The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
Estimating the rate of evolution of the rate of molecular evolution
Open accessAbstract
A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source doesn’t support the claim as written.
In the citing paper
“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]
Checked by a reasoning model — may be wrong.
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]
The cited source says what the claim attributes to it.
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]
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]
The cited source says what the claim attributes to it.
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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gelman, A., Carlin, J. B., Stern, H. S., & Rubin, D. B. (2003) · doi:10.1201/9780429258480 · Cited by 27,276
Monte Carlo sampling methods using Markov chains and their applications.
Hastings, W. K. (1970) · Biometrika · doi:10.1093/biomet/57.1.97 · Cited by 15,195
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
The Neutral Theory of Molecular Evolution
Kimura, M. (1979) · Scientific American · doi:10.1038/scientificamerican1179-98 · Cited by 7,687
The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 7,003
Evolutionary divergence and convergence in proteins.
ZUCKERKANDL, E., & PAULING, L. (1965) · Evolving Genes and Proteins · doi:10.1016/b978-1-4832-2734-4.50017-6 · Cited by 3,020
Kendall's Advanced Theory of Statistics.
Aa, Stuart, A., & Ord, K. (1995) · Journal of the American Statistical Association · doi:10.2307/2291187 · Cited by 2,663
Bayes and Empirical Bayes Methods for Data Analysis
Carlin, B. P., & Louis, T. A. (2001) · Technometrics · doi:10.1198/tech.2001.s608 · Cited by 2,110
Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference
Rannala, B. H., & Yang, Z. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02338839 · Cited by 1,751
Research works printed but not linked: 1
- [8]8. KARLIN, S., and H. M. TAYLOR. 1975. A first course in sto- chastic processes. 2nd edition. Academic Press, San Diego.
Cited by
Sorted by citations
Items 901–998 of 998
Holmes, R. S., Chan, J., Cox, L. A., Murphy, W. J., & VandeBerg, J. L. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-54 · Cited by 15
“Estimates of Evolutionary Dates for CES Gene Duplication Events We estimated the times of divergence for the CES gene family and its members using a relaxed clock approach [52, 53 ], an amino acid alignment, and three major calibration points: mouse-human, eutherian-marsupial, and synapsid-diapsid divergence times est…”
Earth History and the Evolution of Caribbean BatsPreprint
Dávalos, L. M. (2009) · Nature Precedings · doi:10.1038/npre.2009.3901.1 · Cited by 15
“Divergence times were estimated using the program multidivtime (Kishino et al. 2001; Thorne et al. 1998).”
Shrinkage-based Random Local Clocks with Scalable Inference
Fisher, A. A., Ji, X., Nishimura, A., Baele, G., Lemey, P., & Suchard, M. A. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad242 · Cited by 14
“To begin, let i and j be both daughters of node k in F , then We next turn our attention to the gradient of the log-prior, Since p ( ϕ | λ , μ ) is Gaussian, the first term gradient unwinds, Numerical solutions to the second term in equation (11) involve the change-of-variable Jacobian ( ∂ / ∂ ϕ k ) log | d ϕ / d r |…”
BackgroundInfluentialSchram, F. R. (2009) · Crustacean issues · doi:10.1201/9781420092592-c1 · Cited by 15
“This approach was built on the continual improvements of molecular clock theory and applications (Kishino et al. 2001; Thorne et al. 1998).”
The Molecular Clock and Evolutionary Rates Across the Tree of Life
Ho, S. Y. W. (2020) · Springer eBooks · doi:10.1007/978-3-030-60181-2_1 · Cited by 16
Les datations moléculaires à l’heure de la génomique
Douzery, E., Delsuc, F., & Philippe, H. (2006) · médecine/sciences · doi:10.1051/medsci/2006224374 · Cited by 19
“Ce modèle d’assouplissement de l’hypothèse de l’horloge moléculaire a été appliqué dans un cadre statistique bayésien [17, 21].”
dos Reis, M. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0128 · Cited by 15
Ruiz‐García, M., Chacón, D., Plese, T., Schuler, I., & Shostell, J. M. (2017) · Mitochondrial DNA Part A · doi:10.1080/24701394.2016.1275602 · Cited by 14
“Also, by using relaxed clock models, we can account for substitution rate variations among lineages (Thorne et al. 1998).”
