Laurin-Lemay Simon, Rodrigue Nicolas
Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel By Drive, Ottawa, ON, Canada.
Institute of Biochemistry, Carleton University, Ottawa, Canada.
J Mol Evol. 2025 Aug;93(4):465-473. doi: 10.1007/s00239-025-10257-5. Epub 2025 Jul 8.
Methods for the probabilistic mapping of the history of state changes over a phylogeny have been available for the study of molecular evolution for over two decades. In spite of this, such methods have yet to be adopted at large by most molecular evolutionary biologists. Here, we re-emphasize the potential of these stochastic mappings with examples pertaining to the study of the amino acid replacement process. We show how the features targeted by today's top-performing models could have been highlighted in a full phylogenetic context with an amino acid-level Jukes-Cantor model. We also demonstrate how stochastic mappings could be used for detecting CpG hypermutability, a site-dependent feature. We hope for a larger project utilizing mapping-based methods to provide of more fulsome characterization of molecular evolution, and to prioritize and assess modeling efforts. Finally, we draw attention to the options available within the PhyloBayes(-MPI) software for producing mappings under a large set of evolutionary models.
二十多年来，用于在系统发育树上对状态变化历史进行概率映射的方法一直可用于分子进化研究。尽管如此，大多数分子进化生物学家尚未广泛采用这些方法。在这里，我们通过与氨基酸替换过程研究相关的例子，再次强调这些随机映射的潜力。我们展示了如何使用氨基酸水平的朱克斯 - 坎托模型在完整的系统发育背景下突出当今表现最佳的模型所针对的特征。我们还演示了随机映射如何用于检测CpG高变异性，这是一种位点依赖性特征。我们希望有一个更大的项目利用基于映射的方法来更全面地描述分子进化，并对建模工作进行优先级排序和评估。最后，我们提请注意PhyloBayes(-MPI)软件中可用于在大量进化模型下生成映射的选项。
