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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]
The cited source says what the claim attributes to it.
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]
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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]
The cited source says what the claim attributes to it.
In the citing paper
“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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In the citing paper
“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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Montagna, M., Tong, K. J., Magoga, G., Strada, L., Tintori, A., Ho, S. Y. W., & Lo, N. C. (2019) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2019.1854 · Cited by 73
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“To guard against the assumption of a strict molecular clock, we used a relaxed Bayesian clock (Thorne et al., 1998) as implemented in the package PAML, version 3.”
MethodPopular molecular markers in bacteria
Liu, W., Li, L., Khan, M. A., & Zhu, F. (2012) · Molecular Genetics Microbiology and Virology · doi:10.3103/s0891416812030056 · Cited by 68
Dalebout, M. L., Steel, D. J., & Baker, C. S. (2008) · Systematic Biology · doi:10.1080/10635150802559257 · Cited by 68
“14 (Yang, 1997) and ESTBRANCHES (Thorne et al., 1998; Kishino et al., 2001) were used to estimate branch lengths for the COMBO data set ML topology, using a F84+G model with five rate categories, following the recommendations of Rutschmann (2005).”
MethodInfluentialWhittle, C.-A., & Johnston, M. O. (2003) · Journal of Molecular Evolution · doi:10.1007/s00239-002-2395-0 · Cited by 68
“In order to attribute rate variation to minimum generation time or annual/perennial life history, it is imperative that the compared taxa be as closely related as possible to minimize all other differences differences between them (Thorne et al. 1998).”
BackgroundLebedev, V. S., Bannikova, A. A., Tesakov, A. S., & Abramson, N. I. (2007) · Zoologica Scripta · doi:10.1111/j.1463-6409.2007.00300.x · Cited by 67
“Bayesian estimation of divergence times under the relaxedclock model was performed using MULTIDIVTIME package (Thorne et al. 1998; Kishino et al. 2001; Thorne & Kishino 2002).”
MethodPhylogenetic position of Myriapoda revealed by 454 transcriptome sequencing
Rehm, P., Meusemann, K., Borner, J., Misof, B. Y., & Burmester, T. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.04.007 · Cited by 66
“Three relaxed clock models were applied: i. the uncorrelated gamma multipliers (Drummond et al., 2006), ii. the autocorrelated log-normal model (Thorne et al., 1998) and iii. the CIR process (Cox et al., 1985; Lepage et al., 2006).”
MethodBiogeography of the túngara frog, Physalaemus pustulosus: a molecular perspective
Weigt, L. A., Crawford, A. J., Rand, A. S., & Ryan, M. J. (2005) · Molecular Ecology · doi:10.1111/j.1365-294x.2005.02707.x · Cited by 69
ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis
Duchêne, S., Molak, M., & Ho, S. Y. W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt665 · Cited by 61
Li, X., Musikasinthorn, P., & Kumazawa, Y. (2006) · Ichthyological Research · doi:10.1007/s10228-005-0321-3 · Cited by 74
“The estbranches/ multidivtime programs (Thorne et al., 1998) were then used to estimate divergence times by the Bayesian Markov Chain Monte Carlo method.”
MethodSynchronous intercontinental splits between assemblages of woodpeckers suggested by molecular data
Fuchs, J., Ohlson, J. I., Ericson, P. G. P., & Pasquet, É. (2006) · Zoologica Scripta · doi:10.1111/j.1463-6409.2006.00267.x · Cited by 66
“Bayesian approaches for the divergence time estimates were performed using the MULTIDISTRIBUTE package (Thorne et al. 1998; Thorne & Kishino 2002).”
MethodBiogeography of Cedrela (Meliaceae, Sapindales) in Central and South America
Muellner-Riehl, A. N., Pennington, T. D., Köcke, A. V., & Renner, S. S. (2010) · American Journal of Botany · doi:10.3732/ajb.0900229 · Cited by 66
“The program estbranches ( Thorne et al., 1998 ) was then used to calculate branch lengths and their variance, given the sequence data (32 ITS sequences of a length of 941 nt), the model parameter values from PAML, and the specifi ed rooted topology.”
