Abstract：
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.
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.
摘要：
进化史的准确时间尺度对于检验有关历史事件和过程的影响的假设至关重要，进化的时间尺度越来越多地来自DNA序列的分析。但是分子进化速率的变化使DNA对时间的推断变得复杂。许多因素的证据越来越多，比如生活史和栖息地，这与突变和固定的分子过程以及宏观进化多样化的速度有关。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的时钟，分子测年方法很少针对复杂的速率变化模型进行测试。在分子测年中没有考虑的一种关系是分子取代率和物种形成之间相互作用的潜力，这种关系得到了越来越多分类群实证研究的支持。如果这些关系如目前的证据所表明的那样广泛，它们可能对分子日期有重大影响。
我们在三种不同的实际速率变化模型下模拟系统发育和分子序列，其中一种是物种形成率和取代率都不同，但没有联系，一种是它们连续地相互变化，一种是分子变化集中在物种形成事件中的标点符号模型，使用经验案例研究来参数化现实模拟。我们针对这些现实的模拟测试了三种常用的“放松时钟”分子测年方法，以探索每种模型下分子日期的误差程度。我们发现，平均发散时间推断误差范围从使用BEAST2在不相关速率下重建时未链接模型的节点年龄的12％到使用PAML在自相关先验下重建在标点模型下进化的序列时高达91％。
我们证明了当物种形成率和取代率在谱系之间变化时，分子日期可能会出现重大错误。这项研究强调了对根据经验参数和已知关系生成的速率变化的现实模型进行分子测年方法测试的必要性。
我们在三种不同的实际速率变化模型下模拟系统发育和分子序列，其中一种是物种形成率和取代率都不同，但没有联系，一种是它们连续地相互变化，一种是分子变化集中在物种形成事件中的标点符号模型，使用经验案例研究来参数化现实模拟。我们针对这些现实的模拟测试了三种常用的“放松时钟”分子测年方法，以探索每种模型下分子日期的误差程度。我们发现，平均发散时间推断误差范围从使用BEAST2在不相关速率下重建时未链接模型的节点年龄的12％到使用PAML在自相关先验下重建在标点模型下进化的序列时高达91％。
我们证明了当物种形成率和取代率在谱系之间变化时，分子日期可能会出现重大错误。这项研究强调了对根据经验参数和已知关系生成的速率变化的现实模型进行分子测年方法测试的必要性。