MethodCo-estimation of phylogeny and divergence times of Argonautoidea using relaxed phylogenetics
Strugnell, J. M., & Allcock, A. L. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.11.017 · Cited by 13
Shedko, S. V., Мирошниченко, И. Л., & Nemkova, G. A. (2008) · Russian Journal of Genetics · doi:10.1134/s1022795408070090 · Cited by 14
“of this, to transform the tree in Fig. 2 into mtDNA chronogram, a method assuming nonstrict molecular clock [ 19 , 20] and realized within the Bayesian approach in the Estbranches and Multidivtime programs (http://statgen.ncsu.edu/thorne/multidivtime.html) was used.”
MethodEvolution of genes and taxa: a primer
Doyle, J. J., & Gaut, B. S. (2000) · Springer eBooks · doi:10.1007/978-94-011-4221-2_1 · Cited by 14
Barido‐Sottani, J., Żyła, D., & Heath, T. A. (2022) · Systematic Biology · doi:10.1093/sysbio/syac073 · Cited by 13
“When combined with models characterizing the distribution of substitution rates among branches (such as “relaxed clock” models like those described by Thorne et al., 1998; Drummond et al., 2006; Lepage et al., 2007, and many others), these advances led to the introduction of new Bayesian approaches…”
MethodUncertainty in Divergence Time Estimation
Carruthers, T., & Scotland, R. W. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa096 · Cited by 15
Beavan, A. J. S., Pisani, D., & Donoghue, P. C. J. (2021) · Science Advances · doi:10.1126/sciadv.abf2257 · Cited by 13
“s t, t ′ = − ────────────── − exp(− ( − ) ( t ′ − t ) ) (2)”
Triant, D., & DeWoody, J. (2009) · Journal of Mammalogy · doi:10.1644/08-mamm-a-149r1.1 · Cited by 13
“The time when the numt clade arose was estimated with a Bayesian relaxed molecular clock approach as implemented in the multidistribute package (Kishino et al. 2001; Thorne and Kishino 2002; Thorne et al. 1998).”
MethodSlovák, M., Kučera, J., Lack, H. W., Ziffer‐Berger, J., Melichárková, A., Záveská, E., & Vďačný, P. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.11.006 · Cited by 13
Augustine, A., & Imelda, J. (2018) · Biocatalysis and Agricultural Biotechnology · doi:10.1016/j.bcab.2018.05.009 · Cited by 13
Martn-Bravo, S., & Escudero, M. (2012) · InTech eBooks · doi:10.5772/32313 · Cited by 13
Nikaido, M., Cao, Y., Okada, N., & Hasegawa, M. (2003) · Genes & Genetic Systems · doi:10.1266/ggs.78.107 · Cited by 13
“We used the method of Thorne et al. (1998) to estimate branching dates without assuming a molecular clock, with the same calibration and constraints as those used by Nikaido et al. (2001), and estimated the timing of the divergence of the two individual tenrecs examined as 3.3 ± 0.8 MyrBP.”
MethodInfluentialBattistuzzi, F. U., Filipski, A. J., & Kumar, S. (2011) · Wiley eBooks · doi:10.1002/9780470015902.a0001803.pub2 · Cited by 12
“Following this hypothesis, the autocorrelation model of evolutionary rates was developed and implemented in the first relaxed clockmethods (Sanderson, 1997; Thorne et al., 1998).”
MethodLindsey, C. R., Knoll, A. H., Herron, M. D., & Rosenzweig, F. (2024) · BMC Biology · doi:10.1186/s12915-024-01878-1 · Cited by 12
“2 and Table 1), and four relaxed clock models: autocorrelated lognormal (LN) [93] and Cox-Ingersoll-Ross (CIR) [94] models, and the uncorrelated gamma (UGAM) and white -noise (WN) models [95].”
