We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times.
Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation.
The benchmarks for determining the mutation rate are often fossil or archaeological dates.
The molecular clock was first tested in 1962 on the haemoglobin protein variants of various animals, and is commonly used in molecular evolution to estimate times of speciation or radiation.
We illustrate the method's utility on three example data sets involving mammal, primate and influenza evolution.
Finally, we explore methods to visualize the complex posterior distribution that results from inference under such models.
Published shallow phylogenies (Black bass, Primate-sucking lice, 0.1 (95% of rates fall within 0.0082-0.0121 subs/site/Ma when σ = 0.1, for a mean rate of 0.01).