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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In Bayesian treatments of the relaxed clock, rates are either assigned to branches or to nodes.
“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]
The Hierarchical Model of Rate Evolution defines rates on the branches of the rooted tree and treats node times as separate variables. The Rate Proposal Steps likewise propose a new rate for each branch. This contradicts the node-assigned rates attributed to this paper by the citation attached to “nodes.” (LLM, conf=0.89)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredAssigning 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.
“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]
In “Multivariate Normal Approximation” (page unavailable), the paper says its implementation assumes the topology relating the sequences is known before estimating divergence times. This supports the fixed-tree limitation for this implementation, but not the broader assertion that assigning a node age is only possible under that assumption. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe model permits independent gain and loss of conservation on multiple lineages and encourages nearby branches to have the same state and substitution rate, which is reasonable for closely related species and branches in a phylogeny.
“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
The Hierarchical Model of Rate Evolution section allows rates to differ among branches and models autocorrelation between ancestral and descendant branch rates. It does not model conservation states or independent gains and losses of conservation. The Discussion and Conclusions section also says widely used phylogeny-reconstruction methods ignore the potential information from rate autocorrelation, rather than establishing it as a common assumption. (LLM, conf=0.88)
Experimental — accuracy not yet measuredIntermediate models employing relaxed molecular clocks have been described.
“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]
Bayesian relaxed-clock methods model the molecular rate among lineages as varying in an autocorrelated manner, with the rate in each branch drawn a priori from a parametric distribution whose mean is a function of the rate on the parent branch.
“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]
The molecular clock assumption can be relaxed in a variety of ways.
“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]
The first relaxed-clock model described assigned rates to the midpoints of branches and used an assumed lognormal prior distribution relating the midpoint of the ancestral branch to the midpoint of the derived branch.
“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]
In the autocorrelated relaxed-clock models that have been described, including the commonly used lognormal model, it is necessary to specify the degree of autocorrelation as a prior.
“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]
Thorne, Kishino, and Painter and Aris-Brosou and Yang implemented parametric models in which the descendant rate is a priori related to the parent rate.
“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
The relaxed clock approach retrieves the true divergence times when substitution rates are distributed according to the autocorrelated-rate model developed by Thorne et al.
“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]
Protein evolution is not homogeneous.
“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]
Different sites and lineages accumulate substitutions at different rates.
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Gelman, A., Carlin, J. B., Stern, H. S., Dunson, D. B., Vehtari, A., & Rubin, D. B. (2013) · doi:10.1201/b16018 · Cited by 27,276 · see citing works
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 · see citing works
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571 · see citing works
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 · see citing works
The Neutral Theory of Molecular Evolution
Kimura, M. (1979) · Scientific American · doi:10.1038/scientificamerican1179-98 · Cited by 7,698 · see citing works
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 6,916 · see citing works
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 · see citing works
Kendall's Advanced Theory of Statistics.
Aa, Stuart, A., & Ord, K. (1995) · Journal of the American Statistical Association · doi:10.2307/2291187 · Cited by 2,657 · see citing works
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 · see citing works
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 · see citing works
Huber, P. J. (1997) · Springer series in statistics · doi:10.1007/978-1-4612-0667-5_6 · Cited by 1,556 · see citing works
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method
Yang, Z., & Rannala, B. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025811 · Cited by 1,274 · see citing works
The causes of molecular evolution
Gillespie, J. H. (1992) · Choice Reviews Online · doi:10.5860/choice.30-2064 · Cited by 1,244 · see citing works
A 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 · see citing works
Simple methods for testing the molecular evolutionary clock hypothesis.
Tajima, F. (1993) · Genetics · doi:10.1093/genetics/135.2.599 · Cited by 948 · see citing works
Evidence for higher rates of nucleotide substitution in rodents than in man.