MethodMitogenomics of the Old World monkey tribe Papionini
Liedigk, R., Roos, C., Brameier, M., & Zinner, D. P. (2014) · BMC Evolutionary Biology · doi:10.1186/s12862-014-0176-1 · Cited by 66
Cusimano, N., Zhang, L.-B., & Renner, S. S. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm241 · Cited by 66
Molecular evolution of the plastid genome during diversification of the cotton genus
Chen, Z., Grover, C. E., Li, P., Wang, Y., Nie, H., Zhao, Y., Wang, M., Liu, F., Zhou, Z., Wang, X., et al. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.04.014 · Cited by 68
“, 2009), the autocorrelated Lognormal relaxedclock mode (Thorne et al., 1998), and the tree generated from the above dataset and the CAT + GTR model.”
MethodMatsudaira, K., & Ishida, T. (2010) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2010.01.032 · Cited by 65
Dornburg, A., Beaulieu, J. M., Oliver, J. C., & Near, T. J. (2011) · Systematic Biology · doi:10.1093/sysbio/syr019 · Cited by 65
Wáng, B., Ma, J., McKenna, D. D., Yan, E. V., Zhang, H., & Jarzembowski, E. A. (2013) · Journal of Systematic Palaeontology · doi:10.1080/14772019.2013.806602 · Cited by 65
“Divergence times were estimated using relaxed molecular clock methods in the program MULTIDIVTIME (Thorne et al. 1998; Kishino et al. 2001; Thorne & Kishino 2002).”
MethodThe Diversity Of Eukaryotes And The Root Of The Eukaryotic Tree
Brinkmann, H., & Philippe, H. (2008) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-74021-8_2 · Cited by 67
Roure, B., & Philippe, H. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-17 · Cited by 64
“The same observation has been made for evolutionary rates, leading to local molecular clock [48] or auto-correlated relaxed molecular clock models [49].”
BackgroundArroyave, J., & Stiassny, M. L. J. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.04.016 · Cited by 64
Li, Y., Ren, Z., Shedlock, A. M., Wu, J., Sang, L., Tersing, T., Hasegawa, M., Yonezawa, T., & Zhong, Y. (2013) · Gene · doi:10.1016/j.gene.2012.12.096 · Cited by 67
“Since molecular clock was not hold in our data set (Table S4), divergence times were estimated by the Bayesian relaxed clock method (Thorne et al., 1998) using the MCMCTREE program of PAML (version 4.”
MethodMolecular Phylogenetic Analysis of Petunia Juss. (Solanaceae)
Kulcheski, F. R., Muschner, V. C., Lorenz, A. P., Stehmann, J. R., Bonatto, S. L., Salzano, F. M., & Freitas, L. B. (2006) · Genetica · doi:10.1007/s10709-005-1427-2 · Cited by 64
“The divergence time estimation was inferred by a Bayesian method with the MULTIDIVTIME package ( Thorne, Kishino, & Painter, 1998; Thorne & Kishino, 2002).”
MethodPrimary Controls on Species Richness in Higher Taxa
Rabosky, D. L. (2010) · Systematic Biology · doi:10.1093/sysbio/syq060 · Cited by 64
Evolutionary history of the seagrass genus Posidonia
Aires, T., Marbà, N., Cunha, R., Kendrick, G. A., Walker, D. I., Serrão, E. Á., Duarte, C. M., & Arnaud‐Haond, S. (2010) · Marine Ecology Progress Series · doi:10.3354/meps08879 · Cited by 64
“Divergence time estimation The divergence time obtained with Multidivtime (Thorne et al. 1998, Kishino et al. 2001) between the 2 major clades (Mediterranean and Australian) was estimated to be 68.0 (65.6; 70.5) Myr BP (Fig.”
MethodInfluentialVargas‐Ramírez, M., Castaño-Mora, O. V., & Fritz, U. (2008) · Organisms Diversity & Evolution · doi:10.1016/j.ode.2008.10.001 · Cited by 64
“Divergence times for nodes were estimated using the Bayesian relaxed molecular clock as implemented in the MULTIDISTRIBUTE package (Thorne et al. 1998; Thorne and Kishino 2002).”
