Data from: Molecular dating, evolutionary rates, and the age of the grasses

Many questions in evolutionary biology require an estimate of divergence times but, for groups with a sparse fossil record, such estimates rely heavily on molecular dating methods. The accuracy of these methods depends on both an adequate underlying model and the appropriate implementation of fossil evidence as calibration points. We explore the effect of these in Poaceae (grasses), a diverse plant lineage with a very limited fossil record, focusing particularly on dating the early divergences in the group. We show that molecular dating based on a dataset of plastid markers is strongly dependent on the model assumptions. In particular, an acceleration of evolutionary rates at the base of Poaceae followed by a deceleration in the descendants strongly biases methods that assume an autocorrelation of rates. This problem can be circumvented by using markers that have lower rate variation, and we show that phylogenetic markers extracted from complete nuclear genomes can be a useful complement to the more commonly used plastid markers. However, estimates of divergence times remain strongly affected by different implementations of fossil calibration points. Analyses calibrated with only macrofossils lead to estimates for the age of core Poaceae around 51-55 Ma, but the inclusion of microfossil evidence pushes this age to 74-82 Ma and leads to lower estimated evolutionary rates in grasses. These results emphasize the importance of considering markers from multiple genomes and alternative fossil placements when addressing evolutionary issues that depend on ages estimated for important groups.进化生物学领域的诸多问题均需估算类群的分化时间，但对于化石记录稀疏的类群，这类估算高度依赖分子定年方法（molecular dating methods）。此类方法的准确性，既取决于所采用的基础模型是否合理，也依赖于化石证据作为校准点的恰当应用。本研究以禾本科（Poaceae）——一类物种多样性极高但化石记录极为有限的植物支系——为研究对象，重点探讨该类群的早期分化事件定年问题，并考察上述两类因素的影响。研究表明，基于质体标记（plastid markers）数据集的分子定年结果，强烈依赖于模型假设。具体而言，禾本科基部演化速率的加速，以及后续类群中演化速率的减缓，会显著偏倚那些假设速率自相关（autocorrelation of rates）的定年方法。这一问题可通过使用速率变异更低的标记予以规避，本研究证实，从完整核基因组（nuclear genomes）中提取的系统发育标记，可作为当前常用质体标记的有效补充。然而，分化时间的估算结果仍会受到化石校准点不同应用方式的强烈影响。仅使用大化石（macrofossils）作为校准点的分析显示，核心禾本科的起源时间约为51–55 Ma，但纳入微化石（microfossils）证据后，该起源时间被推至74–82 Ma，同时估算得到的禾本科演化速率也有所降低。上述研究结果强调，在探究依赖重要类群估算年龄的演化问题时，考虑来自多个基因组的标记以及不同的化石校准方案，具有重要意义。