Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI 02912, USA; Department of Biology & Burke Museum of Natural History and Culture, University of Washington, 24 Kincaid Hall, Seattle, WA 98195, USA; Department of Ecology and Evolution, Biophore, Quartier Sorge, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge, University of Lausanne, 1015 Lausanne, Switzerland.
Syst Biol. 2014 Mar;63(2):153-65. doi: 10.1093/sysbio/syt072. Epub 2013 Nov 28.
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 data set 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 ∼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.
许多进化生物学问题都需要估计分歧时间，但对于化石记录稀疏的群体，这些估计很大程度上依赖于分子年代测定方法。这些方法的准确性取决于适当的基础模型和化石证据作为校准点的适当实施。我们探讨了这些因素在禾本科（草）中的作用，禾本科是一个具有非常有限化石记录的多样化植物谱系，特别关注该群体早期分歧的年代测定。我们表明，基于质体标记数据集的分子年代测定强烈依赖于模型假设。特别是，禾本科基部的进化率加速，随后在后代中减速，这强烈偏向于假设速率自相关的方法。通过使用具有较低速率变化的标记可以规避这个问题，我们表明从完整核基因组中提取的系统发育标记可以作为更常用的质体标记的有用补充。然而，分歧时间的估计仍然受到化石校准点不同实现的强烈影响。仅用宏观化石校准的分析导致核心禾本科的年龄约为 51-55 Ma，但包括微化石证据将这个年龄推至 74-82 Ma，并导致禾本科的估计进化率降低。这些结果强调了在解决依赖于重要群体估计年龄的进化问题时，考虑来自多个基因组和替代化石位置的标记的重要性。
