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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.
In the citing paper
“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
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
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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In the citing paper
“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 cited source says what the claim attributes to it.
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
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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
Clarridge, J. E. (2004) · Clinical Microbiology Reviews · doi:10.1128/cmr.17.4.840-862.2004 · Cited by 2,291
Sanderson, M. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003974 · Cited by 1,977
“The CV criterion proposed here provides an empirical method for comparing other recently proposed rate and time estimation procedures (Thorne, Kishino, and Painter 1998; Huelsenbeck, Larget, and Swofford 2000), which have mainly been evaluated on an absolute scale by simulation studies (Sanderson…”
BackgroundMethodSanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906
“This has prompted considerable work aimed at developing methods for estimating rates and times in the absence of a clock (Huelsenbeck et al. , 2000; Kishino et al. , 2001; Rambaut and Bromham, 1998; Sanderson, 1997, 2002; Takezaki et al. , 1995; Thorne et al. , 1998).”
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
“…been proposed, such as mixture models, accounting for site-specific effects (Huelsenbeck and Suchard, 2007; Lartillot and Philippe, 2004; Le et al., 2008a, b; Pagel and Meade, 2004; Wang et al., 2008), or flexible molecular clocks (Drummond et al., 2006; Lepage et al., 2007; Thorne et al., 1998).”
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
“In large part, this has been driven by the rapid increase in sequence data that have become available in recent years, as well as the development of methods that accommodate rate variation in estimating divergence times and their confidence intervals (Drummond, et al., 2006; Kumar, et al., 2005; Sanderson, 1997; Thorn…”
BackgroundTreeTime: Maximum-likelihood phylodynamic analysis
Sagulenko, P., Puller, V., & Neher, R. A. (2017) · Virus Evolution · doi:10.1093/ve/vex042 · Cited by 1,185
“These models typically regularize the clock-rate through a prior and penalize rapid changes of the rate by coupling the rate along branches – known as autocorrelated or local molecular clock (Aris-Brosou et al. , 2002; Thorne et al. , 1998).”
BackgroundComputational Molecular Evolution
Yang, Z. (2006) · doi:10.1093/acprof:oso/9780198567028.001.0001 · Cited by 1,152
Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times
Ho, S. Y. W., Phillips, M. J., Cooper, A., & Drummond, A. J. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi145 · Cited by 1,061
“Unlike previous relaxed-clock methods for rate estimation (Thorne, Kishino, and Painter 1998; Aris-Brosou and Yang 2002; Sanderson 2002), however, BEAST does not require a user-specified tree topology.”
MethodDrummond, A. J., Nicholls, G. K., Rodrigo, A. G., & Solomon, W. (2002) · Genetics · doi:10.1093/genetics/161.3.1307 · Cited by 1,059
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
Divergence time and evolutionary rate estimation with multilocus data.
Thorne, J. L., & Kishino, H. (2002) · Systematic Biology · doi:10.1080/10635150290102456 · Cited by 962
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
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
“0.5, 0.9) by simulating a continuous character for each fossil under a geometric Brownian-motion model. This model is identical to the autocorrelated log-normal model for relaxing the molecular clock [3, 7, 10, 11] and produces an autocorrelated sampling/preservation rate over the tree with closely related fossils ass…”
MethodInfluentialA 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
“…shown that the rate of molecular evolution varies significantly over time and among lineages, and it is now standard practice to accommodate such rate variation using relaxedclock models (Drummond et al. 2006; Lepage et al. 2007; Linder et al. 2011; Thorne et al. 1998; Thorne and Kishino 2002).”
BackgroundResultYang, Z., & Rannala, B. H. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj024 · Cited by 917
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 906
Placental mammal diversification and the Cretaceous–Tertiary boundary
Springer, M. S., Murphy, W. J., Eizirik, E., & O’Brien, S. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0334222100 · Cited by 846
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 840
“The rates could be drawn from an autocorrelated process (Thorne et al. 1998; Thorne and Kishino 2002), any type of independent-rates model (Drummond et al.”
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
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 808
The origin and evolution of model organisms
Hedges, S. B. (2002) · Nature Reviews Genetics · doi:10.1038/nrg929 · Cited by 806
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
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
“In doing so, we further the frameworks of Thorne, Kishino, and Painter (1998) and Huelsenbeck, Larget, and Swofford (2000) in several important ways.”
