Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds

Abstract

A limiting factor in many molecular dating studies is shortage of reliable calibrations. Current methods for choosing calibrations (e.g. cross-validation) treat them as either correct or incorrect, whereas calibrations probably lie on a continuum from highly accurate to very poor. Bayesian relaxed clock analysis permits inclusion of numerous candidate calibrations as priors: provided most calibrations are reliable, the model appropriate and the data informative, the accuracy of each calibration prior can be evaluated. If a calibration is accurate, then the analysis will support the prior so that the posterior estimate reflects the prior; if a calibration is poor, the posterior will be forced away from the prior. We use this approach to test two fossil dates recently proposed as standard calibrations within vertebrates. The proposed bird-crocodile calibration (approx. 247Myr ago) appears to be accurate, but the proposed bird-lizard calibration (approx. 255Myr ago) is substantially too recent.

Figure 1

Consensus ultrametric tree obtained using combined data and lognormal priors. Left hand node bars indicate prior distributions; right hand node bars, posterior distributions (95% HPD). Time-scale in millions of years.

Figure 2

Consensus ultrametric tree obtained using combined data with hard uniform bounds for all calibrations. Time-scale in millions of years. Thickness of each branch proportional to rate of evolution in substitutions per site per Myr (based on 10 000 post-burnin trees filtered for topological concordance).