Journal
GENOME BIOLOGY AND EVOLUTION
Volume 10, Issue 6, Pages 1631-1636Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evy118
Keywords
molecular clocks; phylogenomics; RelTime
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Funding
- National Aeronautics and Space Administration [NNX16AJ30G]
- National Science Foundation [1661218]
- National Institutes of Health [GM012487]
- Tokyo Metropolitan University [DB105]
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1661218] Funding Source: National Science Foundation
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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 in which evolutionary rates are variable. Lozano-Fernandez et al. (2017) found that the application of RelTime to one metazoan data set (Erwin et al. 2011) produced equal rates for several ancient lineages, which led them to 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 difference was 5% for many deep metazoan lineages for the Erwin et al. (2011) data set, so the rate equality was not rejected. In fact, RelTime analyses with and without the option to test rate differences produced very similar time estimates. We also found that the Bayesian time estimates vary widely 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.
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