil BAMM 在这种情况下的表现。我们推断出第一批鸟臀目恐龙的尖端树木，并将它们与化石出现数据相结合，以测试进化枝是否经历了白垩纪末期的衰退。然后，我们在经验约束下模拟系统发育和化石记录，以确定宏观进化和保存率是否可以在古生物学现实条件下分开。我们获得了关于鸟臀目宏观进化的不一致推论，包括长期的物种形成率下降 (BAMM)，大多数是平坦的速率，急剧的多样化下降 (PyRate) 或没有一个 (BAMM)，以及难以置信地加速物种形成和灭绝的事件 (PyRate)。模拟显示物种形成和保存之间几乎没有混淆，但产生了虚假相关的物种形成和灭绝估计，同时时间涂抹全树变化 (BAMM) 或高估了它们的数量 (PyRate)。我们的结果表明，脊椎动物古生物学家可用的小型系统发育数据集和当前基于模型的方法所做的假设结合起来，产生了关于已灭绝进化枝多样化的潜在不可靠推论。我们根据现有方法的局限性提供解释现有方法结果的指南，并建议如何减轻后者。[BAMM; 多样化; 化石；宏观进化率；鸟臀目; PyRate。]