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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.
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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
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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“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
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A Bayesian statistical analysis of human T-cell lymphotropic virus evolutionary rates
Lemey, P., Pybus, O. G., Dooren, S. V., & Vandamme, A. (2004) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2004.04.005 · Cited by 38
“This model is best described as a Brownian motion process that operates on the logarithm of the rates of molecular evolution (Thorne et al., 1998).”
BackgroundMethodDating branches on the tree of life using DNA.
Wray, G. A. (2001) · Genome biology · doi:10.1186/gb-2001-3-1-reviews0001 · Cited by 37
“This method builds on information provided by the investigator about phylogenetic relationships and divergence times (called the ‘prior’) to calculate a refined estimate of the variables to be assessed (the ‘posterior’), given both the sequence data available and an explicit model of evolution [15, 31 ].”
MethodThe mouth, the anus, and the blastopore—open questions about questionable openings
Hejnol, A., & Martindale, M. Q. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0004 · Cited by 37
Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics
Boden, J. S., Zhong, J., Anderson, R. E., & Stüeken, E. E. (2024) · Nature Communications · doi:10.1038/s41467-024-47914-0 · Cited by 36
“…mother and daughter lineages: These were the autocorrelated lognormal (LN) and Cox-Ingersoll-Ross (CIR) models where substitution rates are inherited from parent lineages 43,86 , and the uncorrelated gamma multipliers (UGAM) model where substitution rates are chosen independent of ancestry 87 .”
Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry
Fourment, M., & Holmes, E. C. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0410-5 · Cited by 38
“Methods that model rate heterogeneity include auto-correlation of rates among lineages [20], and uncorrelated models that allow rates assigned to lineages to be drawn from an underlying probability distribution [21].”
BackgroundMarkov invariants, plethysms, and phylogenetics
Sumner, J. G., Charleston, M., Jermiin, L. S., & Jarvis, P. (2008) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2008.04.001 · Cited by 30
Phylogenetic relationships of elephant‐shrews (Afrotheria, Macroscelididae)
Smit, H. A. P., van Vuuren, B. J., O’Brien, P. C. M., Ferguson-Smith, M. A., Yang, F., & Robinson, T. J. (2011) · Journal of Zoology · doi:10.1111/j.1469-7998.2011.00790.x · Cited by 37
Molins, A., García-Breijo, F., Reig-Armiñana, J., del Campo, E. M., Casano, L. M., & Barreno, E. (2013) · Vieraea Folia scientiarum biologicarum canariensium · doi:10.31939/vieraea.2013.41.23 · Cited by 36
Noonan, B. P., Pramuk, J. B., Bezy, R. L., Sinclair, E. A., de Queiroz, K., & Sites, J. W. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.05.017 · Cited by 37
ORIGIN AND RAPID DIVERSIFICATION OF A TROPICAL MOSS
Wall, D. P. (2005) · Evolution · doi:10.1111/j.0014-3820.2005.tb01792.x · Cited by 37
Fuchs, J., Cruaud, C., Couloux, A., & Pasquet, É. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.10.014 · Cited by 37
Bayesian Inference in molecular Phylogenetics
Yang, Z. (2005) · Oxford University Press eBooks · doi:10.1093/oso/9780198566106.003.0003 · Cited by 36
Bellot, S., & Renner, S. S. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.07.005 · Cited by 36
“To accommodate such situations, workers have assumed either that substitution rates of ancestors and descendants are correlated (Sanderson, 1997, 2002; Thorne et al., 1998; Rannala and Yang, 2007) or that rate variation is unrelated to species relationships (Drummond et al.”
BackgroundVerneau, O., du Preez, L. H., Laurent, V., Raharivololoniaina, L., Glaw, F., & Miguel Vences, B. (2009) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2008.1530 · Cited by 36
Duchêne, S., Giallonardo, F. D., & Holmes, E. C. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv207 · Cited by 38
Divergence dating using mixed effects clock modelling: An application to HIV-1
Bletsa, M., Suchard, M. A., Ji, X., Gryseels, S., Vrancken, B., Baele, G., Worobey, M., & Lemey, P. (2019) · Virus Evolution · doi:10.1093/ve/vez036 · Cited by 32
Feng, C., Manchester, S. R., & Xiang, Q. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.01.017 · Cited by 36
Xiang, Q., Thorne, J. L., Seo, T., Zhang, W., Thomas, D. T., & Ricklefs, R. E. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.07.010 · Cited by 36
Self-citationJing, M., Yu, H., Wu, S.-H., Wang, W., & Zheng, X. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.04.003 · Cited by 36
“The divergence time between species were estimated through Bayesian molecular dating using PAML/ MULTIDIVTIME developed by Kishino et al. (2001), Thorne et al. (1998) and Yang and Yoder (2003).”