BackgroundMethodBest 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
“Most studies use a Bayesian framework for estimating divergence dates with probability curves between a minimum and a maximum bound to represent calibrations (time priors) (Thorne et al. 1998; Drummond et al. 2006; Yang 2006; Yang and Rannala 2006).”
BackgroundMolecular phylogenetics: principles and practice
Yang, Z., & Rannala, B. H. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3186 · Cited by 813
“Since the pioneering work of Thorne and colleagues 107,108 , models of evolutionary rate drift over time have been developed to relax the molecular clock 72,109 .”
BackgroundSmooth 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 695
“…a time-aware GMRF prior based on midpoint distances between intercoalescent intervals, d k 5 u k þ u k þ 1 2 : ð9Þ Midpoint distances have been successfully used before in molecular evolution by Thorne et al. (1998) to construct an autocorrelated prior for evolutionary rates on genealogy branches.”
MethodPhylogeography 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 687
“Autocorrelated relaxed clock models preceded uncorrelated relaxed clocks (Thorne et al. 1998) and are also available in BEAST.”
MethodEstimating 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 674
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
“The details of our MCMC implementation are somewhat tedious, and the general procedure has already been described (Thorne, Kishino, and Painter 1998).”
BackgroundMethodInfluentialSelf-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 648
“The methods based on explicit models, known as relaxed-clock models, used Bayesian estimation to obtain posterior distributions of node times (Aris-Brosou & Yang 2002, Thorne et al. 1998).”
MethodThe 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
Phylogeny estimation: traditional and Bayesian approaches
Holder, M. T., & Lewis, P. O. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1044 · Cited by 648
“Thorne et al.(37) and others have proposed methods of estimating the dates associated with branch points in a phylogenetic tree.”
BackgroundMethodEXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES
Rabosky, D. L. (2009) · Evolution · doi:10.1111/j.1558-5646.2009.00926.x · Cited by 600
“I refer to this model as a “relaxedrate” model of rate variation, analogous to relaxed-clock methods of modeling molecular evolutionary rate variation (Thorne et al. 1998; Drummond et al. 2006).”
MethodA 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
“the strict molecular clock, the log-normal (Kishino et al., 2001; Thorne et al., 1998 ), and the”
BackgroundMethodInfluentialBattistuzzi, F. U., Feijao, A., & Hedges, S. B. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-44 · Cited by 609
“All time estimates were calculated with a Bayesian local clock approach [97] utilizing concatenated data sets of multiple proteins and a JTT+gamma model of substitution [19,98,99].”
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 574
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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
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
“These sources of uncertainty were not adequately addressed in molecular clock studies that supported particularly ancient dates of placental diversification [5,16].”
Taxon sampling and the accuracy of phylogenetic analyses
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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 544
Bayesian Evolutionary Analysis with BEAST
Drummond, A. J., & Bouckaert, R. (2015) · Cambridge University Press eBooks · doi:10.1017/cbo9781139095112 · Cited by 526
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 536
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
“This relaxedclock model imposes a correlation of rates between ancestral and descendant branches by modeling rate change on the tree as a geometric Brownian diffusion process [53, 54].”
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
“Recent work has suggested the possibility of estimating dates without assuming a global molecular clock (Sanderson 1997; Rambaut and Bromham 1998; Thorne, Kishino, and Painter 1998; Huelsenbeck, Larget, and Swofford 2000).”
BackgroundMethodYoder, A. D., & Nowak, M. D. (2006) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev.ecolsys.37.091305.110239 · Cited by 512
“Using multiple gene loci and Bayesian divergence age analysis (Kishino et al. 2001, Thorne & Kishino 2002, Thorne et al. 1998), along with area cladogram analysis, this study concludes that these three taxa reside in Madagascar owing to a vicariant history (Noonan & Chippendale 2006).”
BackgroundInferring speciation times under an episodic molecular clock
Rannala, B., & Yang, Z. (2007) · Systematic Biology · doi:10.1080/10635150701420643 · Cited by 475
“The general framework has been described before (see, e.g., Thorne et al., 1998).”
BackgroundMethodResultInfluentialRecently 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
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
“When we performed a single MULTIDIVTIME run on third codon positions using the whole data set and the same fossil calibration points, the ratio between the most extreme estimated substitution rates was only 10, that is, severely underestimated (data not shown).”
