Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA.
Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, Warsaw 00-818, Poland.
Syst Biol. 2021 Dec 16;71(1):153-171. doi: 10.1093/sysbio/syab045.
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.].
物种形成和灭绝速率的变化是类群多样化动态的关键，但从现存物种的系统发育推断这些变化面临着挑战。能够综合现存和化石物种信息的方法为随时间变化的多样化速率变化提供了新的见解，但对于分析完全灭绝的类群时它们的行为知之甚少。在这里，我们使用经验数据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。我们推断了鸟臀目恐龙的首个有时间标记的树，并将它们与化石出现数据相结合，以检验该类群是否在白垩纪末期经历了下降。然后，我们模拟了系统发育和化石记录，以在经验约束下确定在古生物学上现实的条件下是否可以区分宏观进化和保存速率。我们对鸟臀目恐龙的宏观进化得出了不一致的推断，包括长期的物种形成率下降（BAMM）、大部分平坦的速率和急剧的多样化下降（PyRate）或没有下降（BAMM），以及不合理的加速物种形成和灭绝的阶段（PyRate）。模拟结果表明，物种形成和保存之间几乎没有混淆，但在时间模糊树宽变化（BAMM）或高估其数量（PyRate）时产生了虚假相关的物种形成和灭绝估计。我们的结果表明，可供脊椎动物古生物学家使用的小的系统发育数据集以及当前基于模型的方法的假设相结合，导致了对灭绝类群多样化的潜在不可靠推断。我们提供了根据其局限性解释现有方法结果的指南，并提出了如何减轻后者的影响。[BAMM；多样化；化石；宏观进化率；鸟臀目；PyRate]。
