Warnock Rachel C M, Parham James F, Joyce Walter G, Lyson Tyler R, Donoghue Philip C J
School of Earth Sciences, University of Bristol, Bristol, UK National Evolutionary Synthesis Center, Durham, NC, USA Department of Paleobiology, Smithsonian Institution, Washington DC, USA
John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA, USA.
Proc Biol Sci. 2015 Jan 7;282(1798):20141013. doi: 10.1098/rspb.2014.1013.
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.
校准是每次分子钟分析中的速率决定步骤，因此，人们在开发区分良好校准与不良校准的方法上投入了大量精力。这些方法可分为对内在化石证据的先验评估，以及通过交叉验证对一致性的后验评估。我们对比了这些相互竞争的方法，并探讨了对化石证据的不同解释对贝叶斯分歧时间估计的影响。结果表明，后验方法可能导致选择错误的校准。贝叶斯后验估计也被证明对时间限制的概率解释极为敏感。此外，在分析中单独使用以及与其他校准以不同组合使用时，各个校准所采用的有效时间先验是不同的。这损害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一起使用时影响相同。因此，确定基于化石校准质量的最有效方法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，除非在校分歧时间分析中如实实施，否则在建立校准方面所做的努力将得不到回报。
