RelTime Relaxes the Strict Molecular Clock throughout the Phylogeny

Area of Science:

• Evolutionary Biology
• Molecular Phylogenetics
• Computational Biology

Background:

• The RelTime method estimates divergence times in phylogenies with lineage-specific evolutionary rate variation.
• Previous studies suggested RelTime might impose a strict molecular clock on deep divergences, a claim this study addresses.

Purpose of the Study:

• To clarify that RelTime does not impose a strict molecular clock.
• To explain the observation of equal rates in previous analyses.
• To compare RelTime divergence estimates with Bayesian methods.

Main Methods:

• Theoretical analyses of the RelTime method.
• Application of RelTime to empirical and simulated datasets with variable evolutionary rates.
• Comparison of RelTime estimates with Bayesian divergence time estimates using different root priors.

Main Results:

• RelTime successfully relaxes the strict molecular clock assumption for varying evolutionary rates.
• Observed rate equality in prior studies was due to a specific RelTime option for statistically non-significant rate differences.
• Bayesian divergence time estimates are sensitive to root priors, with less restrictive priors yielding results concordant with RelTime.

Conclusions:

• RelTime is a robust method for estimating divergence times under relaxed molecular clock conditions.
• The perceived imposition of a strict clock by RelTime was a misinterpretation of its statistical options.
• Careful consideration of root priors is essential for reliable Bayesian divergence time estimation and method comparison.