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 complemen...进化生物学领域的诸多问题均需要估算类群的分化时间，而对于化石记录稀缺的类群而言，这类估算高度依赖分子定年方法。此类方法的准确性同时取决于合适的基础模型，以及将化石证据作为校准点的合理应用方式。我们以禾本科（Poaceae）——一类物种多样但化石记录极度匮乏的植物演化支——为研究对象，探究了上述两类因素的影响，尤其聚焦于该类群的早期分化定年问题。研究表明，基于质体标记（plastid markers）数据集的分子定年结果，强烈依赖于模型的假设前提。具体而言，禾本科基部类群的演化速率先发生加速，后续衍生类群的速率又随之减缓，这会对假定速率自相关（autocorrelation of rates）的定年方法造成强烈偏差。此类问题可通过选用速率变异程度更低的标记来规避；我们的研究还证实，从完整核基因组（nuclear genomes）中提取的系统发育标记（phylogenetic markers），可作为一种有效的补充...