Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617, Brazil.
Genome Biol Evol. 2024 Sep 3;16(9). doi: 10.1093/gbe/evae199.
Relaxing the molecular clock using models of how substitution rates change across lineages has become essential for addressing evolutionary problems. The diversity of rate evolution models and their implementations are substantial, and studies have demonstrated their impact on divergence time estimates can be as significant as that of calibration information. In this review, we trace the development of rate evolution models from the proposal of the molecular clock concept to the development of sophisticated Bayesian and non-Bayesian methods that handle rate variation in phylogenies. We discuss the various approaches to modeling rate evolution, provide a comprehensive list of available software, and examine the challenges and advancements of the prevalent Bayesian framework, contrasting them to faster non-Bayesian methods. Lastly, we offer insights into potential advancements in the field in the era of big data.
使用替代率在谱系间变化的模型来放松分子钟已经成为解决进化问题的关键。速率演化模型及其实现的多样性非常大，研究表明，它们对分歧时间估计的影响与校准信息一样重要。在这篇综述中，我们追溯了从分子钟概念的提出到处理系统发育中速率变化的复杂贝叶斯和非贝叶斯方法的速率演化模型的发展。我们讨论了各种建模速率演化的方法，提供了可用软件的综合列表，并研究了流行的贝叶斯框架的挑战和进展，将其与更快的非贝叶斯方法进行了对比。最后，我们对大数据时代该领域的潜在进展提出了一些见解。