MethodHarris, A., Xiang, Q., & Thomas, D. T. (2009) · Taxon · doi:10.1002/tax.581012 · Cited by 64
Biogeography of Nymphaeales: extant patterns and historical events
Löhne, C., Yoo, M., Borsch, T., Wiersema, J. H., Wilde, V., Bell, C. D., Barthlott, W., Soltis, P. S., & Soltis, P. S. (2008) · Taxon · doi:10.1002/tax.574008 · Cited by 64
Nikaido, M., Harada, M., Cao, Y., Hasegawa, M., & Okada, N. (2000) · Journal of Molecular Evolution · doi:10.1007/s002390010094 · Cited by 64
“The Bayesian method of Thorne et al. (1998) is useful for this purpose, and we applied it to a subset of our data, namely, the data for Chiroptera, Carnivora, Perissodactyla, Cetartiodactyla, Proboscidea (elephant), and Tubulidentata (aardvark) with Xenarthra (armadillo) as an outgroup.”
MethodWinterton, S. L., Wiegmann, B. M., & Schlinger, E. I. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.08.015 · Cited by 63
“Recent approaches for estimating divergence times use stochastic methods that do not assume a constant rate of evolution and therefore account for this rate heterogeneity between lineages (Sanderson, 1997, 2002; Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002).”
BackgroundZhang, M., Rao, D., Yang, J., Yu, G., & Wilkinson, J. A. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.10.019 · Cited by 63
“Because the data did not conform to expectations of clock-like evolution (X2 = 496, d.f. = 87, P 0.01), we used Bayesian molecular dating (Thorne et al., 1998) to date splits using the MULTIDIVTIME package of Thorne and Kishino (2002).”
MethodInfluentialBayesian Estimation of Divergence Times from Large Sequence Alignments
Guindon, S. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq060 · Cited by 63
“Approximation of the Likelihood Function Thorne et al. (1998) used a multivariate normal density to approximate the likelihood function.”
BackgroundMethodResultInfluentialTimetree of Aselloidea Reveals Species Diversification Dynamics in Groundwater
Morvan, C., Malard, F., Paradis, E., Tristan, L., Konecny‐Dupré, L., & Douady, C. J. (2013) · Systematic Biology · doi:10.1093/sysbio/syt015 · Cited by 63
“This computation was implemented on the 2 Multidivtime chronograms as well as on 2000 randomly sampled trees from MCMC sampling (after burn-in removal) for all BEAST analyses (lognormal and exponential models on threshold and GMYC data sets) to account for dating and topology uncertainties.”
MethodInfluentialSteiper, M. E., & Young, N. M. (2008) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.20177 · Cited by 63
Did Kauri (Agathis: Araucariaceae) Really Survive the Oligocene Drowning of New Zealand?
Biffin, E., Hill, R. S., & Lowe, A. J. (2010) · Systematic Biology · doi:10.1093/sysbio/syq030 · Cited by 62
“…relative to those employed by Knapp et al. (2007, penalized likelihood, Sanderson 2002, and the Bayesian relaxed clock implementation, Multidivtime, Thorne et al. 1998; Thorne and Kishino 2002) including the simultaneous estimation of topology and branch lengths (divergence times) from the aligned…”
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Irisarri, I., Uribe, J. E., Eernisse, D. J., & Zardoya, R. (2020) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1573-2 · Cited by 62
A likelihood look at the supermatrix–supertree controversy
Ren, F., Tanaka, H., & Yang, Z. (2008) · Gene · doi:10.1016/j.gene.2008.04.002 · Cited by 61
“For example, in our simulation on divergence time estimation, we ignored possible violations of the molecular clock (Thorne et al., 1998) and uncertainties in the fossil record (Drummond et al.”