MethodInfluentialSkyline‐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 481
“The two steps are described in detail below.”
BackgroundMethodVidal, N., & Hedges, S. B. (2005) · Comptes Rendus Biologies · doi:10.1016/j.crvi.2005.10.001 · Cited by 462
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
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
Vanneste, K., Baele, G., Maere, S., & de Peer, Y. V. (2014) · Genome Research · doi:10.1101/gr.168997.113 · Cited by 447
“other methods/software to avoid propagation of branch length errors (Thorne et al. 1998).”
MethodFast 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 438
Gaunt, M. W., & Miles, M. A. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004133 · Cited by 440
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 441
“…a molecular timescale for placental mammals using a large nuclear+mitochondrial data set (Springer et al. 2003; Roca et al. 2004) and a Bayesian relaxed clock approach (Thorne et al. 1998; Kishino et al. 2001), adding a constraint on the monophyly of Afrotheria+Xenartha (Atlantogenata).”
BackgroundMethodBarraclough, T. G., & Nee, S. (2001) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(01)02161-9 · Cited by 431
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
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
“This contrasts with most previous Bayesian MCMC relaxed clock models that favor many small or smoothly changing events [3,7,19,20].”
BackgroundResultSauquet, 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 422
“2007), and Bayesian relaxed clocks (Thorne et al. 1998) also permit the incorporation of multiple age constraints in the tree.”
BackgroundRocks 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
“Smith and colleagues compared several methods for best fit to the data: the Langley-Fitch strict clock method [32], and a variety of relaxed clock methods that allow for the rate heterogeneity observed in the data, including parametric Bayesian [ 33 ], nonparametric rate smoothing Box 1. Why fossils cannot indicate ac…”
MethodEstablishment 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 418
“X 398 [374-422] 70 [49-93] 396 [370-419] 383”
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 416
“However, although methods for divergence time estimation using molecular data are common (e.g., Thorne et al. 1998; Sanderson 2002; Drummond et al. 2006), there have been few explicit techniques developed for inferring node ages for trees containing fossils (e.g., Magallón 2010).”
MethodMolecular clocks: four decades of evolution
Kumar, S. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1659 · Cited by 422
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
“…molecular clock models act as prior distributions on lineage-specific substitution rates and their introduction has greatly improved divergence dating methods (Thorne et al. 1998; Drummond et al. 2006; Rannala and Yang 2007; Drummond and Suchard 2010; Heath et al. 2012; Li and Drummond 2012).”
BackgroundMolecular clocks: when timesare a-changin'
HO, S., & LARSON, G. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.11.006 · Cited by 402
“... somewhat circular, however, because it is necessary to have a reasonable idea of what the true date might be to select a suitable calibration; (ii) If reliable ancient DNA data are available, use radiocarbon-dated sequences [9,46] to decrease the amount of extrapolation required to estimate the age of the root of…”
MethodBayesian 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 372
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 378
“Both of these methods allow different rates on different lineages, but assume that rates are constant on individual branches (Thorne et al., 1998).”
BackgroundMethodInfluentialCalibrating 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
“Placing minimum bounds on the ages of nodes is possible in a range of available relaxed-clock methods (Sanderson 1997, Thorne et al. 1998, Sanderson 2002, Drummond et al. 2006).”
MethodBayesian 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
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
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 369
“In Bayesian methods, this is usually carried out by specifying an informative prior distribution for the age of the corresponding node (Thorne et al. 1998; Drummond et al. 2006).”
BackgroundMethodInfluentialThe importance of proper model assumption in bayesian phylogenetics.
Lemmon, A. R., & Moriarty, E. C. (2004) · Systematic Biology · doi:10.1080/10635150490423520 · Cited by 356
“, 1994; Galtier and Gouy, 1998), temporal variation in rates of evolution (Sanderson, 1997; Thorne et al., 1998; Huelsenbeck et al., 2000; Kishino et al., 2001), base-pairing interactions of RNA (Muse, 1995; Tillier and Collins, 1998), correlation between rates of adjacent sites (Felsenstein and Churchill, 1996), diff…”
BackgroundCouch, 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
“The ACE1-vir1 allele was specifithe host shift from Setaria millet to rice (Thorne et al. 1998; cally amplified using the primer pairs CM28-X438 (5 -TTT Sanderson 2002).”
