Data from: Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

Calibration is the rate-determining step in every molecular clock analysis
and, hence, considerable effort has been expended in the development of
approaches to distinguish good from bad calibrations. These can be
categorized into a priori evaluation of the intrinsic fossil evidence, and
a posteriori evaluation of congruence through cross-validation. We
contrasted these competing approaches and explored the impact of different
interpretations of the fossil evidence upon Bayesian divergence time
estimation. The results demonstrate that a posteriori approaches can lead
to the selection of erroneous calibrations. Bayesian posterior estimates
are also shown to be extremely sensitive to the probabilistic
interpretation of temporal constraints. Furthermore, the effective time
priors implemented within an analysis differ for individual calibrations
when employed alone and in differing combination with others. This
compromises the implicit assumption of all calibration consistency
methods, that the impact of an individual calibration is the same when
used alone or in unison with others. Thus, the most effective means of
establishing the quality of fossil-based calibrations is through a priori
evaluation of the intrinsic palaeontological, stratigraphic,
geochronological and phylogenetic data. However, effort expended in
establishing calibrations will not be rewarded unless they are implemented
faithfully in divergence time analyses.

校准确认是所有分子钟分析中的速率决定步骤，因此，人们已投入大量精力开发区分优质与劣质校准的方法。这些方法可分为两类：基于内在化石证据的先验评估（a priori evaluation），以及通过交叉验证进行的一致性后验评估（a posteriori evaluation）。我们对比了这些相互竞争的方法，并探究了对化石证据的不同解读对贝叶斯分歧时间估计（Bayesian divergence time estimation）的影响。结果表明，后验方法可能导致错误校准的选择。贝叶斯后验估计（Bayesian posterior estimates）也被证明对时间约束的概率解读极为敏感。此外，在分析中应用的有效时间先验（effective time priors），对于单独使用的校准与和其他校准组合使用的校准而言，存在差异。这违背了所有校准一致性方法的隐含假设——即单个校准单独使用或与其他校准联合使用时的影响是相同的。因此，确定基于化石的校准质量的最有效手段，是通过对内在古生物学、地层学、地质年代学和系统发育数据的先验评估。然而，除非校准在分歧时间分析中得到忠实应用，否则投入在建立校准上的精力将无法获得回报。