Quantifying the error of secondary vs. distant primary calibrations in a simulated environment

Using calibrations to obtain absolute divergence times is standard practice in molecular clock studies. While the use of primary (e.g., fossil) calibrations is preferred, this approach can be limiting because of their rarity in fast-growing datasets. Thus, alternatives need to be explored, such as the use of secondary (molecularly-derived) calibrations that can anchor a timetree in a larger number of nodes. However, the use of secondary calibrations has been discouraged in the past because of concerns in the error rates of the node estimates they produce with an apparent high precision. Here, we quantify the amount of errors in estimates produced by the use of secondary calibrations relative to true times and primary calibrations placed on distant nodes. We find that, overall, the inaccuracies in estimates based on secondary calibrations are predictable and mirror errors associated with primary calibrations and their confidence intervals. Additionally, we find comparable error rates in estimated times from secondary calibrations and distant primary calibrations, although the precision of estimates derived from distant primary calibrations is roughly twice as good as that of estimates derived from secondary calibrations. This suggests that increasing dataset size to include primary calibration may produce divergence times that are about as accurate as those from secondary calibrations, albeit with a higher precision. Overall, our results suggest that secondary calibrations may be useful to explore the parameter space of plausible evolutionary scenarios when compared to time estimates obtained with distant primary calibrations.