MethodFreeze tolerance evolution among anurans: Frequency and timing of appearance
Voituron, Y., Barré, H., Ramløv, H., & Douady, C. J. (2009) · Cryobiology · doi:10.1016/j.cryobiol.2009.01.001 · Cited by 36
Uniform phenotype conceals double colonization by reed‐warblers of a remote Pacific archipelago
Cibois, A., Thibault, J., & Pasquet, É. (2007) · Journal of Biogeography · doi:10.1111/j.1365-2699.2007.01703.x · Cited by 36
“…that do not assume a global molecular clock but allow for geological or fossil calibrations to be included in the analysis in the form of constraints on divergence times (the multidistribute package, Thorne et al., 1998; Kishino et al., 2001) following the protocols used in Cibois et al. (2004).”
BackgroundMethodPatou, M., Debruyne, R., Jennings, A. P., Zubaid, A., Rovie‐Ryan, J. J., & Veron, G. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.03.026 · Cited by 36
Phylogeny mandalas for illustrating the Tree of Life
Hasegawa, M. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.11.001 · Cited by 35
Phylogenetic Methodology for Detecting Protein Interactions
Waddell, P. J., Kishino, H., & Ota, R. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl193 · Cited by 35
“Understanding how to best estimate rates is still developing, but the meth-ods of Sanderson (1997), Thorne et al. (1998), and Thorne and Kishino (2002) are popular.”
BackgroundSelf-citationSummarizing a Posterior Distribution of Trees Using Agreement Subtrees
Cranston, K., & Rannala, B. H. (2007) · Systematic Biology · doi:10.1080/10635150701485091 · Cited by 35
“An evolutionary study may require one or more trees in order to study such topics as divergence times (Sanderson, 2002; Thorne et al., 1998 ), selection (Yang et al., 2005), or phylogeography (Knowles and Maddison, 2002; Hewitt, 2001).”
BackgroundLiede‐Schumann, S., Kong, H., Meve, U., & Thiv, M. (2012) · Taxon · doi:10.1002/tax.614007 · Cited by 35
Matschiner, M. (2018) · Hydrobiologia · doi:10.1007/s10750-018-3686-9 · Cited by 35
Arnaiz‐Villena, A., Ruiz-del-Valle, V., Gómez-Prieto, P., Reguera, R., Parga-Lozano, C., & Serrano-Vela, J. I. (2009) · The Open Ornithology Journal · doi:10.2174/1874453200902010029 · Cited by 35
“The original tree was constructed assuming GTR+I+G model of evolution (chosen by Modeltest), with branch lengths estimated according to Thorne's model.”
MethodFuchs, J., Fjeldså, J., & Pasquet, É. (2006) · Zoologica Scripta · doi:10.1111/j.1463-6409.2006.00238.x · Cited by 35
“Bayesian approaches for the divergence time estimates were performed using the MULTIDIVERGENCE software package (Thorne et al. 1998; Thorne & Kishino 2002).”
MethodZhao, Q., Liu, H., Luo, L.-G., & Ji, X. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2010.12.017 · Cited by 34
“We used the program estbranches in the Multidivtime package to estimate the maximum likelihood of the branch lengths of the tree and the variance– covariance matrix.”
