ArticleGenome biology and evolution2018
RelTime Relaxes the Strict Molecular Clock throughout the Phylogeny.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
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- The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites.Genome biology and evolution · 2024Article
- Phylogenomics of the psychoactive mushroom genusProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity.Science advances · 2023Article
- Molecular timetrees using relaxed clocks and uncertain phylogenies.Frontiers in bioinformatics · 2023Article
- Assessing the relative performance of fast molecular dating methods for phylogenomic data.BMC genomics · 2022Article
- Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating.Genome biology and evolution · 2021Article
- Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches.Molecular ecology resources · 2021Article
- Horizontal transmission and recombination maintain forever young bacterial symbiont genomes.PLoS genetics · 2020Article
- Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation.Genome biology and evolution · 2020Article
- Highlight: New Solutions and Open Questions in Computational Evolutionary Biology.Genome biology and evolution · 2019Article
- On estimating evolutionary probabilities of population variants.BMC evolutionary biology · 2019Article
- East African cichlid lineages (Teleostei: Cichlidae) might be older than their ancient host lakes: new divergence estimates for the east African cichlid radiation.BMC evolutionary biology · 2019Article
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5 authors.
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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.
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