RelTime relaxes the strict molecular clock throughout the phylogeny

Abstract

© The Author(s) 2018. The RelTime method estimates divergence times when evolutionary rates vary among lineages. Theoretical analyses show that RelTime relaxes the strict molecular clock throughout a molecular phylogeny, and it performs well in the analyses of empirical and computer simulated data sets inwhich evolutionary rates are variable. Lozano-Fernandez et al. (2017) found that the application of RelTime to onemetazoan data set (Erwin et al. 2011) produced equal rates for several ancient lineages, which led themto speculate that RelTime imposes a strict molecular clock for deep animal divergences. RelTime does not impose a strict molecular clock. The pattern observed by Lozano-Fernandez et al. (2017)was a result of the use of an option to assign the same rate to lineages in RelTime when the rates are not statistically significantly different. The median rate differencewas 5% for many deep metazoan lineages for the Erwin et al. (2011) data set, so the rate equalitywas not rejected. In fact, RelTime analyseswith andwithout the option to test rate differences produced very similar time estimates.We also found that the Bayesian time estimates varywidely depending on the root priors assigned, and that the use of less restrictive priors produces Bayesian divergence times that are concordant with those from RelTime for the Erwin et al. (2011) data set. Therefore, it is prudent to discuss Bayesian estimates obtained under a range of priors in any discourse about molecular dating, including method comparisons.