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Genome Biol Evol. 2018 Jun 1;10(6):1631-1636. doi: 10.1093/gbe/evy118.

RelTime Relaxes the Strict Molecular Clock throughout the Phylogeny.

Author information

1
Department of Biological Sciences, Oakland University.
2
Center for Data Science and Big Data Analytics, Oakland University.
3
Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia.
4
Department of Biology, Temple University, Philadelphia.
5
Department of Biological Sciences, Tokyo Metropolitan University, Japan.
6
Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Japan.
7
Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia.

Abstract

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.

PMID:
29878203
PMCID:
PMC6022624
DOI:
10.1093/gbe/evy118
[Indexed for MEDLINE]
Free PMC Article

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