MethodGoodall-Copestake, W. P., Harris, D. J., & Hollingsworth, P. M. (2009) · Botanical Journal of the Linnean Society · doi:10.1111/j.1095-8339.2009.00948.x · Cited by 36
Temporal and spatial diversification of the African disjunct genus Androcymbium (Colchicaceae)
del Hoyo, A., García‐Marín, J., & Pedrola‐Monfort, J. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.08.005 · Cited by 34
Phylogeography of the Central American lancehead Bothrops asper (SERPENTES: VIPERIDAE)
Saldarriaga‐Córdoba, M., Parkinson, C. L., Daza, J. M., Wüster, W., & Sasa, M. (2017) · PLoS ONE · doi:10.1371/journal.pone.0187969 · Cited by 34
“This method incorporates heterogeneity rates based on Bayesian inference and allows the simultaneous use of different evolutionary parameters for each dataset [51, 52].”
MethodSchmitz, P., Cibois, A., & Landry, B. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.05.010 · Cited by 34
“The Bayesian relaxed molecular clock approach was applied using the program package MULTIDIVTIME ( Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002).”
MethodEstabrook, G. F., Smith, G. R., & Dowling, T. E. (2007) · Evolution · doi:10.1111/j.1558-5646.2007.00089.x · Cited by 34
Molecular Evidence for the Last Survivor of an Ancient Kangaroo Lineage
Westerman, M., Burk, A., Amrine‐Madsen, H., Prideaux, G. J., Case, J. A., & Springer, M. S. (2002) · Journal of Mammalian Evolution · doi:10.1023/a:1022697300092 · Cited by 34
“Divergence times were estimated using the mt and combined data sets and the relaxed clock method of Thorne et al. (1998) and Kishino et al. (2001), which is implemented in the estbranches and divtime5b programs.”
MethodPitra, C., D'aloia, M. E., Lieckfeldt, D., & Combreau, O. (2004) · Conservation Genetics · doi:10.1023/b:coge.0000030004.51398.28 · Cited by 34
“These molecular dates should also be confirmed in the future using other dating methods, such as for example the Bayesian approach of Thorne et al. (1998).”
MethodPhylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome
Kosiol, C., Bofkin, L., & Whelan, S. (2005) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2005.08.003 · Cited by 34
“…purely of empirical parameters have proved very useful for other topics related to phylogenetics, including homology detection (e.g., the PAM [37] and BLOSUM [38] matrices used by BLAST [39]), and sequence alignment (e.g., CLUSTAL contains implicit descriptions of character replacement [40]).”
BackgroundComparative analysis reveals that polyploidy does not decelerate diversification in fish
Zhan, S. H., Glick, L., Tsigenopoulos, C. S., Otto, S. P., & Mayrose, I. (2014) · Journal of Evolutionary Biology · doi:10.1111/jeb.12308 · Cited by 33
“…for each data set using MrBayes, version 3.2.1 (Huelsenbeck & Ronquist, 2001), under a relaxed molecular clock according to a Brownian motion model (Thorne et al., 1998), running for 2 000 000 steps with a sampling frequency of once per 2000 steps; the initial 50% of the steps were discarded as…”
MethodInfluentialPhylogenetic evidence for cladogenetic polyploidization in land plants
Zhan, S. H., Drori, M., Goldberg, E. E., Otto, S. P., & Mayrose, I. (2016) · American Journal of Botany · doi:10.3732/ajb.1600108 · Cited by 32
The phylogeny of lance lacewings ( N europtera: O smylidae)
Winterton, S. L., Zhao, Y., Garzón‐Orduña, I. J., Wang, Y., & Liu, Z. (2017) · Systematic Entomology · doi:10.1111/syen.12231 · Cited by 33
“…2017 The Royal Entomological Society, Systematic Entomology, 42, 555–574 3.3 (Lartillot et al., 2009) two chains of an autocorrelated log-normal (Thorne et al., 1998) relaxed clock model (LN) were run for 17 000 cycles and assuming a birth–death speciation model on the divergence times.”
MethodInfluentialRose, J. P., Xiang, C., Sytsma, K. J., & Drew, B. T. (2021) · Botanical Journal of the Linnean Society · doi:10.1093/botlinnean/boab104 · Cited by 33
Lavin, M. (2006) · Systematics Association special volume · doi:10.1201/9781420004496.ch19 · Cited by 33
Bayesian Phylogenetic Inference Using a Combinatorial Sequential Monte Carlo Method
Wang, L., Bouchard‐Côté, A., & Arnaud Doucet, B. (2015) · Journal of the American Statistical Association · doi:10.1080/01621459.2015.1054487 · Cited by 35
“There has been work on generalizing ultrametric models to handle nonconstant evolutionary rates (Thorne, Kishino, and Painter 1998; Drummond and Suchard 2010), but due to the higher dimensional parameters of these models, nonclock models are still widely used.”