BackgroundMethodWang, F., Wang, S., Wu, Y., Jiang, D., Yi, Q., Zhang, M., Yu, H. J., Yuan, X., Li, M., Li, G., et al. (2025) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13819 · Cited by 12
“MCMCTree performs Bayesian estimation of species divergence times using the divergence time of P. trifoliata at 9.5 Mya and DYC002 at 7.5 Mya as constraints with the approximate likelihood method (Thorne et al., 1998; Wu et al., 2018).”
InfluentialMolecular Evolution of Hemagglutinin (H) Gene in Measles Virus Genotypes D3, D5, D9, and H1
Saitoh, M., Takeda, M., Gotoh, K., Takeuchi, F., Sekizuka, T., Kuroda, M., Mizuta, K., Ryo, A., Tanaka, R., Ishii, H., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0050660 · Cited by 12
“The time of the most recent common ancestor (tMRCA) with a 95% highest posterior density (HPD) was estimated by Bayesian molecular dating as described previously [9,10].”
MethodYang, Q., Zhu, Y., Xiong, B., & Liu, H. (2011) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.28.158 · Cited by 12
“MULTIDIVTIME was used to estimate the posterior ages of branching events, their standard deviations, and the 95% credibility intervals via Markov chain Monte Carlo.”
MethodDai, Y., Winterton, S. L., Garzón‐Orduña, I. J., Liang, F., & Liu, X. (2016) · Austral Entomology · doi:10.1111/aen.12220 · Cited by 12
“In the analysis using PhyloBayes, we ran a chain of an autocorrelated lognormal relaxed clock model (Thorne et al. 1998) and a birth-death process as the tree prior for 50000 cycles with the first 2000 cycles discarded as burnin.”
MethodA road map for phylogenetic models of species trees
Cornuault, J., & Sanmartín, I. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107483 · Cited by 12
Barraclough, T. G., & Davies, T. J. (2001) · Cambridge University Press eBooks · doi:10.1017/cbo9780511614927.018 · Cited by 12
Between a Rock and a Hard Place: Applications of the “Molecular Clock” in Systematic Biology
Bell, C. D. (2015) · Systematic Botany · doi:10.1600/036364415x686297 · Cited by 12
The Use of Bioinformatics for Studying HIV Evolutionary and Epidemiological History in South America
Bello, G., Soares, M. A., & Schrago, C. G. (2011) · AIDS Research and Treatment · doi:10.1155/2011/154945 · Cited by 12
“This is mainly because the BI allows the usage of sophisticated models of evolutionary rate evolution, such as correlated [62] and uncorrelated models [59].”
BackgroundCennamo, P., Guacchio, E. D., Paino, L., CASTRO, O. D., Menale, B., Vasquez-Torres, M., & Caputo, P. (2013) · Phytotaxa · doi:10.11646/phytotaxa.141.1.3 · Cited by 12
Studying language evolution in the age of big data
Tanmoy Bhattacharya, A., Retzlaff, N., Blasi, D. E., Croft, W., Cysouw, M., Hruschka, D. J., Maddieson, I., Müller, L., Smith, E., Stadler, P. F., et al. (2018) · Journal of Language Evolution · doi:10.1093/jole/lzy004 · Cited by 12
“6 Second, models that allow a drift of the underlying process parameters, such as rates of change (Thorne et al. 1998) or patterns of covariation (Penny et al. 2001), have been developed and used, and with enough data, the extra parameters introduced can indeed be estimated.”