BackgroundThe coevolution of fungus-ant agriculture
Schultz, T. R., Sosa‐Calvo, J., Kweskin, M., Lloyd, M. W., Dentinger, B. T. M., Kooij, P. W., Vellinga, E. C., Rehner, S. A., Rodrigues, A. L., Montoya, Q. V., et al. (2024) · Science · doi:10.1126/science.adn7179 · Cited by 69
Nie, Z., Sun, H., Li, H., & Wen, J. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.03.012 · Cited by 61
“tion of rates and time (Thorne et al., 1998; Thorne and Kishino, 2002; Yang and Yoder, 2003).”
MethodThe determinants of the molecular substitution process in turtles
LourençO, J. M., Glémin, S., Chiari, Y., & Galtier, N. (2012) · Journal of Evolutionary Biology · doi:10.1111/jeb.12031 · Cited by 62
“…most of this evidence comes from endothermic vertebrates, mammals (Sarich & Wilson, 1973; Mindell et al., 1996; Sayres et al., 2001; Bromham, 2002b; Hwang & Green, 2004; Nabholz et al., 2008; Welch et al., 2008; Tsantes & Steiper, 2009) and birds (Mooers & Harvey, 1994; Nabholz et al., 2009).”
BackgroundMolecular phylogeny of the extinct giant deer, Megaloceros giganteus
Hughes, S., Hayden, T. J., Douady, C. J., Tougard, C., Germonpré, M., Stuart, A. J., Lbova, L., Carden, R. F., Hänni, C., & Say, L. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.02.004 · Cited by 61
Barba‐Montoya, J., dos Reis, M., & Yang, Z. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.07.005 · Cited by 64
“(3) 183 This is equivalent to the Dirichlet time prior used by Thorne et al. (1998).”
MethodWu, J., Yonezawa, T., & Kishino, H. (2017) · Current Biology · doi:10.1016/j.cub.2017.08.043 · Cited by 61
Self-citationErséus, C., Williams, B. W., Horn, K. M., Halanych, K. M., Santos, S. R., James, S. W., Châtelliers, M. C. D., & Anderson, F. E. (2020) · Zoologica Scripta · doi:10.1111/zsc.12426 · Cited by 62
Arensburger, P., Simon, C., & Holsinger, K. E. (2004) · Journal of Biogeography · doi:10.1111/j.1365-2699.2004.01098.x · Cited by 60
“Figure 3 Age estimates of nodes on the maximum likelihood Kikihia tree using a modified Thorne et al. (1998) program.”
MethodInfluentialPollination, biogeography and phylogeny of oceanic island bellflowers (Campanulaceae)
Olesen, J. M., Alarcón, M., Ehlers, B., Aldasoro, J. J., & Roquet, C. (2012) · Perspectives in Plant Ecology Evolution and Systematics · doi:10.1016/j.ppees.2012.01.003 · Cited by 60
The expanded cattle KIR genes are orthologous to the conserved single-copy KIR3DX1 gene of primates
Guethlein, L. A., Abi‐Rached, L., Hammond, J. A., & Parham, P. (2007) · Immunogenetics · doi:10.1007/s00251-007-0214-x · Cited by 60
“Divergence time analysis was performed using the Bayesian relaxed molecular clock approach with the MULTIDISTRIBUTE program package ( Thorne et al. 1998; Thorne and Kishino 2002), as previously described (Abi-Rached and Parham 2005).”
MethodSchaefer, H., & Renner, S. S. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.01.030 · Cited by 60
“Bayesian relaxed clock dating was performed using the approach developed by Thorne and Kishino (2002) and Thorne et al. (1998).”
MethodCalibrated Birth–Death Phylogenetic Time-Tree Priors for Bayesian Inference
Heled, J., & Drummond, A. J. (2014) · Systematic Biology · doi:10.1093/sysbio/syu089 · Cited by 60
“In order to produce results on an absolute time scale it is necessary to either provide information on the rate of molecular evolution or alternatively calibrate a subset of internal nodes with a calibration density [Thorne et al., 1998, Yang and Rannala, 2006, Drummond et al., 2006].”