BackgroundSpeciation on islands: what are we learning?
Emerson, B. C. (2008) · Biological Journal of the Linnean Society · doi:10.1111/j.1095-8312.2008.01120.x · Cited by 33
Robust support for tardigrade clades and their ages from three protein‐coding nuclear genes
Regier, J. C., Shultz, J. W., Kambic, R. E., & Nelson, D. R. (2004) · Invertebrate Biology · doi:10.1111/j.1744-7410.2004.tb00145.x · Cited by 34
Wan, Q., Zeng, C., Ni, X., Pan, H., & Fang, S. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004147 · Cited by 33
“Molecular dating by MULTIDISTRIBUTE was achieved through three programs, PAML [52], ESTBRANCHES [53], and MULTIDIVTIME [51,53].”
MethodInfluentialSoltis, P. S., Moore, M. J., Burleigh, G., & Soltis, P. S. (2009) · Critical Reviews in Plant Sciences · doi:10.1080/07352680802665297 · Cited by 33
“…discoveries have resulted not only from the compilation of large data sets, but also from impressive developments in algorithms (e.g., Bayesian relaxed clock (BRC) Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002; and penalized likelihood (PL) approaches; Sanderson, 2002).”
BackgroundMello, B., Tao, Q., Barba‐Montoya, J., & Kumar, S. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13249 · Cited by 32
Pirie, M. D., Chatrou, L. W., Erkens, R. H. J., Maas, J. W., van der Niet, T., Mols, J. B., & Richardson, J. E. (2005) · Socio-Environmental Systems Modeling · Cited by 32
Segar, S. T., López‐Vaamonde, C., Rasplus, J., & Cook, J. M. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.05.030 · Cited by 32
“We implemented the log-normal relaxed clock with autocorrelation (Thorne et al., 1998) and ran two chains in parallel for 8000 cycles.”
MethodRELATIONSHIPS AND DIVERGENCE TIMES AMONG THE ORDERS AND FAMILIES OF MARSUPIALIA
Meredith, R. W., Krajewski, C., Westerman, M., & Springer, M. S. (2009) · Cited by 32
Divergence times in the termite genus Macrotermes (Isoptera: Termitidae)
Brandl, R., Hyodo, F., von Korff-Schmising, M., Maekawa, K., Miura, T., Takematsu, Y., Matsumoto, T., Abe, T., Bagine, R. K. N., & Kaib, M. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.07.007 · Cited by 32
“The selected approach implements a probabilistic model to describe the correlated change in evolutionary rate over time (program MULTIDIVTIME; Thorne et al., 1998; Thorne and Kishino, 2002).”
MethodHalf a Century of Controversy: The Neutralist/Selectionist Debate in Molecular Evolution
Galtier, N. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae003 · Cited by 31
“…research was sustained by a remarkable effort to develop models of sequence evolution and statistical methods of substitution rate estimation (e.g. Thorne et al. 1998; Yang and Nielsen 2008; Lartillot and Poujol 2011), which, in turn, opened exciting opportunities such as, among other things, the…”
MethodMagallón, S. (2014) · Botanical Sciences · doi:10.17129/botsci.37 · Cited by 30
Conceptual issues in Bayesian divergence time estimation
Rannala, B. H. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0134 · Cited by 31
“I will also assume that the fossils are direct ancestors that can be assigned to lineages [2,10].”
BackgroundAguileta, G., Bielawski, J. P., & Yang, Z. (2006) · Gene · doi:10.1016/j.gene.2006.04.019 · Cited by 31
“Bayesian method for divergence date estimation We used a Bayesian MCMC approach (Thorne et al., 1998) as implemented in a program package written by Jeff Thorne.”
