Research School of Biological Sciences, Australian National University, Robertson Building, 134 Linnaeus Way, Canberra, ACT 2600, Australia.
Mathematical Sciences Institute, Australian National University, Canberra, ACT 2600, Australia.
BMC Ecol Evol. 2022 May 10;22(1):61. doi: 10.1186/s12862-022-02015-8.
An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates.
We simulate phylogenies and molecular sequences under three different realistic rate variation models-one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used "relaxed clock" molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML.
We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.
准确的进化历史时间尺度对于检验历史事件和过程的影响假说至关重要，并且进化时间尺度越来越多地来自 DNA 序列分析。但是，分子进化率的变化使得从 DNA 推断时间变得复杂。越来越多的证据表明，许多因素（如生活史和栖息地）与突变和固定的分子过程以及宏观进化多样化的速率都有关联。然而，最广泛使用的方法依赖于理想的速率变化模型，例如不相关和自相关时钟，并且很少针对复杂的速率变化模型测试分子定年方法。在分子定年中没有考虑到的一个关系是分子替代率与物种形成之间相互作用的可能性，越来越多的分类群中的经验研究支持了这种关系。如果这些关系像当前证据表明的那样广泛，它们可能会对分子日期产生重大影响。
我们使用经验案例研究来参数化现实模拟，根据三种不同的现实速率变化模型（一种是物种形成率和替代率都在变化但没有关联的模型，一种是它们连续协变的模型，一种是分子变化集中在物种形成事件的模型）模拟系统发育和分子序列。我们使用三种常用的“松弛时钟”分子定年方法来测试这些现实模拟，以探讨在每种模型下分子日期的误差程度。我们发现，当在 BEAST 2 中使用不相关的速率先验对无关联模型进行重建时，平均分歧时间推断误差范围为节点年龄的 12%，而当在 punctuated 模型下进化的序列在 PAML 下使用自相关先验进行重建时，误差高达 91%。
当谱系之间的物种形成率和替代率都发生变化时，我们证明了分子日期可能存在重大错误。这项研究强调了需要针对从经验参数和已知关系生成的现实速率变化模型测试分子定年方法。