Bawono, P., & Heringa, J. (2014) · Elsevier eBooks · doi:10.1016/b978-0-444-53632-7.01108-4
Soria‐Hernanz, D. F., Braverman, J. M., & Hamilton, M. B. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn074 · Cited by 13
Deciphering deuterostome phylogeny: molecular, morphological, and palaeontological perspectives
Smith, A. B., & Swalla, B. J. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0009 · Cited by 13
The evolution of nervous system centralization
Arendt, D., Denes, A. S., Jékely, G., & Tessmar‐Raible, K. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0007 · Cited by 12
Bayesian Inference of Phylogenetics Revisited: Developments and Concerns
Randle, C. P., Mort, M. E., & Crawford, D. J. (2005) · Taxon · doi:10.2307/25065298 · Cited by 12
Rates of molecular evolution and their application to neotropical avian biogeography
Witt, C. C. (2004) · Louisiana State University · doi:10.31390/gradschool_dissertations.3296 · Cited by 12
Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family
Li, G., Janecka, J. E., & Murphy, W. J. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msq281 · Cited by 12
“We estimated divergence times for feline CES7 gene orthologs using the software ‘‘estbranches’’ (F84 model) and ‘‘multidivtime’’ (Thorne et al. 1998; Kishino et al. 2001; Thorne and Kishino 2002), using published fossil constraints (Johnson et al. 2006).”
MethodHernández, R., van den Berg, C., Mendoza, C. G., Cevallos, M. P., Efraín Freire, M., Lemmon, E. M., Lemmon, A. R., & Magallón, S. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.850521 · Cited by 13
A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution
Gemmell, P., Sackton, T. B., Edwards, S. V., & Liu, J. S. (2024) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1011995 · Cited by 11
Probabilistic models of eukaryotic evolution: time for integration
Lartillot, N. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0338 · Cited by 11
Nguembock, B., Fjeldså, J., Cruaud, C., & Pasquet, É. (2008) · Zoologica Scripta · doi:10.1111/j.1463-6409.2008.00344.x · Cited by 11
“4 Chronogram obtained from the Bayesian relaxed-clock method of Thorne et al. (1998) and Thorne & Kishino (2002) and using the Bayesian topology obtained with the combined data set partitioned by gene and codon position.”
MethodDating species divergences using rocks and clocks
Yang, Z., & Donoghue, P. C. J. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0126 · Cited by 11
“The past decade has seen exciting developments in clock-dating methodologies, especially in the Bayesian framework, such as stochastic models of evolutionary rate change to deal with the sloppiness of the clock [5–7], flexible calibration curves to accommodate uncertain fossil information [8].”
MethodNguembock, B., Cibois, A., Bowie, R. C. K., Cruaud, C., & Pasquet, É. (2009) · Journal of Avian Biology · doi:10.1111/j.1600-048x.2009.04410.x · Cited by 11
Pereira, S. L., & Wajntal, A. (2008) · Genetics and Molecular Biology · doi:10.1590/s1415-47572008005000021 · Cited by 11
“Estimates of the Bayesian posterior distribution of di- vergence times were performed using the Multidivtime package (Thorne and Kishino, 2002; Thorne et al., 1998), which assumes a stochastic model of change in rates of DNA substitution over time.”
BackgroundMethodInfluentialPeterson, K. J., Cotton, J. A., Gehlîng, J. G., & Pisani, D. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0002 · Cited by 12
A new survey on knowledge discovery and data mining
Mhamdi, F., & Elloumi, M. (2008) · International Conference on Research Challenges in Information Science (RCIS) · doi:10.1109/rcis.2008.4632134 · Cited by 11
“Justify Temperature < 37.5”
BackgroundInfluentialMolecular paleobiology — Progress and perspectives
Wörheide, G., Dohrmann, M., & Yang, Q. (2016) · Palaeoworld · doi:10.1016/j.palwor.2015.01.005 · Cited by 10
Relative Time Constraints Improve Molecular Dating
Szöllõsi, G. J., Höhna, S., Williams, T. A., Schrempf, D., Daubin, V., & Boussau, B. (2022) · Systematic Biology · doi:10.1093/sysbio/syab084 · Cited by 23
Kovacs, T. G. L., Walker, J., Hellemans, S., Bourguignon, T., Tatarnic, N. J., McRae, J. M., Ho, S. Y. W., & Lo, N. C. (2024) · Systematic Biology · doi:10.1093/sysbio/syae002 · Cited by 10
“The most widely used relaxed clocks either treat the branch rates as autocorrelated 53 (Thorne et al. 1998; Sanderson 2002; Lepage et al. 2006), where they are assumed to be 54 related between adjacent branches, or uncorrelated, where they are drawn independently from 55 a chosen parametric distribution (Drummond et a…”
BackgroundPractical Guide and Review of Fossil Tip-Dating in Phylogenetics
Heckeberg, N. S., Capobianco, A., Khakurel, B., Darlim, G., & Höhna, S. (2025) · Systematic Biology · doi:10.1093/sysbio/syaf050 · Cited by 13
“The strict morphological clock assumption can be relaxed similar to molecular relaxed clocks ( Thorne et al. 1998 ; Huelsenbeck et al. 2000 ; Drummond et al. 2006 ).”