Wu, C., & Li, W. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.6.1741 · Cited by 926 · see citing works
An examination of the constancy of the rate of molecular evolution
Langley, C. H., & Fitch, W. M. (1974) · Journal of Molecular Evolution · doi:10.1007/bf01797451 · Cited by 474 · see citing works
Relative rates of nucleotide substitution at the rbcl locus of monocotyledonous plants
Gaut, B. S., Muse, S. V., Clark, W. D., & Clegg, M. T. (1992) · Journal of Molecular Evolution · doi:10.1007/bf00161167 · Cited by 284 · see citing works
Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution
Goldman, N., Thorne, J. L., & Jones, D. T. (1998) · Genetics · doi:10.1093/genetics/149.1.445 · Cited by 281 · see citing works
Self-citationPhylogenetic Inference for Binary Data on Dendograms Using Markov Chain Monte Carlo
Mau, B., & Newton, M. A. (1997) · Journal of Computational and Graphical Statistics · doi:10.1080/10618600.1997.10474731 · Cited by 177 · see citing works
Very slightly deleterious mutations and the molecular clock
Ohta, T. (1987) · Journal of Molecular Evolution · doi:10.1007/bf02111276 · Cited by 101 · see citing works
Allison, L., & Wallace, C. S. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160274 · Cited by 38 · see citing works
Estimating times of divergence with a change of rate: the orangutan/African ape divergence
Penny, D., Murray‐McIntosh, R. P., & Hendy, M. D. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025962 · Cited by 11 · see citing works
Flagged first, then by citations
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 · see citing works
BEAST: Bayesian evolutionary analysis by sampling trees
Drummond, A. J., & Rambaut, A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-214 · Cited by 12,898 · see citing works
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 · see citing works
“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 · see citing works
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 · see citing works
Clarridge, J. E. (2004) · Clinical Microbiology Reviews · doi:10.1128/cmr.17.4.840-862.2004 · Cited by 2,198 · see citing works
Sanderson, M. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003974 · Cited by 1,977 · see citing works
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906 · see citing works
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
Lartillot, N., Lepage, T., & Blanquart, S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp368 · Cited by 1,297 · see citing works
TimeTree: A public knowledge-base of divergence times among organisms
Hedges, S. B., Dudley, J., & Kumar, S. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl505 · Cited by 1,234 · see citing works
TreeTime: Maximum-likelihood phylodynamic analysis
Sagulenko, P., Puller, V., & Neher, R. A. (2017) · Virus Evolution · doi:10.1093/ve/vex042 · Cited by 1,201 · see citing works
Computational Molecular Evolution
Yang, Z. (2006) · doi:10.1093/acprof:oso/9780198567028.001.0001 · Cited by 1,143 · see citing works
Ho, S., Phillips, M., Cooper, A., & Drummond, A. (2005) · Molecular biology and evolution · doi:10.1093/molbev/msi145 · Cited by 1,065 · see citing works
Drummond, A. J., Nicholls, G. K., Rodrigo, A. G., & Solomon, W. (2002) · Genetics · doi:10.1093/genetics/161.3.1307 · Cited by 1,059 · see citing works
Timing the ancestor of the HIV-1 pandemic strains.
Korber, B., Muldoon, M., Theiler, J., Gao, F., Gupta, R., Lapedes, A., Hahn, B. H., Wolinsky, S., & Bhattacharya, T. (2000) · Science · doi:10.1126/science.288.5472.1789 · Cited by 1,021 · see citing works
Divergence time and evolutionary rate estimation with multilocus data.
