Consequences of Secondary Calibrations on Divergence Time Estimates

Area of Science:

• Evolutionary Biology
• Computational Biology
• Phylogenetics

Background:

• Secondary calibrations are frequently used in molecular dating when fossil data is scarce.
• The impact of secondary calibrations within relaxed-clock models remains incompletely understood.
• Previous studies have not fully explored the consistency of age and uncertainty estimates when using secondary calibrations.

Purpose of the Study:

• To investigate the consequences of applying secondary calibrations in relaxed-clock divergence time analyses.
• To determine if using posterior estimates from primary studies as priors in secondary studies yields consistent age and uncertainty.
• To evaluate the accuracy and precision of age estimates derived from secondary calibrations.

Main Methods:

• Simulated divergence time analyses using 100 randomly replicated secondary trees.
• Compared age and uncertainty estimates between primary and secondary calibration approaches.
• Analyzed the influence of prior distribution shape (normal vs. uniform) on error.

Main Results:

• Secondary calibration estimates were significantly younger and narrower (more precise) than primary estimates on average.
• Primary and secondary age estimates differed significantly in 97% of replicates.
• Error magnitude increased with deeper nodes and was positively related to tree size and age; normal priors increased error compared to uniform priors.

Conclusions:

• Secondary calibrations can provide a misleading impression of precision in divergence time estimates.
• Age distributions derived from secondary calibrations shift away from primary analyses.
• Further research is needed to model the increased uncertainty associated with secondary calibrations before they are solely relied upon for time-dependent hypothesis testing.