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 601–700 of 998
Courcelle, M., Tilak, M., Leite, Y. L. R., Douzery, E., & Fabre, P. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.03.007 · Cited by 55
“We used a Bayesian relaxed molecular clock with rate autocorrelation along the branches of the tree (Thorne et al. 1998; Thorne and Kishino 2002) on the reference topology yielded by the supermatrix analysis.”
MethodWerneck, F. P., Giugliano, L. G., Collevatti, R. G., & Colli, G. R. (2008) · Molecular Ecology · doi:10.1111/j.1365-294x.2008.03999.x · Cited by 51
“We estimated divergence times based on a Bayesian relaxed molecular clock approach implemented in MULTIDISTRIBUTE (Thorne et al. 1998; Kishino et al. 2001; Thorne & Kishino 2002).”
MethodThiv, M., Thulin, M., Hjertson, M., Kropf, M., & Linder, H. P. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.10.009 · Cited by 50
“The Bayesian dating method (Thorne et al., 1998; Thorne and Kishino, 2002) uses a probabilistic model to describe the change in evolutionary rate over time and uses the Markov chain Monte Carlo (MCMC) procedure to derive the posterior distribution of rates and time.”
MethodZou, X., Yang, Z., Doyle, J. J., & Ge, S. (2013) · New Phytologist · doi:10.1111/nph.12230 · Cited by 50
Hardman, M., & Hardman, L. M. (2008) · Systematic Biology · doi:10.1080/10635150801902193 · Cited by 50
Liu, J., Li, Y., Arnold, M. L., Wu, C., Wu, S., Lü, X., & Zhang, Y. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-223 · Cited by 50
“Rate constancy was rejected at the 5% level, so we employed the relaxed Bayesian methods to estimate divergence times [92,93].”
MethodPhylogenetic Inference Using RevBayes
Höhna, S., Landis, M. J., & Heath, T. A. (2017) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.22 · Cited by 48
Mangiagalli, M., Lapi, M., Maione, S., Orlando, M., Brocca, S., Pesce, A., Barbiroli, A. G., Camilloni, C., Pucciarelli, S., Lotti, M., et al. (2020) · FEBS Journal · doi:10.1111/febs.15354 · Cited by 50
Plastid Endosymbiosis: Sources and Timing of the Major Events
Hackett, J. D., Yoon, H. S., Butterfield, N. J. F., Sanderson, M. J., & Bhattacharya, D. (2007) · Elsevier eBooks · doi:10.1016/b978-012370518-1/50008-4 · Cited by 50
Forest, F., Nänni, I., Chase, M. W., Crane, P. R., & Hawkins, J. A. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.08.017 · Cited by 50
“To infer divergence time estimates and associated conWdence intervals, we used a Bayesian dating method (Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002) and followed the procedure outline in Rutschmann (2004), which involves the use of three programs: baseml (PAML package; Yang, 1997), Estbranches…”
MethodInfluentialOkajima, Y., & Kumazawa, Y. (2008) · Gene · doi:10.1016/j.gene.2008.06.011 · Cited by 49
Manos, P. S., & Meireles, J. E. (2015) · American Journal of Botany · doi:10.3732/ajb.1400530 · Cited by 49
Bayesian phylogenetic estimation of fossil ages
Drummond, A. J., & Stadler, T. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0129 · Cited by 46
Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record
Koch, N. M., Thompson, J. R., Hiley, A. S., McCowin, M. F., Armstrong, A. F., Coppard, S. E., Aguilera, F., Bronstein, O., Kroh, A., Mooi, R., et al. (2022) · eLife · doi:10.7554/elife.72460 · Cited by 48
Phylogeny Imbalance: Taxonomic Level Matters
Purvis, A., & Agapow, P. (2002) · Systematic Biology · doi:10.1080/10635150290102546 · Cited by 48
“The development of methods for date estimation in the absence of a molecular clock (e.g., Sanderson, 1997; Rambaut and Bromham, 1998; Thorne et al., 1998; Huelsenbeck et al., 2000) and indeed the increasing use of molecular data for phylogeny reconstruction raise the prospect that a different path…”
MethodVďačný, P. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy071 · Cited by 50
“…per 1 My implemented as a diffuse gamma prior G(1, 5,710) (Vd’a cn y 2015); and 6) the variance of the logarithm of the rate r2 incorporated as a diffuse gamma prior G(1, 145), whose mean represents the reciprocal of prior mean of the root age (see above), as recommended by Thorne et al. (1998).”