Bakiu, R., Korro, K., & Santovito, G. (2015) · The European Zoological Journal · doi:10.1080/11250003.2015.1018352 · Cited by 10
“The TK02 model is a continuous autocorrelated model similar to the one implemented in multidivtime (Thorne et al. 1998; Thorne & Kishino 2002).”
Intercontinental and intracontinental biogeography—patterns and methods
Wen, J., Xiang, Q., Qian, H., Li, J., Wang, X.-Q., & Ickert‐Bond, S. M. (2009) · Journal of Systematics and Evolution · doi:10.1111/j.1759-6831.2009.00052.x · Cited by 10
“To account for the heterogeneity, relaxed molecular clock approaches have been developed (Thorne et al., 1998; Sanderson, 2002; Yang & Yoder, 2003; Drummond et al., 2006) with the availability of computer programs such as r8s, multidivtime, and BEAST (Thorne & Kishino, 2002; Sanderson, 2003; Drummond & Rambaut, 2007;…”
MethodAccounting for Calibration Uncertainty: Bayesian Molecular Dating as a “Doubly Intractable” Problem
Guindon, S. (2018) · Systematic Biology · doi:10.1093/sysbio/syy003 · Cited by 10
“Thorne et al. (1998) devised a similar yet more explicit statistical model of a “relaxed clock” and based the inference on the posterior distribution of model parameters.”
BackgroundMethodDerouiche, L., Irzagh, A., Rahmouni, R., Tahri, R., Hadjeloum, M., Bouhadad, R., & Fernandes, C. (2020) · Gene · doi:10.1016/j.gene.2020.144510 · Cited by 10
Carruthers, T., & Scotland, R. W. (2021) · Systematic Biology · doi:10.1093/sysbio/syab021 · Cited by 10
Gouws, G., Stewart, B. A., & Daniels, S. R. (2010) · Biological Journal of the Linnean Society · doi:10.1111/j.1095-8312.2010.01485.x · Cited by 10
Neutral and adaptive protein evolution
Yang, Z. (2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198567028.003.0008 · Cited by 10
Understanding mammalian evolution using Bayesian phylogenetic inference
Kelly, C. D. (2005) · Mammal Review · doi:10.1111/j.1365-2907.2005.00064.x · Cited by 10
“Recently, Springer et al. (2003) investigated this issue using Murphy et al.’s (2001b) large molecular data set (see below for details), in conjunction with the above-mentioned Bayesian approaches for estimating posterior probabilities of divergence times (Thorne et al., 1998; Kishino et al., 2001).”
BackgroundMethodResultInfluentialLemey, P., Salemi, M., Wang, B., Duffy, M., Hall, W. H., Saksena, N. K., & Vandamme, A. (2003) · FEMS Immunology & Medical Microbiology · doi:10.1016/s0928-8244(03)00239-6 · Cited by 10
Scalable Bayesian Divergence Time Estimation With Ratio Transformations
Ji, X., Fisher, A. A., Su, S., Thorne, J. L., Potter, B. I., Lemey, P., Baele, G., & Suchard, M. A. (2023) · Systematic Biology · doi:10.1093/sysbio/syad039 · Cited by 11
“…much effort and improvement have shaped the molecular clock models to better characterize evolutionary rate heterogeneity along phylogenies (Thorne et al., 1998; Kishino et al., 2001; Drummond et al., 2006; Rannala and Yang, 2007; Lemey et al., 2010; Lartillot et al., 2016; Bletsa et al.,…”
BackgroundSelf-citationTerrestrialization: toward a shared framework for ecosystem evolution
Boyce, C. K., & Nelsen, M. P. (2025) · Paleobiology · doi:10.1017/pab.2024.15 · Cited by 9
“…have improved dramatically with the advent of likelihood-based methods, relaxed clocks, and Bayesian approaches that include diverse tree and node constraint priors (Thorne et al. 1998; Sanderson 2002; Yang and Rannala 2005; Drummond et al. 2006; Drummond and Rambaut 2007; Heath et al. 2014).”
