Quantifying the Error of Secondary vs. Distant Primary Calibrations in a Simulated Environment

Area of Science:

• Evolutionary Biology
• Molecular Phylogenetics
• Computational Biology

Background:

• Molecular clock dating relies on calibrations to estimate divergence times.
• Primary calibrations (e.g., fossils) are preferred but often rare in large datasets.
• Secondary (molecular) calibrations offer more anchoring points but have faced skepticism due to perceived error rates.

Purpose of the Study:

• To quantify errors in divergence time estimates derived from secondary calibrations.
• To compare these errors against those from primary calibrations on distant nodes.
• To assess the utility of secondary calibrations in molecular clock analyses.

Main Methods:

• Simulated datasets to generate divergence time estimates using both primary and secondary calibrations.
• Statistical analysis to compare error rates and precision between calibration methods.
• Evaluation of predictability of inaccuracies associated with secondary calibrations.

Main Results:

• Inaccuracies from secondary calibrations are predictable and mirror primary calibration errors.
• Error rates for secondary calibrations are comparable to distant primary calibrations.
• Distant primary calibrations offer approximately twice the precision of secondary calibrations.

Conclusions:

• Secondary calibrations are a useful tool for molecular clock dating, especially when primary calibrations are limited.
• Their predictable error rates make them reliable for exploring evolutionary scenarios.
• Increasing dataset size with primary calibrations may yield similar accuracy but higher precision compared to secondary calibrations.