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There has been concern in the literature about the methodology of usingsecondary calibration timepoints when estimating evolutionary divergence dates.Such timepoints are divergence time estimates that have been derived from onemolecular data set on the basis of a primary external calibration timepoint,and which are then used independently on a second data set. Logically, theprimary and secondary calibration points must be mutually consistent, in thesense that it must be possible to predict each time point from the other.However, the attempt by Shaul and Graur (2002, Gene 300: 59-61) to assess thereliability of secondary timepoints is flawed because they presented timeestimates without presenting confidence intervals on those estimates, and so itwas not possible to make any explicit hypothesis tests of divergence times.Also, they inappropriately excluded some of the data, which leads to a verybiased estimate of one of the divergence times. Here, I present a re-analysisof the same data set, with more appropriate methodology, and come to theconclusion that no inconsistencies are involved. However, it is clear from theanalysis that molecular data often have such large confidence intervals thatthey are uninformative, and thus cannot be used for reliable hypothesis tests.

Counting chickens before they hatch: reciprocal consistency of calibration points for estimating divergence dates