BackgroundMethodInfluentialGonzález, J., Castro, G. D., García‐del‐Rey, E., Berger, C., & Wink, M. (2008) · Journal für Ornithologie · doi:10.1007/s10336-008-0360-4 · Cited by 30
“…fossils as time constraints (Pereira et al. 2007), a Bayesian inference method that takes into account the variation among substitution rates (Thorne et al. 1998; Kishino et al. 2001; Thorne and Kishino 2002), and a multiple gene approach which is recommended for estimations of divergence…”
MethodACCOUNTING FOR RATE VARIATION AMONG LINEAGES IN COMPARATIVE DEMOGRAPHIC ANALYSES
Hope, A. G., Ho, S. Y. W., Malaney, J. L., Cook, J. A., & Talbot, S. L. (2014) · Evolution · doi:10.1111/evo.12469 · Cited by 30
“These include relaxed molecular clocks (e.g., Thorne et al. 1998; Sanderson 2002; Drummond et al. 2006), which allow evolutionary timescales to be estimated in the presence of rate variation among lineages.”
BackgroundUsing multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data
Duchêne, S., & Ho, S. Y. W. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.04.010 · Cited by 29
Fourment, M., & Holmes, E. C. (2014) · BMC Evolutionary Biology · doi:10.1186/s12862-014-0163-6 · Cited by 30
Ritchie, A. M., Hua, X., Cardillo, M., Yaxley, K. J., Dinnage, R., & Bromham, L. D. (2020) · Diversity and Distributions · doi:10.1111/ddi.13179 · Cited by 30
“For example, most methods rely on modelling substitution rates based on simple parametric distributions, either independently for each lineage (Drummond et al., 2006) or determining the rate for each new lineage from the rate of its parent (Ho et al., 2005; Thorne et al., 1998).”
MethodCarruthers, T., Sun, M., Baker, W. J., Smith, S. A., de Vos, J. M., & Eiserhardt, W. L. (2022) · Systematic Biology · doi:10.1093/sysbio/syac012 · Cited by 32
“Since then, methods have developed that attempt to account for the complexity of ways that molecular sequences evolve—with a particular focus being on how best to account for differences in substitution rates (r) among lineages (Sanderson 1997, 2002; Thorne et al. 1998; Kishino et al. 2001; Drummond et al. 2006; dos R…”
Vďačný, P. (2015) · European Journal of Protistology · doi:10.1016/j.ejop.2015.06.008 · Cited by 30
Zheng, Y., Fu, J., & Li, S. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.03.026 · Cited by 30
“Consequently, dating analysis was performed using both penalized likelihood (Sanderson, 2002) and Thorne and Kishino’s Bayesian (Thorne et al., 1998; Kishino et al., 2001) approaches.”
MethodDoyon, J., Hamel, S., & Chauve, C. (2011) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2011.64 · Cited by 30
“The branch length (in Million of Years) of the species tree S were computed by a Bayesian framework that takes as input homologous DNA sequences and assumes that the rates of nucleotide substitutions is constant over any branch, but it can differ among the branches (relaxed molecular clock) [22].”
MethodGenomic analysis of emerging pathogens: methods, application and future trends
Li, L. M., Grassly, N. C., & Fraser, C. (2014) · Genome biology · doi:10.1186/s13059-014-0541-9 · Cited by 33
“Incorporating sampling times helps to convert a phylogeny specified in units of nucleotide substitutions to a phylogeny specified in units of time [24].”
MethodPolyploid evolution in Oryza officinalis complex of the genus Oryza
Wang, B., Ding, Z., Liu, W., Pan, J., Li, C., Ge, S., & Zhang, D. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-250 · Cited by 30
“Divergence times were estimated by Bayesian dating methods [44-46], using the programs Baseml [47], Estbranches [44] and Multidivtime [46].”
MethodEfficient Methods for Dating Evolutionary Divergences
Tao, Q., Tamura, K., & Kumar, S. (2020) · Springer eBooks · doi:10.1007/978-3-030-60181-2_12 · Cited by 28
Habib, K. A., Neogi, A. K., Rahman, M., Oh, J., Lee, Y.-H., & Kim, C. (2021) · PLoS ONE · doi:10.1371/journal.pone.0255110 · Cited by 29
Miyazaki, J.-I., Dobashi, M., Tamura, T., Beppu, S., Sakai, T., Mihara, M., & Hosoya, K. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.05.005 · Cited by 29
Šorfová, P., Škeřı́ková, A., & Hypša, V. (2008) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2008.02.004 · Cited by 29
Bell, C. D. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.03.013 · Cited by 29
“For these data, I used several recently proposed Bayesian methods that relax the assumption of a strict molecular clock (Thorne et al., 1998; Kishino et al., 2001; Aris-Brosou and Yang, 2002, 2003).”
