Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
Methods Mol Biol. 2022;2569:327-342. doi: 10.1007/978-1-0716-2691-7_16.
Phylogenetic comparative methods (PCMs) combine statistics and evolutionary models to infer the dynamics of trait evolution and diversification that underlie the observed phylogeny. While PCMs have been used to study macro-evolutionary processes and evolutionary transitions of macroorganisms, their application to microbes is still limited. With the abundance of publicly available genomic and trait character data for diverse microbes nowadays, applications of PCMs on these data can provide insights into the fundamental principles that govern microbial evolution. Here, we introduce the Binary-State Speciation and Extinction (BiSSE) model, which is a relatively simple yet powerful approach for analyzing trait evolution. We begin by explaining the theoretical background and intuition behind the BiSSE model. Then, R commands for running the BiSSE model are presented. Finally, we introduce a case study that successfully applied the BiSSE model to investigate generalist and specialist microbial lifestyle evolution.
系统发育比较方法（PCMs）将统计学和进化模型相结合，以推断出进化和多样化的特征，这些特征构成了所观察到的系统发育。虽然 PCMs 已被用于研究宏观进化过程和宏观生物的进化转变，但它们在微生物中的应用仍然有限。如今，由于大量公开可用的基因组和特征数据，PCMs 在这些数据上的应用可以深入了解微生物进化的基本原理。在这里，我们介绍了二元状态物种形成和灭绝（BiSSE）模型，这是一种相对简单但功能强大的分析特征进化的方法。我们首先解释 BiSSE 模型的理论背景和直觉。然后，我们给出了运行 BiSSE 模型的 R 命令。最后，我们介绍了一个成功应用 BiSSE 模型的案例研究，该研究调查了微生物生活方式的通才和专家进化。