BackgroundComparing Patterns of Natural Selection Across Species Using Selective Signatures
Shapiro, B. J., & Alm, E. J. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0040023 · Cited by 48
“The time scale for the phylogeny was estimated using a Bayesian relaxed molecular clock model [52].”
MethodGroussin, M., Hobbs, J. K., Szöllősi, G. J., Gribaldo, S., Arcus, V. L., & Gouy, M. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu305 · Cited by 48
“The Log-normal autocorrelated relaxed clock model (Thorne et al. 1998) was chosen to allow substitution rates to vary in time.”
MethodThomas, D. T. (2008) · Cited by 48
Schulte, J. A. (2013) · International Journal of Evolutionary Biology · doi:10.1155/2013/628467 · Cited by 48
“The TK02 model is a continuous autocorrelated model similar to the one implemented in multidivtime [29, 32].”
Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations
Duchêne, D. A., Duchêne, S., Holmes, E. C., & Ho, S. Y. W. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv154 · Cited by 49
“The primary differences among the various clock models include the number of distinct substitution rates across the tree and the degree to which rates are treated as a heritable trait (Thorne et al. 1998; Drummond et al. 2006; Drummond and Suchard 2010; for a review see Ho and Duchêne 2014).”
BackgroundAssembling the spiralian tree of life
Giribet, G., Dunn, C. W., Edgecombe, G. D., Hejnol, A., Martindale, M. Q., & Rouse, G. W. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0006 · Cited by 50
Schweizer, G., Münch, K., Mannhaupt, G., Schirawski, J., Kahmann, R., & Dutheil, J. Y. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy023 · Cited by 48
“The PhyloBayes version 4.1 software (Lartillot et al. 2009) was used with the auto-correlated model of Thorne et al. (Thorne et al. 1998) under a GTR + CAT model.”
MethodInfluentialDivergence times and origin of neotropical sheath-tailed bats (Tribe Diclidurini) in South America
Lim, B. K. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.09.003 · Cited by 48
SYSTEMATICS OF A RARE SPECIES OF POCKET GOPHER, PAPPOGEOMYS ALCORNI
Demastes, J. W., Butt, A. L., Hafner, M. S., & Light, J. E. (2003) · Journal of Mammalogy · doi:10.1644/1545-1542(2003)084 · Cited by 21
New Guinea uplift opens ecological opportunity across a continent
Roycroft, E., Fabre, P., MacDonald, A. J., Moritz, C. C., Moussalli, A., & Rowe, K. C. (2022) · Current Biology · doi:10.1016/j.cub.2022.08.021 · Cited by 50
Boatwright, J. S., Savolainen, V., Wyk, B.-E. V., Schutte-Vlok, A. L., Forest, F., & van der Bank, M. (2008) · Systematic Botany · doi:10.1600/036364408783887500 · Cited by 47
“…likelihood score without clock = 16,435.28640; = 1,000.23634; Dƒ = 196; p < 0.0001), we used two dating methods to estimate time, the nonparametric rate smoothing method (NPRS; Sanderson 1997) and a Bayesian relaxed clock (Thorne et al. 1998; Kishino et al. 2001; Thorne and Kishino 2002).”
MethodInfluentialChloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species
Chen, Z., Feng, K., Grover, C. E., Li, P., Liu, F., Wang, Y., Xu, Q., MingZhao, S., Zhou, Z., Cai, X., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0157183 · Cited by 47
“3f [47], using the autocorrelated Lognormal relaxed-clock mode [48] and the tree generated from the above dataset and CAT+GTR model.”