MethodFoster, C. S. P., & Ho, S. Y. W. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx198 · Cited by 28
“An 182 advantage of MCMCTREE is the option to use approximate likelihood calculation, which is much 183 faster than full likelihood calculation (Thorne et al. 1998; dos Reis and Yang 2011).”
BackgroundMethodInfluentialRates and Rocks: Strengths and Weaknesses of Molecular Dating Methods
Guindon, S. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00526 · Cited by 28
“The first model explicitly accommodating for autocorrelation was proposed by Thorne et al. (1998). Instead of modeling instantaneous rates at times s and t, corresponding to the end nodes of the first and second edge respectively, they focused on the rates at times s : = s/2 and t : = (t + s)/2, i.”
BackgroundLi, G., Liang, B., Wang, Y.-N., Zhao, H.-B., Helgen, K., Lin, L.-K., Jones, G. E. B., & Zhang, S.-Y. (2007) · Journal of Mammalogy · doi:10.1644/06-mamm-a-273r.1 · Cited by 35
“We utilized the software packages PAML 3.14 (Yang 1997), ESTBRANCHES, and MULTIDIVITIME (Kishino et al. 2001; Thorne and Kishino 2002; Thorne et al. 1998) for these analyses.”
MethodInfluentialEdwards, D., & Hawkins, J. A. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.09.014 · Cited by 28
Gene trees and species trees: irreconcilable differences
Swenson, K. M., & El-Mabrouk, N. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-s19-s15 · Cited by 28
Flores-Carrasco, S. V., Evans, A. L., & McAllister, B. F. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-33 · Cited by 28
“Bayesian dating (BD) was performed as implemented in Multidivtime, which allows multiple data partitions [ 92 ,93].”
MethodBiogeographical history of Japanese freshwater fishes
Watanabe, K., Takahashi, H., Kitamura, A., Yokoyama, R., Kitagawa, T., Takeshima, H., Sato, S., Yamamoto, S., Takehana, Y., Mukai, T., et al. (2006) · Japanese Journal of Ichthyology · doi:10.11369/jji1950.53.1 · Cited by 28
Mizuta, K., Tsukagoshi, H., Ikeda, T., Aoki, Y., Abiko, C., Itagaki, T., Nagano, M., Noda, M., & Kimura, H. (2014) · Journal of Medical Microbiology · doi:10.1099/jmm.0.068189-0 · Cited by 27
“The Bayesian Markov chain Monte Carlo (MCMC) method enables the evolutionary timescale to be estimated (Thorne et al., 1998; Lepage et al., 2007).”
MethodAge at first reproduction explains rate variation in the strepsirrhine molecular clock
Tsantes, C., & Steiper, M. E. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906686106 · Cited by 27
Kuchta, S. R., Brown, A. D., Converse, P. E., & Highton, R. (2016) · PLoS ONE · doi:10.1371/journal.pone.0150022 · Cited by 27
The Essentials of Computational Molecular Evolution
Aris‐Brosou, S., & Rodrigue, N. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-582-4_4 · Cited by 25
Muellner-Riehl, A. N., Greger, H., & Pannell, C. M. (2009) · Blumea - Biodiversity Evolution and Biogeography of Plants · doi:10.3767/000651909x476175 · Cited by 27
Evolving Perceptions on the Antiquity of the Modern Avian Tree
Brown, J. W., & van Tuinen, M. (2011) · Wiley eBooks · doi:10.1002/9781119990475.ch12 · Cited by 27
PAML (Phylogenetic Analysis by Maximum Likelihood)
Cummings, M. P. (2004) · Wiley eBooks · doi:10.1002/9780471650126.dob0515.pub2 · Cited by 27
Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera)
Lavrov, D. V., Díaz, M. C., Maldonado, M., Morrow, C. C., Pérez, T., Pomponi, S. A., & THACKER, R. W. (2023) · PLoS ONE · doi:10.1371/journal.pone.0287281 · Cited by 26
“We used the 180 log normal (Brownian) autocorrelated clock [61] (-ln) model for the analysis and ran two 181 chains for >15,000 cycles.”
