Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS UMR 8079, 91405 Orsay, France.
Syst Biol. 2012 Mar;61(2):289-313. doi: 10.1093/sysbio/syr116. Epub 2011 Dec 26.
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.
尽管时间校准被广泛认为对于使用分子年代测定方法获得准确的分歧时间估计至关重要，但很少有研究评估不同校准策略导致的变化。根据可用信息，研究人员通常使用来自化石记录的主要校准或来自先前分子年代测定研究的次要校准。在开花植物的分析中，主要校准数据可以从宏观和中化石（例如，叶子、花朵和果实）或微化石（例如，花粉）中获得。化石数据在准确性和精度上可能有很大差异，在选择适当的校准值时会面临困难的选择。在这里，我们测试了对于具有特别丰富和经过充分研究的化石记录的植物属 Nothofagus（山毛榉科，壳斗目）的八个合理校准方案的影响。为此，我们回顾了 38 个 Nothofagus 和其他壳斗目植物的化石分类群的系统发育位置和地质年代，并为壳斗目系统发育的 18 个节点确定了最小年龄约束。使用最大似然法（RAxML+r8s）和贝叶斯法（BEAST）对来自叶绿体和核基因组六个区域的序列数据进行了每个方案的分子年代测定分析。使用内外群约束或两者，导致了相似的年龄估计，除了在具有强烈影响的校准节点附近。除了使用“安全但较晚”的约束外，还使用“早期但风险大”的化石约束，或者使用扩散假设而不是化石约束，导致了较老的年龄估计。相反，使用次要校准点会导致年龄估计急剧变小。这项实证研究强调了校准对分子年代测定分析的关键影响。即使在最好的情况下，有许多经过彻底审查的化石可用，估计分歧时间仍可能存在很大的不确定性。例如，我们对 Nothofagus 冠群年龄的估计在我们的全部校准方案范围内从 13 到 113 Ma 不等。我们建议，在校准过程的所有阶段都应该进行更多的背景研究，以尽可能减少错误，从验证化石的地质年代数据到对其系统发育位置进行关键重新评估。