Thorne, J. L., & Kishino, H. (2002) · Systematic Biology · doi:10.1080/10635150290102456 · Cited by 962 · see citing works
Self-citationThe timescale of early land plant evolution
Morris, J. L., Puttick, M. N., Clark, J., Edwards, D., Kenrick, P., Pressel, S., Wellman, C. H., Yang, Z., Schneider, H., & Donoghue, P. C. J. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1719588115 · Cited by 926 · see citing works
The fossilized birth-death process for coherent calibration of divergence-time estimates
Heath, T. A., Huelsenbeck, J. P., & Stadler, T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319091111 · Cited by 834 · see citing works
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
Ronquist, F., Klopfstein, S., Vilhelmsen, L., Schulmeister, S., Murray, D. L., & Rasnitsyn, A. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys058 · Cited by 930 · see citing works
Yang, Z., & Rannala, B. H. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj024 · Cited by 904 · see citing works
Accounting 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 879 · see citing works
Placental mammal diversification and the Cretaceous–Tertiary boundary
Springer, M. S., Murphy, W. J., Eduardo Eizirik, C., & O’Brien, S. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0334222100 · Cited by 837 · see citing works
Höhna, S., Landis, M. J., Heath, T. A., Boussau, B., Lartillot, N., Moore, B. R., Huelsenbeck, J. P., & Ronquist, F. (2016) · Systematic Biology · doi:10.1093/sysbio/syw021 · Cited by 815 · see citing works
The age and diversification of the angiosperms re‐revisited
Bell, C. D., Soltis, P. S., & Soltis, P. S. (2010) · American Journal of Botany · doi:10.3732/ajb.0900346 · Cited by 824 · see citing works
Potential Applications and Pitfalls of Bayesian Inference of Phylogeny
Huelsenbeck, J. P., Larget, B. R., Miller, R. E., & Ronquist, F. (2002) · Systematic Biology · doi:10.1080/10635150290102366 · Cited by 811 · see citing works
Bayesian Selection of Continuous-Time Markov Chain Evolutionary Models
Suchard, M. A., Weiss, R. E., & Sinsheimer, J. S. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003872 · Cited by 791 · see citing works
The origin and evolution of model organisms
Hedges, S. B. (2002) · Nature Reviews Genetics · doi:10.1038/nrg929 · Cited by 806 · see citing works
Testing macro–evolutionary models using incomplete molecular phylogenies
Pybus, O. G., & Harvey, P. (2000) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2000.1278 · Cited by 802 · see citing works
Best Practices for Justifying Fossil Calibrations
Parham, J. F., Donoghue, P. C. J., Bell, C. J., Calway, T. D., Head, J. J., Holroyd, P. A., Inoue, J. G., Irmis, R. B., Joyce, W. G., Ksepka, D. T., et al. (2012) · Systematic Biology · doi:10.1093/sysbio/syr107 · Cited by 780 · see citing works
Molecular phylogenetics: principles and practice
Yang, Z., & Rannala, B. H. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3186 · Cited by 762 · see citing works
Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics
Minin, V. N., Bloomquist, E. W., & Suchard, M. A. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn090 · Cited by 680 · see citing works
Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time
Lemey, P., Rambaut, A., Welch, J. J., & Suchard, M. A. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq067 · Cited by 688 · see citing works
Estimating divergence times in large molecular phylogenies
Tamura, K., Battistuzzi, F. U., Billing-Ross, P., Murillo, O. D., Filipski, A., & Kumar, S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1213199109 · Cited by 660 · see citing works
Performance of a divergence time estimation method under a probabilistic model of rate evolution.
Kishino, H., Thorne, J. L., & Bruno, W. J. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003811 · Cited by 633 · see citing works
Self-citationSimon, C., Buckley, T. R., Frati, F., Stewart, J. B., & Beckenbach, A. T. (2006) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev.ecolsys.37.091305.110018 · Cited by 644 · see citing works
The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
Douzery, E. J. P., Snell, E. A., Bapteste, E., Delsuc, F., & Philippe, H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403984101 · Cited by 638 · see citing works
