The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.
Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates
Open accessAbstract
RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.
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Citations
Cites
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst197 · Cited by 47,205
Self-citationMEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
Kumar, S., Stecher, G., & Tamura, K. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw054 · Cited by 44,059
Self-citationPAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463 · cited 2×
“2001), the independent rate (IR) model (Drummond et al. 2006), as well as a model that contains multiple distributions of rates (hybrid rates [HR]).”
BackgroundMethodSanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906
Rambaut, A., & Grass, N. C. (1997) · Bioinformatics · doi:10.1093/bioinformatics/13.3.235 · Cited by 1,574
Estimating the rate of evolution of the rate of molecular evolution
Thorne, J. L., Kishino, H., & Painter, I. S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025892 · Cited by 1,317 · cited 5×
“This is, however, different from the autocorrelation rate model of Thorne et al. (1998) in which ancestral and descendant branch rates are autocorrelated throughout the tree.”
BackgroundMethodInfluentialA nonparametric approach to estimating divergence times in the absence of rate constancy.
Sanderson, M. J. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025731 · Cited by 1,156 · cited 1×
“RRF is also different from non-parametric and semi-parametric approaches based on the idea of Sanderson (1997), because RRF minimizes lineage rate changes rather than branch rate changes and RRF does not attempt to estimate a universal penalty for how quickly rates change throughout the tree.”
MethodAccounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times
Ho, S. Y. W., & Phillips, M. J. (2009) · Systematic Biology · doi:10.1093/sysbio/syp035 · Cited by 887
Metadata
- Authors
- Tamura, K., Tao, Q., & Kumar, S.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-03-20
- Volume
- 35
- Issue
- 7
- Pages
- 1770-1782
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2949972517
- Cited by
- 258
- References
- 54
- FWCI
- 5.81
- Type
- journal article
- Language
- en
- Open access
- hybrid
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