The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
Estimating the rate of evolution of the rate of molecular evolution
Open accessAbstract
A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.
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“To convert this tree from units of time to molecular evolutionary units, the rates are either assigned to branches [ 15, 17] or to nodes [ 53, 54].”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
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Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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“Assigning an age to a particular node is only possible when the tree itself is assumed to be known and fixed, a limitation of previous relaxed-clock implementations [ 15, 17, 54].”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Such a model permits independent gain and loss of conservation on multiple lineages and also encourages nearby branches to have the same state and substitution rate, which is reasonable for closely related species and branches in a phylogeny and is also a common assumption in phylogenetics”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Thorne et al. 1998
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In the citing paper
“Recently, it has been realized that less drastic alternatives to the unrooted model of phylogeny may exist. Instead of dispensing with the molecular clock entirely, attempts have been made to relax the molecular clock assumption by allowing the rate to vary across the tree [ 13– 15].”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
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In the citing paper
“These model the molecular rate among lineages as varying in an autocorrelated manner, with the rate in each branch being drawn (a priori) from a parametric distribution whose mean is a function of the rate on the parent branch.”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
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“The molecular clock assumption can be relaxed in a variety of ways [ 13– 15, 17, 49– 52].”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
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In the citing paper
“The first such model to be described [ 15] assigned rates to the midpoints of branches and the assumed lognormal prior distribution relating the midpoint of the ancestral branch to the midpoint of the derived branch.”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
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“In the autocorrelated relaxed-clock models that have been described, including the commonly used lognormal model [ 15, 17, 55], it is also necessary to specify the degree of autocorrelation as a prior.”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
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“Thorne, Kishino, and Painter (1998) and Aris-Brosou and Yang (2002) implemented parametric models in which the rate in a given branch (the descendant rate) is a priori related to the rate in the branch immediately ancestral to it (the parent rate).”
From Accuracy of Rate Estimation Using Relaxed-Clock Models with a Critical Focus on the Early Metazoan Radiation (2005) · cites this paper as Thorne, Kishino, and Painter 1998
In the citing paper
“Moreover, the relaxed clock approach retrieves the true divergence times (Table 1) when substitution rates are distributed according to the autocorrelated-rate model developed by Thorne et al. (32).”
From The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? (2004) · cites this paper as [32]
In the citing paper
“However, protein evolution is not homogeneous.”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [68]
In the citing paper
“Different sites and lineages accumulate substitutions at different rates (e.g., [67-69])”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [68]
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Citations
Cites
Gelman, A., Carlin, J. B., Stern, H. S., & Rubin, D. B. (2003) · doi:10.1201/9780429258480 · Cited by 27,276
Monte Carlo sampling methods using Markov chains and their applications.
Hastings, W. K. (1970) · Biometrika · doi:10.1093/biomet/57.1.97 · Cited by 15,195
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
The Neutral Theory of Molecular Evolution
Kimura, M. (1979) · Scientific American · doi:10.1038/scientificamerican1179-98 · Cited by 7,687
The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 7,003
Evolutionary divergence and convergence in proteins.
ZUCKERKANDL, E., & PAULING, L. (1965) · Evolving Genes and Proteins · doi:10.1016/b978-1-4832-2734-4.50017-6 · Cited by 3,020
Kendall's Advanced Theory of Statistics.
Aa, Stuart, A., & Ord, K. (1995) · Journal of the American Statistical Association · doi:10.2307/2291187 · Cited by 2,663
Bayes and Empirical Bayes Methods for Data Analysis
Carlin, B. P., & Louis, T. A. (2001) · Technometrics · doi:10.1198/tech.2001.s608 · Cited by 2,110
Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference
Rannala, B. H., & Yang, Z. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02338839 · Cited by 1,751
Research works printed but not linked: 1
- [8]8. KARLIN, S., and H. M. TAYLOR. 1975. A first course in sto- chastic processes. 2nd edition. Academic Press, San Diego.
Cited by
Sorted by citations
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879
“This is similar to the MULTIDIVTIME program (Thorne, Kishino, and Painter 1998; Kishino, Thorne, and Bruno 2001) and can be used to analyze data of multiple gene loci, incorporating multiple fossil calibrations and allowing the evolutionary rate to drift over time.”
MethodBEAST: Bayesian evolutionary analysis by sampling trees
Drummond, A. J., & Rambaut, A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-214 · Cited by 13,104
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
“For models that assign rates to nodes, it is necessary to treat the root node in a special way, as it does not have a parent node [15].”
BackgroundMethodInfluentialPhylogenies and Community Ecology
Webb, C. O., Ackerly, D. D., McPeek, M. A., & Donoghue, M. J. (2002) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.33.010802.150448 · Cited by 4,559
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
Huelsenbeck, J. P., Ronquist, F., Nielsen, R., & Bollback, J. P. (2001) · Science · doi:10.1126/science.1065889 · Cited by 2,737
Metadata
- Authors
- Thorne, J. L., Kishino, H., & Painter, I. S.
- Affiliations
- North Carolina State University (US)
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 1998-12-01
- Volume
- 15
- Issue
- 12
- Pages
- 1647-1657
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2051296828
- Cited by
- 1,317
- References
- 23
- Citations by year
- 2026: 20 · 2025: 19 · 2024: 29 · 2023: 32 · 2022: 27 · 2021: 28 · 2020: 48 · 2019: 41 · 2018: 27 · 2017: 29 · 2016: 35 · 2015: 43 · 2014: 68 · 2013: 46 · 2012: 63
- FWCI
- 4.54
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (P01-GM45344, P01GM045344)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- molecular evolution rate, rate heterogeneity, Bayesian model, divergence time estimation, nucleotide substitution models, rbcL, protein sequences, molecular clock
- MeSH terms
- Algorithms, Biological Evolution, Models, Genetic, Phylogeny, Plant Proteins, Plants, Ribulose-Bisphosphate Carboxylase, Time, Models, Statistical, Evolution, Molecular
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