Genomic analysis reveals cryptic diversity in aphelids and sheds light on the emergence of Fungi
Mikhailov, K. V., Karpov, S. A., Letcher, P. M., Lee, P. A., Logacheva, M. D., Penin, A. A., Nesterenko, M. A., Pozdnyakov, I. R., Potapenko, E. V., Sherbakov, D. Y., et al. (2022) · Current Biology · doi:10.1016/j.cub.2022.08.071 · Cited by 25
Diversity of HIV-1 Subtype B: Implications to the Origin of BF Recombinants
Leal, E. D. S., & Villanova, F. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011833 · Cited by 26
“We also used a Bayesian Markov chain Monte Carlo (BMCMC) coalescent framework, implemented in the BEAST package [45], that uses DNA sequences to estimate ancestral genealogies using relaxed molecular clock models (lognormal) that have advantages over traditional clock models [46,47].”
Nakamine, H., & Takeda, M. (2008) · Journal of Insect Science · doi:10.1673/031.008.7001 · Cited by 26
de Oliveira, L. L., Aguiar, B. O., & Schrago, C. G. (2012) · Evolutionary Bioinformatics · doi:10.4137/ebo.s9008 · Cited by 26
Siver, P. A., Wolfe, A. P., Rohlf, F. J., Shin, W., & Jo, B. Y. (2013) · Geobiology · doi:10.1111/gbi.12023 · Cited by 26
“Relaxed molecular clocks allow flexible rates of molecular evolution between taxa, including ancestral and descendent forms, and thus constitute a significant advance over previous models that assume constant rates of evolution for the entire tree (Thorne et al., 1998; Drummond et al., 2006).”
BackgroundRaterman, D., Meredith, R. W., Ruedas, L. A., & Springer, M. S. (2006) · Australian Journal of Zoology · doi:10.1071/zo05067 · Cited by 26
“Multidivtime The phylogeny shown in Fig.”
MethodInfluentialMcConway, K., & Sims, H. J. (2004) · Evolution · doi:10.1111/j.0014-3820.2004.tb01569.x · Cited by 26
“…evidence that rates of molecular evolution are heterogeneous among lineages, among genes, and over time (e.g., Ayala 1997; Sanderson 1997; Kumar and Hedges 1998; Thorne et al. 1998; Foote et al. 1999; Cutler 2000; Huelsenbeck et al. 2000; Sanderson and Doyle 2001; Bromham 2002; Soltis et al. 2002).”
BackgroundRoycroft, E., Achmadi, A. S., Callahan, C. M., Esselstyn, J. A., Good, J. M., Moussalli, A., & Rowe, K. C. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab103 · Cited by 27
Dating the origin of the major lineages of Branchiopoda
Sun, X., Xia, X., & Yang, Q. (2015) · Palaeoworld · doi:10.1016/j.palwor.2015.02.003 · Cited by 25
Zhang, A., & Sota, T. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.07.003 · Cited by 25
“We used a Bayesian relaxed clock approach to estimated the divergence times (Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002), because this method allows evolutionary rates to vary among lineages and among gene partitions.”
MethodEvolution of Pollen/Ovule Ratios and Breeding System in Erodium (Geraniaceae)
Alarcón, M. L., Roquet, C., & Aldasoro, J. J. (2011) · Systematic Botany · doi:10.1600/036364411x583637 · Cited by 25
“…times of the Geraniaceae nodes, the Multidivtime software package was used following the procedure outlined in Rutschmann (2005) , which involves the use of the Baseml (PAML, Yang 1997 ), Estbranches ( Thorne et al. 1998 ) and Multidivtime ( Kishino et al. 2001 ; Thorne and Kishino 2002 ) programs.”
MethodThiv, M., Thulin, M., Kilian, N., & Linder, H. P. (2006) · Systematic Botany · doi:10.1600/036364406778388683 · Cited by 25
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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