MethodUnderstanding the Tripartite Approach to Bayesian Divergence Time Estimation
Warnock, R. C. M., & Wright, A. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108954365 · Cited by 47
Campbell, 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. (2021) · Heredity · doi:10.1038/s41437-021-00446-5 · Cited by 49
Self-citationBorges, A., Bermingham, E., Herrera, N., Alfonzo, M. J., & Sanjur, O. I. (2009) · Toxicon · doi:10.1016/j.toxicon.2009.09.011 · Cited by 47
“…a Markov chain Monte Carlo (MCMC) approach to estimate posterior probability distributions of absolute divergence times following the method of Thorne et al. (1998) and Kishino et al. (2001), and implemented for multigenic data (Thorne and Kishino, 2002) in Thorne’s software package…”
MethodCALIBRATION AGE AND QUARTET DIVERGENCE DATE ESTIMATION
Brochu, C. A. (2004) · Evolution · doi:10.1111/j.0014-3820.2004.tb01715.x · Cited by 47
Synonymous Substitutions Substantially Improve Evolutionary Inference from Highly Diverged Proteins
Seo, T., & Kishino, H. (2008) · Systematic Biology · doi:10.1080/10635150802158670 · Cited by 47
“Under the Bayesian framework, incorrect branch length estimates may result in wrong estimations of divergence time (Thorne et al., 1998) or mistaken trend estimations of selective pressure (Seo et al., 2004).”
BackgroundSelf-citationAmer, S. A. M., & Kumazawa, Y. (2005) · Gene · doi:10.1016/j.gene.2004.11.014 · Cited by 47
Hillis, D. M. (2000) · Science · doi:10.1126/science.288.5472.1757 · Cited by 47
Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses
Zhong, B., Yonezawa, T., Zhong, Y., & Hasegawa, M. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005297 · Cited by 46
“To estimate divergence times and molecular evolutionary rates, a Bayesian method implemented in MCMCTREE (in PAML [19]) was applied either with the CR model [12,13] or with the IR model [15] (using the GTR model with a discrete gamma distribution with five rate categories (C5) for nucleotide substitutions), and multip…”
BackgroundMethodMeredith, R. W., Mendoza, M. A., Roberts, K. K., Westerman, M., & Springer, M. S. (2010) · Journal of Mammalian Evolution · doi:10.1007/s10914-010-9129-7 · Cited by 46
“In contrast, Multidivtime requires a rooted tree topology, only allows for fixed minimum and maximum constraints, and assumes autocorrelated rates of molecular evolution among lineages ( Thorne et al. 1998; Kishino et al. 2001; Thorne and Kishino 2002).”
BackgroundBayesian Phylogenetics and Its Influence on Insect Systematics
Ronquist, F., & DEANS, A. R. (2009) · Annual Review of Entomology · doi:10.1146/annurev.ento.54.110807.090529 · Cited by 47
Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts
Magee, A. F., Höhna, S., Vasylyeva, T. I., Leaché, A. D., & Minin, V. N. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007999 · Cited by 48
“On each branch of T, evolution proceeds at a rate governed by a molecular clock model [33, 34, 35].”
BackgroundReconstructing ancestral ecologies: challenges and possible solutions
Hardy, C. R. (2005) · Diversity and Distributions · doi:10.1111/j.1366-9516.2006.00207.x · Cited by 46
Triant, D. A., & DeWoody, J. A. (2007) · Gene · doi:10.1016/j.gene.2007.07.003 · Cited by 45
“the multidistribute package (Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino 2002).”
InfluentialA 15-Myr-Old Genetic Bottleneck
Paape, T. D., Igić, B., Smith, S. D., Olmstead, R. G., Bohs, L., & Kohn, J. R. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn016 · Cited by 45
“Because the data do not conform to a strict molecular clock (see Results), a Bayesian method (Thorne et al. 1998; Thorne and Kishino 2002; Drummond et al. 2006) of relaxing this assumption was used to estimate divergence times among species.”
