do Rosario Petrucci Bruno, May Michael R, Heath Tracy A
Department of Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA.
Philos Trans R Soc Lond B Biol Sci. 2025 Feb 13;380(1919):20230313. doi: 10.1098/rstb.2023.0313. Epub 2025 Feb 20.
The effect of traits on diversification rates is a major topic of study in the fields of evolutionary biology and palaeontology. Many researchers investigating these macroevolutionary questions currently make use of the extensive suite of state-dependent speciation and extinction (SSE) models. These models were developed for, and are almost exclusively used with, phylogenetic trees of extant species. However, analyses considering only extant taxa are limited in their power to estimate extinction rates. Furthermore, SSE models can erroneously detect associations between neutral traits and diversification rates when the true associated trait is not observed. In this study, we examined the impact of including fossil data on the accuracy of parameter estimates under the binary-state speciation and extinction (BiSSE) model. This was achieved by combining SSE models with the fossilized birth-death process. We show that the inclusion of fossils improves the accuracy of extinction-rate estimates for analyses applying the BiSSE model in a Bayesian inference framework, with no negative impact on speciation-rate and state transition-rate estimates when compared with estimates from trees of only extant taxa. However, even with the addition of fossil data, analyses under the BiSSE model continued to incorrectly identify correlations between diversification rates and neutral traits.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.
性状对物种多样化速率的影响是进化生物学和古生物学领域的一个主要研究课题。目前，许多研究这些宏观进化问题的研究人员都在使用一系列广泛的状态依赖物种形成和灭绝（SSE）模型。这些模型是为现存物种的系统发育树而开发的，并且几乎只与现存物种的系统发育树一起使用。然而，仅考虑现存分类单元的分析在估计灭绝速率方面的能力有限。此外，当未观察到真正相关的性状时，SSE模型可能会错误地检测中性性状与物种多样化速率之间的关联。在本研究中，我们研究了在二态物种形成和灭绝（BiSSE）模型下纳入化石数据对参数估计准确性的影响。这是通过将SSE模型与化石出生-死亡过程相结合来实现的。我们表明，在贝叶斯推断框架中应用BiSSE模型进行分析时，纳入化石可提高灭绝速率估计的准确性，与仅使用现存分类单元树的估计相比，对物种形成速率和状态转变速率估计没有负面影响。然而，即使添加了化石数据，在BiSSE模型下的分析仍会继续错误地识别物种多样化速率与中性性状之间的相关性。本文是主题为“进化的数学理论”：可追溯到100年前的系统发育模型的一部分。