BackgroundMethodInfluentialCorrelating Early Evolution of Parasitic Platyhelminths to Gondwana Breakup
Badets, M., Whittington, I. D., Lalubin, F., Allienne, J., Maspimby, J.-L., Bentz, S., du Preez, L. H., Barton, D. P., Hasegawa, H., Tandon, V., et al. (2011) · Systematic Biology · doi:10.1093/sysbio/syr078 · Cited by 60
“ML branch lengths and their variance–covariance matrix were estimated with the estbranches program (Thorne et al. 1998).”
MethodCuenca, A., Lange, C. B. A., & Borchsenius, F. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.10.010 · Cited by 59
“14 packages (Yang, 1997) and multidivtime (Kishino et al., 2001; Thorne and Kishino, 2002; Thorne et al., 1998); and the non-parametric rate smoothing approach, penalized likelihood (PL; Sanderson, 1997), as implemented in the program r8s v.”
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Zhong, B., Fong, R., Collins, L. J., McLenachan, P. A., & Penny, D. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu087 · Cited by 59
“Various substitution models that relax the assumption of the strict molecular clock have been developed to account for rate heterogeneity between lineages in molecular phylogenetics (e.g., Thorne et al. 1998; Sanderson 2002; Drummond et al. 2006).”
BackgroundSmedmark, J. E. E., & Anderberg, A. A. (2007) · American Journal of Botany · doi:10.3732/ajb.94.9.1491 · Cited by 59
Lartillot, N., Phillips, M. J., & Ronquist, F. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0132 · Cited by 63
“The most well-known example of an autocorrelated model is the lognormal (or Brownian) relaxed clock, which makes the assumption that the logarithm of the substitution rate evolves according to a Brownian motion [3,5,6].”
BackgroundMethodInfluentialHo, S. Y. W., & Lo, N. C. (2013) · Australian Journal of Entomology · doi:10.1111/aen.12018 · Cited by 57
Lavin, M. (2006) · CRC Press eBooks · doi:10.1201/9781420004496-19 · Cited by 58
Molecular Clocks without Rocks: New Solutions for Old Problems
Tiley, G. P., Poelstra, J. W., dos Reis, M., Yang, Z., & Yoder, A. D. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.06.002 · Cited by 60
“Different models of rate variation among branches are available, including autocorrelation among lineages [2,35], uncorrelated rates [3,30,36], or a mixture of the two [37].”
BackgroundEvolution of BK Virus Based on Complete Genome Data
Nishimoto, Y., Takasaka, T., Hasegawa, M., Zheng, H.-Y., Chen, Q., Sugimoto, C., Kitamura, T., & Yogo, Y. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-005-0092-5 · Cited by 58
“The Bayesian method of Thorne and colleagues (Thorne et al. 1998; Kishino et al. 2001) is useful for this purpose as shown by Hasegawa et al. (2003) and other authors.”
MethodResultInfluentialBayesian Dating of Shallow Phylogenies with a Relaxed Clock
Brown, R. P., & Yang, Z. (2009) · Systematic Biology · doi:10.1093/sysbio/syp082 · Cited by 57
“,Yang and Rannala 2006), together with a greater availability of software that implement different algorithms (Thorne et al. 1998; Thorne and Kishino 2002; Drummond and Rambaut 2007; Yang 2007; Lepage et al. 2008), have made the Bayesian MCMC approach increasingly popular in phylogenetic studies.”
InfluentialPhylogeny of Basal Hexapod Lineages and Estimates of Divergence Times
Regier, J. C., Shultz, J. W., & Kambic, R. E. (2004) · Annals of the Entomological Society of America · doi:10.1603/0013-8746(2004)097[0411:pobhla]2.0.co;2 · Cited by 57
Aoki, S., Uehara, K., Imafuku, M., Hasebe, M., & Itô, M. (2004) · Journal of Plant Research · doi:10.1007/s10265-004-0153-7 · Cited by 57
van Tuinen, M., & Hadly, E. A. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-004-2624-9 · Cited by 57
The Taming of the Skew: Estimating Proper Confidence Intervals for Divergence Dates
Burbrink, F. T., & Pyron, R. A. (2008) · Systematic Biology · doi:10.1080/10635150802040605 · Cited by 57
“Two leading methods of statistical inference are commonly applied that do not require clock-like behavior from the data; relaxed clocks using Bayesian inference (BI) or penalized likelihood (PL; Sanderson, 2002, 2003; Thorne et al., 1998; Thorne and Kishino, 2002).”