MethodA likelihood method for detecting trait-dependent shifts in the rate of molecular evolution
Mayrose, I., & Otto, S. P. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msq263 · Cited by 43
Daniels, S. R., Hofmeyr, M. D., Henen, B. T., & Crandall, K. A. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.08.010 · Cited by 45
“To guard against the assumption of a strict molecular clock we used a relaxed Bayesian clock (Thorn et al., 1998) as implemented in the package PAML version 3.”
MethodMicroRNAs and metazoan phylogeny: big trees from little genes
Sperling, E. A., & Peterson, K. J. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0015 · Cited by 45
Improving the performance of Bayesian phylogenetic inference under relaxed clock models
Zhang, R., & Drummond, A. J. (2020) · BMC Evolutionary Biology · doi:10.1186/s12862-020-01609-4 · Cited by 45
“The introduction of relaxed molecular clocks allowed for the estimation of divergence times [6] and phylogeny [7] in the presence of rate heterogeneity among branches.”
BackgroundMethodRapid Radiation and Rampant Reticulation: Phylogenomics of South AmericanLiolaemusLizards
Esquerré, D., Keogh, J. S., Demangel, D., Morando, M. M., Ávila, L. J., Sites, J. W., Ferri‐Yáñez, F., & Leaché, A. D. (2021) · Systematic Biology · doi:10.1093/sysbio/syab058 · Cited by 49
Lévy, A., Doadrio, I., & Almada, V. C. (2008) · Journal of Biogeography · doi:10.1111/j.1365-2699.2008.01969.x · Cited by 45
“Figure 3 Bayesian topology of the European leuciscin clade, drawn to scale (time in Ma) after Bayesian molecular dating (Rutschmann, 2005), given a relaxed molecular clock, using paml (Yang, 1997) and multidivtime (Thorne et al., 1998; Kishino et al., 2001), which allows for different evolutionary rates among lineages.”
MethodEgan, A. N., & Doyle, J. J. (2010) · Systematic Biology · doi:10.1093/sysbio/syq041 · Cited by 43
“A 95% confidence interval (CI) for PL is provided by bootstrap analyses and a 95% credibility interval is presented for Bayesian analyses (Table S4).”
MethodInfluentialRabbits, if anything, are likely Glires
Douzery, E., & Huchon, D. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.07.014 · Cited by 45
“(1998), implemented in the DIVTIME 5b package.”
MethodInfluentialCrottini, A., Andreone, F., Kosuch, J., Borkin, L., Litvinchuk, S., Eggert, C., & Veith, M. (2007) · Molecular Ecology · doi:10.1111/j.1365-294x.2007.03274.x · Cited by 50
“We therefore applied Bayesian molecular dating (Thorne et al. 1998) to haplotype splits using the multidivtime package of Thorne & Kishino (2002).”
MethodYu, F.-R., Yu, F.-H., Pang, J.-F., Kilpatrick, C., McGuire, P., Wang, Y.-X., Lu, S.-Q., & Woods, C. A. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2005.12.002 · Cited by 43
Wood, D. A., Fisher, R. N., & Reeder, T. W. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.11.014 · Cited by 44
“, 1996; Cranston and Rannala, 2005; Rutschmann, 2006) and agree they should be used with caution, approximate times of lineage divergence were estimated using a Bayesian relaxed clock method, implemented in MULTIDISTRIBUTE (Thorne et al., 1998; Thorne and Kishino, 2002).”