Bužan, E., Pagès, M., MICHAUX, J. R., & Kryštufek, B. (2011) · Zoologica Scripta · doi:10.1111/j.1463-6409.2011.00494.x · Cited by 9
“The Bayesian dating method implemented in Multidivtime accounting for change in evolutionary rate over times (Thorne et al. 1998; Thorne & Kishino 2002) was 40, 6, November 2011, pp 545–553 547 used to estimate divergence dates (following the procedure described in Rutschmann 2005).”
MethodAccounting for the Biological Complexity of Pathogenic Fungi in Phylogenetic Dating
Edwards, H. M., & Rhodes, J. L. (2021) · Journal of Fungi · doi:10.3390/jof7080661 · Cited by 9
Population genomics of decline and local extinction in the endangered Australian Pookila
Burns, P. A., Rowe, K. C., Parrott, M. L., & Roycroft, E. (2023) · Biological Conservation · doi:10.1016/j.biocon.2023.110183 · Cited by 9
Darriba, D., Aberer, A. J., Flouri, T., Heath, T. A., Izquierdo-Carrasco, F., & Stamatakis, A. (2013) · IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum · doi:10.1109/ipdpsw.2013.267 · Cited by 9
“We assume that this disproportional slowdown is associated with the original DPPDiv implementation generating so many denormalized floating point values (and hence exceptions) because it lacks a numerical scaling procedure.”
Jin, H., Yonezawa, T., Zhong, Y., Kishino, H., & Hasegawa, M. (2016) · Genes & Genetic Systems · doi:10.1266/ggs.16-00003 · Cited by 9
Self-citationBarrientos-Villalobos, J., & Schmitter-Soto, J. (2019) · Environmental Biology of Fishes · doi:10.1007/s10641-019-00920-4 · Cited by 10
DNA barcoding of reef‐associated fishes of Saint Martin's Island, Northern Bay of Bengal, Bangladesh
Habib, K. A., Islam, M. J., Sakib, M. N., Brishti, P. S., & Neogi, A. K. (2023) · Ecology and Evolution · doi:10.1002/ece3.10641 · Cited by 9
“Although the absolute rate of change in the 16S rRNA gene sequence is not known, it does mark the evolutionary distance and relatedness of organisms (Kimura, 1980; Pace, 1997; Rajendhran & Gunasekaran, 2011; Thorne et al., 1998).”
BackgroundKiyota, N., Kobayashi, M., Tsukagoshi, H., Ryo, A., Harada, S., Kusaka, T., Obuchi, M., Shimojo, N., Noda, M., & Kimura, H. (2013) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2013.10.024 · Cited by 9
“Another technique, the Bayesian Markov chain Monte Carlo (MCMC) method, enables the time-scaled phylogeny of viral genes to be estimated (Lepage et al., 2007; Thorne et al., 1998).”
MethodBarker, D. (2014) · Biology & Philosophy · doi:10.1007/s10539-014-9455-x · Cited by 9
“Where the area of research seems to demand such models, this is a strong incentive to use a Bayesian rather than a likelihood approach (e.g. Thorne et al. 1998; Drummond et al. 2006; Huelsenbeck et al. 2006; Rannala and Yang 2007).”