Phylogeny estimation: traditional and Bayesian approaches
Holder, M. T., & Lewis, P. O. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1044 · Cited by 631 · see citing works
EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES
Rabosky, D. L. (2009) · Evolution · doi:10.1111/j.1558-5646.2009.00926.x · Cited by 595 · see citing works
A general comparison of relaxed molecular clock models
Lepage, T., Bryant, D., Philippe, H., & Lartillot, N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm193 · Cited by 546 · see citing works
Battistuzzi, F. U., Feijao, A., & Hedges, S. B. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-44 · Cited by 581 · see citing works
Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales
Arbogast, B. S., Edwards, S. V., Wakeley, J., Beerli, P., & Slowinski, J. B. (2002) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.33.010802.150500 · Cited by 568 · see citing works
LIVEZEY, B. C., & ZUSI, R. L. (2007) · Zoological Journal of the Linnean Society · doi:10.1111/j.1096-3642.2006.00293.x · Cited by 574 · see citing works
Basidiomycete yeasts in the cortex of ascomycete macrolichens
Spribille, T., Tuovinen, V., Resl, P., Vanderpool, D., Wolinski, H., Aime, M. C., Schneider, K. L., Stabentheiner, E., Toome‐Heller, M., Thor, G., et al. (2016) · Science · doi:10.1126/science.aaf8287 · Cited by 566 · see citing works
dos Reis, M., Inoue, J., Hasegawa, M., Asher, R. J., Donoghue, P. C. J., & Yang, Z. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.0683 · Cited by 526 · see citing works
Taxon sampling and the accuracy of phylogenetic analyses
(2008) · Journal of Systematics and Evolution · doi:10.3724/sp.j.1002.2008.08016 · Cited by 553 · see citing works
Contemporaneous and recent radiations of the world's major succulent plant lineages
Arakaki, M., Christin, P., Nyffeler, R., Lendel, A., Eggli, U., Ogburn, R. M., Spriggs, E. L., Moore, M. J., & Edwards, E. J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1100628108 · Cited by 533 · see citing works
Bayesian Evolutionary Analysis with BEAST
Drummond, A. J., & Bouckaert, R. (2015) · Cambridge University Press eBooks · doi:10.1017/cbo9781139095112 · Cited by 518 · see citing works
Evolution and metabolic significance of the urea cycle in photosynthetic diatoms
Allen, A. E., Dupont, C. L., Obornı́k, M., Horák, A., Nunes‐Nesi, A., McCrow, J. P., Zheng, H., Johnson, D. A., Hu, H., Fernie, A. R., et al. (2011) · Nature · doi:10.1038/nature10074 · Cited by 518 · see citing works
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales
dos Reis, M., Thawornwattana, Y., Angelis, K., Telford, M. J., Donoghue, P. C. J., & Yang, Z. (2015) · Current Biology · doi:10.1016/j.cub.2015.09.066 · Cited by 471 · see citing works
Estimation of primate speciation dates using local molecular clocks.
Yoder, A. D., & Yang, Z. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026389 · Cited by 494 · see citing works
Yoder, A. D., & Nowak, M. D. (2006) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev.ecolsys.37.091305.110239 · Cited by 512 · see citing works
Inferring speciation times under an episodic molecular clock
Rannala, B., & Yang, Z. (2007) · Systematic Biology · doi:10.1080/10635150701420643 · Cited by 475 · see citing works
Recently formed polyploid plants diversify at lower rates
Mayrose, I., Zhan, S. H., Rothfels, C. J., Magnuson-Ford, K., Barker, M. S., Rieseberg, L. H., & Otto, S. P. (2011) · Science · doi:10.1126/science.1207205 · Cited by 489 · see citing works
Strong Variations of Mitochondrial Mutation Rate across Mammals--the Longevity Hypothesis
Nabholz, B., Glémin, S., & Galtier, N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm248 · Cited by 482 · see citing works
Skyline‐plot methods for estimating demographic history from nucleotide sequences
Ho, S. Y. W., & Shapiro, B. (2011) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2011.02988.x · Cited by 482 · see citing works
Vidal, N., & Hedges, S. B. (2005) · Comptes Rendus Biologies · doi:10.1016/j.crvi.2005.10.001 · Cited by 462 · see citing works
Total-Evidence Dating under the Fossilized Birth–Death Process
Zhang, C., Stadler, T., Klopfstein, S., Heath, T. A., & Ronquist, F. (2016) · Systematic Biology · doi:10.1093/sysbio/syv080 · Cited by 419 · see citing works
