Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK.
Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
Methods Mol Biol. 2023;2545:139-154. doi: 10.1007/978-1-0716-2561-3_7.
The timing of whole-genome duplication (WGD) events is crucial to understanding their role in evolution and underpins many hypotheses linking WGD to increased diversity and complexity. As such, means of estimating the timing of the WGD events relative to their macroevolutionary outcomes are of considerable importance. Molecular clock methods facilitate direct estimation of the absolute timing of WGD events, integrating information on the rate of sequence evolution between species while accommodating the uncertainty inherent to the fossil record. We present an explanation of the best practice for constructing fossil calibrations and estimating the age of WGD events via molecular clock methods in the program MCMCtree, with an example dataset based on a well-characterized WGD event within the flowering dogwoods (Cornus). The approach presented herein allows for the estimation of the age of WGD events and subsequent speciation events, allowing the relationship between WGD and the macroevolutionary outcomes to be explored. In our example, we show that in the case of flowering dogwoods, the WGD event long predates the end-Cretaceous mass extinction and that the two events may be independent.
全基因组复制 (WGD) 事件的时间对于理解它们在进化中的作用至关重要，并为许多将 WGD 与多样性和复杂性增加联系起来的假说提供了依据。因此，估计 WGD 事件相对于其宏观进化结果的时间的方法具有相当重要的意义。分子钟方法促进了对 WGD 事件绝对时间的直接估计，整合了物种之间序列进化率的信息，同时适应了化石记录固有的不确定性。我们介绍了在程序 MCMCtree 中通过分子钟方法构建化石校准和估计 WGD 事件年龄的最佳实践的解释，该方法基于在开花山茱萸 (Cornus) 内的一个特征明确的 WGD 事件的示例数据集。本文提出的方法允许估计 WGD 事件和随后的物种形成事件的年龄，从而可以探索 WGD 与宏观进化结果之间的关系。在我们的例子中，我们表明，在开花山茱萸的情况下，WGD 事件远早于白垩纪末期大灭绝，并且这两个事件可能是独立的。