BackgroundYang, Z., & Yoder, A. D. (2003) · Systematic Biology · doi:10.1080/10635150390235557 · Cited by 357
Lin, C., & Danforth, B. N. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00241-0 · Cited by 353
“…2000b; Lutzoni et al., 2001; Nielson, 2002), analyzing patterns of cospeciation (Huelsenbeck et al., 2000a), estimating ancestral states (Huelsenbeck and Bollback, 2001; Lutzoni et al., 2001), and estimating divergence times (Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002).”
BackgroundEstablishing 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
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 348
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 339
“The primate divergence dates are estimated here using a Bayesian MCMC molecular clock methodology (Thorne and Kishino, 2002; Thorne et al., 1998), which has been applied to a range of taxa (e.g., Crawford and Smith, 2005; Knapp et al., 2005; Raaum et al., 2005; San Mauro et al., 2005; Steiner et…”
MethodPoux, 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
“We used the Bayesian approach (Thorne et al., 1998) as implemented in the MULTIDIVTIME program package (Thorne and Kishino, 2002), which relaxes the molecular clock by allowing continuous autocorrelation of Downloaded from https://academic.oup.com/sysbio/article-abstract/54/5/719/1630184 by guest…”
MethodHuchon, 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 343
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 335
“Furthermore, very little is known about the timeframe of brown algal evolution and our study is a first attempt at building a time-calibrated phylogeny based on Bayesian relaxed molecular clock analysis (Thorne et al., 1998; Drummond et al., 2006).”
Schaefer, H., Heibl, C., & Renner, S. S. (2008) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2008.1447 · Cited by 340
“For the Bayesian approach, we used BASEML from the PAML package (Yang 2007) and MULTIDIVTIME (Thorne et al. 1998; Thorne & Kishino 2002) in LAGOPUS, an R package written by Heibl & Cusimano (2008).”
BackgroundMethodInfluentialPhylogenetic systematics turns over a new leaf
Lewis, P. O. (2001) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(00)02025-5 · Cited by 325
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 332
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
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
“…improvements have also been made, such as the implementation of more biologically realistic yet computationally tractable models that accommodate changes in substitution rates along lineages, also known as “relaxed clocks” (e.g., Thorne et al. 1998; Huelsenbeck et al. 2000; Drummond et al. 2006).”
BackgroundPeterson, 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
“Most modern molecular clock methods (e.g. Sanderson 1997, 2002; Thorne et al. 1998;Drummond et al. 2006) allow constraining, as well as fixing, the age of a calibration point, so that every fossil divergence can be defined using a minimum and a maximum.”
BackgroundYoder, A. D., & Yang, Z. (2004) · Molecular Ecology · doi:10.1046/j.1365-294x.2004.02106.x · Cited by 313
“The Bayes method was used to estimate divergence dates while accounting for stochastic changes in evolutionary rate over time (Thorne et al. 1998; Thorne & Kishino 2002).”
MethodBLANK, C. E., & SÁNCHEZ‐BARACALDO, P. (2010) · Geobiology · doi:10.1111/j.1472-4669.2009.00220.x · Cited by 298
“4 (MDT-na; Thorne et al., 1998) was used for Bayesian inferences of node ages using the SSU–LSU data set, with branch lengths estimated using baseml and the F84 model in PAML v.”
MethodInfluentialUsing 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
“More complex models indeed exist (e.g., Gold-man and Yang, 1994; Muse and Gaut, 1994; Schöniger and von Haeseler, 1994; Thorne et al., 1998; Tuffley and Steel, 1998; Huelsenbeck and Nielsen, 1999; Huelsenbeck, 2002), but their application is still uncommon, mainly because these models have not yet…”
BackgroundEstimating 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 310
“Detailed analyses of primate sequences have revealed extensive departures from rate constancy in several other parts of the tree [4,18,27], calling for the employment of relaxed-clock methods that can explicitly accommodate rate heterogeneity among lineages [41,42].”
BackgroundComplexity 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 331
“Bayesian molecular dating was conducted using MCMCtree 77 v.4.9h, with approximate likelihood calculation 78 and under the GTR + G model.”
MethodMolecular 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 299
Self-citation
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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