MethodRenner, S. S. (2004) · American Journal of Botany · doi:10.3732/ajb.91.9.1427 · Cited by 57
“I therefore adopted a Bayesian approach that does not assume a strict clock and that allows multiple calibration as well as the simultaneous use of different models for data partitions where appropriate (Thorne et al., 1998; Thorne and Kishino, 2002).”
MethodBayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters
Álvarez-Carretero, S., Goswami, A., Yang, Z., & dos Reis, M. (2019) · Systematic Biology · doi:10.1093/sysbio/syz015 · Cited by 59
Hendrixson, B. E., & Bond, J. E. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.09.010 · Cited by 56
The Inference of Stepwise Changes in Substitution Rates Using Serial Sequence Samples
Drummond, A. J., Forsberg, R., & Rodrigo, A. G. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003920 · Cited by 57
Pereira, S. L., & Baker, A. J. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.11.020 · Cited by 54
“The Ostrich Struthio camelus (AF143727, NC_002785) was used as the outgroup to root the tree and had the same fixed rate of change in the rate of DNA substitution at the beginning and at the end of its branch as imposed by the method (Kishino et al., 2001; Thorne et al., 1998 ).”
MethodInfluentialMirand, A., Schuffenecker, I., Henquell, C., Billaud, G., Jugie, G., Falcon, D., Mahul, A., Archimbaud, C., Terletskaia‐Ladwig, E., Diedrich, S., et al. (2010) · Journal of General Virology · doi:10.1099/vir.0.021741-0 · Cited by 56
“Analyses were carried out with a Bayesian approach that does not assume a pre-specified model of demographic history, the Bayesian skyline plot (piecewise skyline model), and with methods that relax the assumption of a strict molecular clock (Drummond et al., 2006; Thorne et al., 1998).”
MethodKaliszewska, Z. A., Seger, J., Rowntree, V. J., Barco, S. G., BENEGAS, R., Best, P. B., Brown, M. W., Brownell, R. L., Carribero, A., Harcourt, R. G., et al. (2005) · Molecular Ecology · doi:10.1111/j.1365-294x.2005.02664.x · Cited by 56
“These authors estimated the ages of internal nodes in their tree using the ‘relaxed clock’ model of Thorne et al. (1998) and Kishino et al. (2001), with calibration provided by two fossil dates.”
Dated Plant Phylogenies Resolve Neogene Climate and Landscape Evolution in the Cape Floristic Region
Hoffmann, V., Verboom, G. A., & Cotterill, F. P. D. (2015) · PLoS ONE · doi:10.1371/journal.pone.0137847 · Cited by 56
“In contrast to the relaxed clock model applied in this study, most published dates were obtained using methods which assume rate autocorrelation (i.e. nonparametric rate smoothing [98], penalized likelihood [99] and the relaxed Bayesian clock implemented in Multidivtime [100,101] and these gave dates that were consist…”
BackgroundTeeling, E. C., Madsen, O., Murphy, W. J., Springer, M. S., & O’Brien, S. J. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00117-9 · Cited by 56
“Divergence times were estimated using the program divtime5b (Kishino et al., 2001; Thorne et al., 1998).”
MethodA multigene timescale and diversification dynamics of Ciliophora evolution
Fernandes, N. M., & Schrago, C. G. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106521 · Cited by 55
Thiv, M., van der Niet, T., Rutschmann, F., Thulin, M., Brune, T., & Linder, H. P. (2010) · American Journal of Botany · doi:10.3732/ajb.1000339 · Cited by 55
Brammer, C. A., & von Dohlen, C. D. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.09.006 · Cited by 55
The evolution of Dscam genes across the arthropods
Armitage, S. A. O., Freiburg, R. Y., Kurtz, J., & Bravo, I. G. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-53 · Cited by 53
Continuous and tractable models for the variation of evolutionary rates
Lepage, T., Lawi, S., Tupper, P. F., & Bryant, D. (2006) · Mathematical Biosciences · doi:10.1016/j.mbs.2005.11.002 · Cited by 57
“This we have for the models [4,22,23,5] and for the CIR model, but not for the models of [21].”
InfluentialEvolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary
Springer, M. S., Foley, N. M., Brady, P. L., Gatesy, J., & Murphy, W. J. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.01241 · Cited by 56
Tinn, O., & Oakley, T. H. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.03.001 · Cited by 54
Molecular dating and biogeography of fig-pollinating wasps
López‐Vaamonde, C., Wikström, N., Kjer, K. M., Weiblen, G. D., Rasplus, J., Machado, C. A., & Cook, J. M. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.05.028 · Cited by 54
“1.70 (Sanderson, 2003); (iii) a model-based Bayesian implementation of rate autocorrelation (Thorne et al., 1998) as implemented in the program Multidivtime ver.”
InfluentialHoward, R. J., Edgecombe, G. D., David, L., Pisani, D., & Lozano-Fernández, J. (2019) · Organisms Diversity & Evolution · doi:10.1007/s13127-019-00390-7 · Cited by 54
“To address these problems, a variety of models have been developed to relax the assumptions of the molecular clock (e.g. Sanderson 1996; Rambaut and Bromham 1998; Thorne et al. 1998; Thorne and Kishino 2002; Drummond et al. 2006; Lepage et al. 2007; Linder et al. 2011; Ronquist et al. 2012).”
A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies
Tao, Q., Tamura, K., Battistuzzi, F. U., & Kumar, S. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz014 · Cited by 50
“This idea led to statistical modeling of the variability of evolutionary rates among branches and formed the basis of the earliest methods for estimating divergence times without assuming a strict molecular clock (Sanderson 1997; Thorne et al. 1998; Kumar 2005; Ho and Duchêne 2014; Kumar and Hedges 2016).”
MethodMolecular evidence for major placental clades
Springer, M. S., Murphy, W. J., Eizirik, E., apos, O., & Brien, S. J. O. (2005) · Cited by 55
Sharpe*, S. C., Eme*, L., Brown, M. W., & Roger, A. J. (2015) · Advances in Marine Genomics · doi:10.1007/978-94-017-9642-2_1 · Cited by 49
Molecular dates for the “cambrian explosion”: The influence of prior assumptions.
Welch, J. J., Fontanillas, E., & Bromham, L. (2005) · Systematic Biology · doi:10.1080/10635150590947212 · Cited by 53
“In common with most previous authors, ArisBrosou and Yang rely on the reasonable assumption that rates change gradually over the tree (see also Sanderson, 1997, 2002; Thorne et al., 1998; Huelsenbeck et al., 2000).”
MethodResultInfluentialEstimation of species divergence times in presence of cross-species gene flow
Tiley, G. P., Flouri, T., Jiao, X., Poelstra, J. W., Xu, B., Zhu, T., Rannala, B. H., Yoder, A. D., & Yang, Z. (2023) · Systematic Biology · doi:10.1093/sysbio/syad015 · Cited by 55
“Sophisticated relaxed-clock methods (Thorne et al. 1998; Drummond et al. 2006; Lepage et al. 2007; Rannala and Yang 2007) exist that can leverage multiple marginal prior distributions that represent external fossil (Benton and Donoghue 2007) or geological (De Baets et al. 2016) calibrations while…”
BackgroundNot so old Archaea – the antiquity of biogeochemical processes in the archaeal domain of life
Blank, C. E. (2009) · Geobiology · doi:10.1111/j.1472-4669.2009.00219.x · Cited by 52
“The third used Bayesian methods (MULTIDIVTIME; Thorne et al., 1998), where branch lengths of the consensus topology were estimated in”
MethodMolecular Phylogeny and Dating of Early Primate Divergences
Eizirik, E., Murphy, W. J., Springer, M. S., & O’Brien, S. J. (2004) · Springer eBooks · doi:10.1007/978-1-4419-8873-7_2 · Cited by 54
Nowak, M. D., Smith, A. B., Simpson, C., & Zwickl, D. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066245 · Cited by 52
“rate variation such as BEAST [13,17], MCMCTREE [18], MultiDivTime [19], PhyloBayes [20], and TimeTree [21].”
