Ho Simon Y W, Duchêne Sebastián
School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
Mol Ecol. 2014 Dec;23(24):5947-65. doi: 10.1111/mec.12953. Epub 2014 Oct 30.
The molecular clock presents a means of estimating evolutionary rates and timescales using genetic data. These estimates can lead to important insights into evolutionary processes and mechanisms, as well as providing a framework for further biological analyses. To deal with rate variation among genes and among lineages, a diverse range of molecular-clock methods have been developed. These methods have been implemented in various software packages and differ in their statistical properties, ability to handle different models of rate variation, capacity to incorporate various forms of calibrating information and tractability for analysing large data sets. Choosing a suitable molecular-clock model can be a challenging exercise, but a number of model-selection techniques are available. In this review, we describe the different forms of evolutionary rate heterogeneity and explain how they can be accommodated in molecular-clock analyses. We provide an outline of the various clock methods and models that are available, including the strict clock, local clocks, discrete clocks and relaxed clocks. Techniques for calibration and clock-model selection are also described, along with methods for handling multilocus data sets. We conclude our review with some comments about the future of molecular clocks.
分子钟提供了一种利用遗传数据估计进化速率和时间尺度的方法。这些估计能够为进化过程和机制带来重要的见解，同时也为进一步的生物学分析提供一个框架。为了应对基因间和谱系间的速率变化，人们开发了各种各样的分子钟方法。这些方法已在各种软件包中实现，它们在统计特性、处理不同速率变化模型的能力、纳入各种校准信息的能力以及分析大数据集的易处理性方面存在差异。选择合适的分子钟模型可能是一项具有挑战性的工作，但有多种模型选择技术可供使用。在这篇综述中，我们描述了进化速率异质性的不同形式，并解释了如何在分子钟分析中对其进行处理。我们概述了现有的各种时钟方法和模型，包括严格时钟、局部时钟、离散时钟和宽松时钟。还描述了校准和时钟模型选择的技术，以及处理多位点数据集的方法。我们在综述结尾对分子钟的未来发表了一些看法。