Rosid radiation and the rapid rise of angiosperm-dominated forests
Wang, H., Moore, M. J., Soltis, P. S., Bell, C. D., Brockington, S. F., Alexandre, R., Davis, C. “., Latvis, M., Manchester, S. R., & Soltis, P. S. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0813376106 · Cited by 442 · see citing works
Vanneste, K., Baele, G., Maere, S., & de Peer, Y. V. (2014) · Genome Research · doi:10.1101/gr.168997.113 · Cited by 438 · see citing works
Fast Dating Using Least-Squares Criteria and Algorithms
To, T., Jung, M., Lycett, S., & Gascuel, O. (2015) · Systematic Biology · doi:10.1093/sysbio/syv068 · Cited by 415 · see citing works
Bayesian random local clocks, or one rate to rule them all
Drummond, A. J., & Suchard, M. A. (2010) · BMC Biology · doi:10.1186/1741-7007-8-114 · Cited by 429 · see citing works
Gaunt, M. W., & Miles, M. A. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004133 · Cited by 435 · see citing works
Using genomic data to unravel the root of the placental mammal phylogenyPreprint
Murphy, W. J., Pringle, T. H., Crider, T. A., Springer, M. S., & Miller, W. (2007) · Genome Research · doi:10.1101/gr.5918807 · Cited by 436 · see citing works
Barraclough, T. G., & Nee, S. (2001) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(01)02161-9 · Cited by 431 · see citing works
Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times
dos Reis, M., & Yang, Z. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr045 · Cited by 431 · see citing works
Sauquet, H., Ho, S. Y. W., Gandolfo, M. A., Jordan, G. J., Wilf, P., Cantrill, D. J., Bayly, M. J., Bromham, L. D., Brown, G. K., Carpenter, R. J., et al. (2011) · Systematic Biology · doi:10.1093/sysbio/syr116 · Cited by 425 · see citing works
Rocks and clocks: calibrating the Tree of Life using fossils and molecules
Donoghue, P. C. J., & Benton, M. J. (2007) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2007.05.005 · Cited by 413 · see citing works
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
du Plessis, L., McCrone, J. T., Zarebski, A. E., Hill, V., Ruis, C., Gutiérrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T. R., et al. (2021) · Science · doi:10.1126/science.abf2946 · Cited by 408 · see citing works
Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia
Pyron, R. A. (2011) · Systematic Biology · doi:10.1093/sysbio/syr047 · Cited by 419 · see citing works
Molecular clocks: four decades of evolution
Kumar, S. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1659 · Cited by 405 · see citing works
Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins
Gavryushkina, A., Heath, T. A., Ksepka, D. T., Stadler, T., Welch, D., & Drummond, A. J. (2016) · Systematic Biology · doi:10.1093/sysbio/syw060 · Cited by 372 · see citing works
Molecular clocks: when timesare a-changin'
HO, S., & LARSON, G. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.11.006 · Cited by 402 · see citing works
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
Gavryushkina, A. “., Welch, D., Stadler, T., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003919 · Cited by 365 · see citing works
Raaum, R. L., Sterner, K. N., Noviello, C., Stewart, C.-B., & Disotell, T. R. (2005) · Journal of Human Evolution · doi:10.1016/j.jhevol.2004.11.007 · Cited by 377 · see citing works
Calibrating molecular estimates of substitution rates and divergence times in birds
Ho, S. Y. M. (2007) · Journal of Avian Biology · doi:10.1111/j.0908-8857.2007.04168.x · Cited by 372 · see citing works
Bayesian molecular clock dating of species divergences in the genomics era
dos Reis, M., Donoghue, P. C. J., & Yang, Z. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.8 · Cited by 339 · see citing works
The genetic basis of a plant–insect coevolutionary key innovation
Wheat, C. W., Vogel, H., Wittstock, U., Braby, M. F., Underwood, D. L. A., & Mitchell‐Olds, T. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706229104 · Cited by 364 · see citing works
Molecular‐clock methods for estimating evolutionary rates and timescales
Ho, S. Y. W., & Duchêne, S. (2014) · Molecular Ecology · doi:10.1111/mec.12953 · Cited by 362 · see citing works
The importance of proper model assumption in bayesian phylogenetics.