Using fossils and molecular data to reveal the origins of the Cape proteas (subfamily Proteoideae)
Sauquet, H., Weston, P. H., Barker, N. P., Anderson, C. L., Cantrill, D. J., & Savolainen, V. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.12.013 · Cited by 52
Building trees of algae: some advances in phylogenetic and evolutionary analysis
Verbruggen, H., & Theriot, E. C. (2008) · European Journal of Phycology · doi:10.1080/09670260802207530 · Cited by 53
Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework
Bloomquist, E. W., & Suchard, M. A. (2009) · Systematic Biology · doi:10.1093/sysbio/syp076 · Cited by 50
“…the past decade, investigators have realized the shortcomings of a strict molecular clock (Zuckerkandl and Pauling 1965; Bromham and Penny 2003) and have introduced several models to relax this assumption for bifurcating trees (Thorne et al. 1998; Aris-Brosou and Yang 2002; Drummond et al. 2006).”
BackgroundBayesian relaxed clock estimation of divergence times in foraminifera
Groussin, M., Pawlowski, J. W., & Yang, Z. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.06.008 · Cited by 51
“The likelihood was calculated under the HKY85 + C 5 model, using both Felsenstein's (1981) exact algorithm and using the normal approximation (Thorne et al., 1998; Yang, 2006: figure 7.10).”
InfluentialBranstetter, M. G., Müller, A., Griswold, T., Orr, M. C., & Zhu, C. (2021) · Systematic Entomology · doi:10.1111/syen.12470 · Cited by 55
“In contrast, mcmctree has a less user-friendly interface, but it implements an approximate method to calculating the likelihood that makes analysing very large datasets tractable (Thorne et al., 1998; dos Reis & Yang, 2011).”
MethodKsepka, D. T. (2009) · Cladistics · doi:10.1111/j.1096-0031.2009.00250.x · Cited by 54
“Molecular sequence data can be used in concert with temporal calibration points to estimate the absolute ages of divergences within a clade (Ayala, 1986; Thorne et al., 1998; Sanderson, 2002, 2003; Thorne and Kishino, 2002; Drummond et al., 2006).”
BackgroundMolecular clocks and the early evolution of metazoan nervous systems
Wray, G. A. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0046 · Cited by 51
Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies
Didelot, X., Siveroni, I. A., & Volz, E. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa193 · Cited by 48
“An alternative class of models is the autocorrelated RC models, where neighboring branches share similar rates (Thorne et al. 1998; Ho et al. 2005; Ho and Duchêne 2014; Bromham et al. 2018).”
Condamine, F. L., Toussaint, E. F. A., Cotton, A. M., Genson, G., Sperling, F. A. H., & Kergoat, G. J. (2012) · Cladistics · doi:10.1111/j.1096-0031.2012.00412.x · Cited by 51
“As the hypothesis of a molecular clock was not statistically supported for our dataset, methods of dating that account for rate variation across lineages were used (Thorne et al., 1998; Sanderson, 2002; Drummond et al., 2006).”
MethodInfluentialPérez‐Collazos, E., SΑNCHEZ‐GÓMEZ, P., Jiménez, J. F., & Catalán, P. (2009) · Molecular Ecology · doi:10.1111/j.1365-294x.2008.04060.x · Cited by 51
“Divergence times and additional parameters were calculated using the programs Baseml (paml package, Yang 1997), Estbranches (Thorne et al. 1998) and Multidivtime (Kishino et al. 2001) using the same settings indicated by Cano-Maqueda et al. (2008) for the western Asian–Mediterranean Campanula…”
MethodZhao, Z., & Li, S. (2017) · Systematic Biology · doi:10.1093/sysbio/syx042 · Cited by 51
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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