MethodRelaxing the Molecular Clock to Different Degrees for Different Substitution Types
Lee, H., Rodrigue, N., & Thorne, J. L. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv099 · Cited by 9
Self-citationPhylogenetic skew: an index of community diversity
Chen, H., Shao, K., & Kishino, H. (2015) · Molecular Ecology · doi:10.1111/mec.13064 · Cited by 9
Self-citationMarrero, Á. (2013) · Vieraea Folia scientiarum biologicarum canariensium · doi:10.31939/vieraea.2013.41.24 · Cited by 9
Zamora, J., Lowy, E., Ruiz-del-Valle, V., Moscoso, J., Serrano-Vela, J. I., Rivero-de-Aguilar, J., & Arnaiz‐Villena, A. (2005) · Journal für Ornithologie · doi:10.1007/s10336-005-0036-2 · Cited by 9
“About 2.6 mya, when the weather became much warmer (Uriarte-Cantolla 2003) and during periods of severe drought, bordering populations of desert finch might have set out from semi-desert areas to more humid habitats and evolved to a greenfinch-like bird (extant or extinct ancestor).”
BackgroundInfluentialZamora, J., Lowy, E., Ruiz-del-Valle, V., Moscoso, J., Serrano-Vela, J. I., Rivero-de-Aguilar, J., & Arnaiz‐Villena, A. (2006) · Journal für Ornithologie · doi:10.1007/s10336-006-0072-6 · Cited by 9
“This linearized tree was constructed by assuming that evolutionary rates between lineages may be different (Thorne et al. 1998).”
BackgroundMethodInfluentialKumar, A., Saha, B., & Singh, S. (2017) · Data in Brief · doi:10.1016/j.dib.2017.10.031 · Cited by 9
Matzig, D. N., Marwick, B., Riede, F., & Warnock, R. C. M. (2024) · Royal Society Open Science · doi:10.1098/rsos.240321 · Cited by 8
Pervasive Mitochondrial tRNA Gene Loss in Clade B of Haplosclerid Sponges (Porifera, Demospongiae)
Lavrov, D. V., Turner, T. L., & Vicente, J. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf020 · Cited by 8
“We used the lognormal (Brownian) autocorrelated clock (Thorne et al. 1998) (-ln) model for the analysis and ran two chains for > 60,000 cycles.”
Phylogenomics and the evolution of larval feeding habits in the blow flies (Diptera: Calliphoridae)
Beza-Beza, C., Soghigian, J., Bailey, E., Johnston, N. P., Cassel, B. K., Bayless, K. M., Wells, J. D., Yeates, D. K., Wallman, J. F., Yan, L., et al. (2025) · Systematic Entomology · doi:10.1111/syen.70018 · Cited by 8
“Additionally, we used the approximate likelihood method of clock dating (Thorne et al., 1998) as implemented in MCMCtree.”
Sequential Bayesian Phylogenetic Inference
Höhna, S., & Hsiang, A. Y. (2024) · Systematic Biology · doi:10.1093/sysbio/syae020 · Cited by 8
The emergence of metabolisms through Earth history and implications for biospheric evolution
Moody, E. R. R., Williams, T. A., Álvarez-Carretero, S., Szöllősi, G. J., Pisani, D., Lenton, T. M., & Donoghue, P. C. J. (2025) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2024.0097 · Cited by 12
“We used MCMCtree (PAML v. 4.10.7; [20]) for divergence time estimation under the independent-rates log-normal (ILN [21,22]; and the geometric Brownian motion (GBM, or autocorrelated-rates model [23,24]) relaxed-clock models.”
InfluentialRomero, M. F., Cerritos, R., & Ximénez, C. (2016) · Journal of Parasitology Research · doi:10.1155/2016/3241027 · Cited by 8
Higher level phylogeny of baleen whales
Gatesy, J., & McGowen, M. R. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-818969-6.00001-7 · Cited by 8
Biogeographic Dating of Phylogenetic Divergence Times Using Priors and Processes
Landis, M. J. (2020) · Springer eBooks · doi:10.1007/978-3-030-60181-2_9 · Cited by 8
Age of the last common ancestor of extant Plasmodium parasite lineages
Hayakawa, T., Tachibana, S., Hikosaka, K., Arisue, N., Matsui, A., Horii, T., & Tanabe, K. (2012) · Gene · doi:10.1016/j.gene.2012.04.037 · Cited by 8
Miyazaki, J.-I., Nakao, K., Mihara, M., Sakai, T., Gunji, Y., Tojo, K., Muraoka, K., & Hosoya, K. (2007) · ZOOLOGICAL SCIENCE · doi:10.2108/zsj.24.666 · Cited by 8
“, 2005), we hypothesized concerning evolutionary processes in Lefua loaches and estimated divergence times by considering rate of variation in molecular evolution (Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002).”
