Aris-Brosou Stéphane, Rodrigue Nicolas
Departments of Biology and Mathematics & Statistics and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, ON, Canada.
Methods Mol Biol. 2012;855:111-52. doi: 10.1007/978-1-61779-582-4_4.
In this chapter, we give a brief yet self-contained introduction to computational molecular evolution. In particular, we present the emergence of the use of likelihood-based methods, review the standard DNA substitution models, and introduce how model choice operates. We also present recent developments in inferring absolute dates and rates on a phylogeny and show how state-of-the-art models take inspiration from diffusion theory to link population genetics, which traditionally focuses at a taxonomic level under that of species, and molecular evolution.
在本章中，我们对计算分子进化进行了简要且自成体系的介绍。特别地，我们阐述了基于似然性方法的使用的出现，回顾了标准的DNA替代模型，并介绍了模型选择是如何运作的。我们还展示了在系统发育树上推断绝对日期和速率方面的最新进展，并说明最先进的模型是如何从扩散理论中获得灵感，从而将传统上聚焦于物种以下分类水平的群体遗传学与分子进化联系起来的。