Lemmon, A. R., & Moriarty, E. C. (2004) · Systematic Biology · doi:10.1080/10635150490423520 · Cited by 356 · see citing works
Couch, B. C., Fudal, I., Lebrun, M., Tharreau, D., Valent, B. S., Kim, P. V., Nottéghem, J., & Kohn, L. M. (2005) · Genetics · doi:10.1534/genetics.105.041780 · Cited by 361 · see citing works
Yang, Z., & Yoder, A. D. (2003) · Systematic Biology · doi:10.1080/10635150390235557 · Cited by 357 · see citing works
Lin, C., & Danforth, B. N. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00241-0 · Cited by 353 · see citing works
Establishing a time‐scale for plant evolution
Clarke, J. T., Warnock, R. C. M., & Donoghue, P. C. J. (2011) · New Phytologist · doi:10.1111/j.1469-8137.2011.03794.x · Cited by 353 · see citing works
A Compound Poisson Process for Relaxing the Molecular Clock
Huelsenbeck, J. P., Larget, B. R., & Swofford, D. L. (2000) · Genetics · doi:10.1093/genetics/154.4.1879 · Cited by 345 · see citing works
Primate molecular divergence dates
Steiper, M. E., & Young, N. M. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.05.021 · Cited by 336 · see citing works
Poux, C., Madsen, O., Marquard, E., Vieites, D. R., JONG, W. W. D., & Miguel Vences, B. (2005) · Systematic Biology · doi:10.1080/10635150500234534 · Cited by 339 · see citing works
Huchon, D., Madsen, O., Sibbald, M. J. J. B., Ament, K., Stanhope, M. J., Catzeflis, F. M., JONG, W. W. D., & Douzery, E. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004164 · Cited by 336 · see citing works
Silberfeld, T., Leigh, J., Verbruggen, H., Cruaud, C., de Reviers, B., & Rousseau, F. (2010) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2010.04.020 · Cited by 332 · see citing works
Schaefer, H., Heibl, C., & Renner, S. S. (2008) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2008.1447 · Cited by 328 · see citing works
Phylogenetic systematics turns over a new leaf
Lewis, P. O. (2001) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(00)02025-5 · Cited by 320 · see citing works
Early photosynthetic eukaryotes inhabited low-salinity habitats
Sánchez‐Baracaldo, P., Raven, J. A., Pisani, D., & Knoll, A. H. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620089114 · Cited by 319 · see citing works
Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals
Feuda, R., Dohrmann, M., Pett, W., Philippe, H., Rota-Stabelli, O., Lartillot, N., Wörheide, G., & Pisani, D. (2017) · Current Biology · doi:10.1016/j.cub.2017.11.008 · Cited by 291 · see citing works
The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates
Soubrier, J., Steel, M., Lee, M. S. Y., Sarkissian, C. S. I. D., Guindon, S., Ho, S. Y. W., & Cooper, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss140 · Cited by 316 · see citing works
Peterson, K. J., Cotton, J. A., Gehling, J. G., & Pisani, D. (2008) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2007.2233 · Cited by 313 · see citing works
Yoder, A. D., & Yang, Z. (2004) · Molecular Ecology · doi:10.1046/j.1365-294x.2004.02106.x · Cited by 313 · see citing works
BLANK, C. E., & SÁNCHEZ‐BARACALDO, P. (2010) · Geobiology · doi:10.1111/j.1472-4669.2009.00220.x · Cited by 298 · see citing works
Using MODELTEST and PAUP * to Select a Model of Nucleotide Substitution
Posada, D. (2003) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0605s00 · Cited by 306 · see citing works
Estimating the phylogeny and divergence times of primates using a supermatrix approach
Chatterjee, H. J., Ho, S. Y. W., Barnes, I., & Groves, C. P. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-259 · Cited by 305 · see citing works
Complexity of avian evolution revealed by family-level genomes
Stiller, J., Feng, S., Chowdhury, A.-A., Rivas-González, I., Duchêne, D. A., Fang, Q., Deng, Y., Kozlov, A. M., Stamatakis, A., Claramunt, S., et al. (2024) · Nature · doi:10.1038/s41586-024-07323-1 · Cited by 307 · see citing works
Molecular evidence on plant divergence times
Sanderson, M. J., Thorne, J. L., Wikström, N., & Bremer, K. (2004) · American Journal of Botany · doi:10.3732/ajb.91.10.1656 · Cited by 295 · see citing works
Self-citation
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