BackgroundArnaiz‐Villena, A. (2012) · The Open Ornithology Journal · doi:10.2174/1874453201205010073 · Cited by 8
“The likelihood scores estimated for that model were used, and linearized estimating the branch lengths according to the model proposed by Thorne [21], which allows the rates not to be constant among the evolutionary lineages.”
Evolution of the SEC1 gene in New World monkey lineages (Primates, Platyrrhini)
Borges, B., Paiva, T. S., & Harada, M. L. (2008) · Genetics and Molecular Research · doi:10.4238/vol7-3gmr452 · Cited by 8
“…with the software ESTBRANCHES from the MULTIDISTRIBUTE package (see Thorne et al., 1998); these were used for Bayesian molecular clock inferences (Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002), performed with the MULTDIVTIME software, also included in aforementioned…”
MethodInvertebrate Problematica: kinds, causes, and solutions
Jenner, R. A., Timothy, D. J., & Littlewood, D. T. J. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0011 · Cited by 7
Reconstructing evolutionary timescales using phylogenomicsPreprint
Tong, K., Lo, N. C., & Ho, S. Y. W. (2016) · doi:10.7287/peerj.preprints.2403v1 · Cited by 8
“Rate variation across lineages can be taken into account using relaxed molecular clocks, which were first developed in the late 1990s (Sanderson, 1997; Thorne et al., 1998).”
BackgroundMethodCampbell, C. R., Tiley, G. P., Poelstra, J. W., Hunnicutt, K. E., Larsen, P. A., Lee, H., Thorne, J. L., dos Reis, M., & Yoder, A. D. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/724880 · Cited by 8
“Phylogenetic approaches, on the other hand, use external calibrations such as fossils or geological events to obtain substitution rates in units of absolute time (Drummond et al, 2006; Sanderson, 2002; Thorne and Kishino, 2002; Thorne et al, 1998).”
BackgroundMethodSelf-citationPractical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC)
Barido‐Sottani, J., Schwery, O., Warnock, R. C. M., Zhang, C., & Wright, A. M. (2024) · Open Research Europe · doi:10.12688/openreseurope.16679.3 · Cited by 7
Rossi, M. E., Keating, J. N., Kenny, N. J., Giacomelli, M., Álvarez-Carretero, S., Schuster, A., Cárdenas, P., Taboada, S., Koutsouveli, V., Donoghue, P. C. J., et al. (2026) · Science Advances · doi:10.1126/sciadv.adx1754 · Cited by 12
“We performed molecular clock analyses under the autocorrelated-rates [AR ( 60 )] relaxed-clock model and the independent-rates [IR ( 61 )] log-normal relaxed-clock model to assess the impact of both”
The Lake Tanganyika cichlid species assemblage: recent advances in molecular phylogenetics
Koblmüller, S., Sefc, K. M., & Sturmbauer, C. (2008) · Springer eBooks · doi:10.1007/978-1-4020-9582-5_1 · Cited by 7
Koch, N. M., & Carmona, P. S. M. (2024) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.14404 · Cited by 7
“…(Kumar & Hedges, 2016), being able to accom - modate among-lineage rate variation through the use of relaxed clocks (Drummond et al., 2006; Thorne et al., 1998 ), exploit di - verse sources of both character and temporal information (O'Reilly et al., 2015 ; Ronquist et al., 2012 ), and…”
Laflamme (2004) · doi:10.1666/0022-3360(2004)078
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