MethodAn Evolving View of Phylogenetic Support
Simon, C. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa068 · Cited by 50
Jonniaux, P., & Kumazawa, Y. (2007) · Gene · doi:10.1016/j.gene.2007.09.023 · Cited by 44
BIOGEOGRAPHY OF EASTERN POLYNESIAN MONARCHS (POMAREA): AN ENDEMIC GENUS CLOSE TO EXTINCTION
Cibois, A., Thibault, J., & Pasquet, É. (2004) · Ornithological Applications · doi:10.1093/condor/106.4.837 · Cited by 44
Seo, T., & Kishino, H. (2009) · Systematic Biology · doi:10.1093/sysbio/syp015 · Cited by 43
Self-citationVeith, M., Fromhage, L., Kosuch, J., & Miguel Vences, B. (2006) · Bijdragen tot de Dierkunde · doi:10.1163/18759866-0750304001 · Cited by 44
“strongly depend on the choice of outgroup (in our case some possible outgroups resulted in a rejection of the assumption of rate constancy) we also applied Bayesian molecular dating (Thorne et al., 1998) using the multidivtime package of Thorne and Kishino (2002).”
MethodResultAssessing parameter identifiability in phylogenetic models using data cloning
Ponciano, J. M., Burleigh, J. G., Braun, E. L., & Taper, M. L. (2012) · Systematic Biology · doi:10.1093/sysbio/sys055 · Cited by 39
“The recognition of the complexity of patterns of genomic and organismal evolution has motivated the development of novel phylogenetic models that attempt to capture a large number of features enhancing biological realism (Drummond et al. 2006; Felsenstein 2004; Fisher 2008; Huelsenbeck et al. 2000; Thorne et al. 1998;…”
BackgroundThe evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth
Mateos, K., Chappell, G., Klos, A., Le, B., Boden, J., Stüeken, E., & Anderson, R. (2023) · Science Advances · doi:10.1126/sciadv.ade4847 · Cited by 43
“To generate chronograms, we tested three different clock models: autocorrelated log normal (LN) (85), uncorrelated gamma multiplier (UGAM) (86), and the autocorrelated Cox-IngersollRoss (CIR) process (42).”
Paraskevis, D. N., Angelis, K., Magiorkinis, G., Kostaki, E. G., Ho, S. Y. W., & Hatzakis, A. E. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.07.010 · Cited by 43
Pasquet, É., Pons, J., Fuchs, J., Cruaud, C., & Bretagnolle, V. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.03.010 · Cited by 43
“Bayesian approaches for the divergence time estimates were performed using a relaxed clock method as implemented in the MULTIDIVTIME package ( Thorne et al., 1998; Thorne and Kishino, 2002).”
A retrospective study of the orthopoxvirus molecular evolution
Babkin, I. V., & Babkina, I. N. (2012) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2012.07.011 · Cited by 43
Hoffmann, F. G., Hoofer, S. R., & Baker, R. J. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.08.002 · Cited by 43
“Then, we used estbranches (Thorne et al., 1998) to estimate branch lengths and their associated variance–covariance matrix for each partition.”
Nicolas, V., Fabre, P., Bryja, J., Denys, C., Verheyen, E., Missoup, A. D., Olayemi, A., Katuala, P., Dudu, A., Colyn, M., et al. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106703 · Cited by 45
May, M. R., Contreras, D. L., Sundue, M., Nagalingum, N. S., Looy, C. V., & Rothfels, C. J. (2021) · Systematic Biology · doi:10.1093/sysbio/syab020 · Cited by 48
“…of models with a long history in Bayesian divergence-time estimation (Heath and Moore 2014), and can accommodate gradual patterns of rate change (Thorne et al. 1998; Thorne and Kishino 2002), rare episodic changes (Huelsenbeck et al. 2000), clade-specific rates (Drummond and Suchard 2010), and…”
BackgroundMethodAmer, S. A. M., & Kumazawa, Y. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm054 · Cited by 43
“Assuming the topological relationships thus obtained, divergence times at nodes were estimated using the multidistribute package (Thorne et al. 1998) after optimizing parameters for the model F84 and the gamma distribution for 8 categories by PAML (Yang 1997).”
MethodMorgan, M. J., Roberts, J. D., & Keogh, J. S. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.12.009 · Cited by 43
“, Li, 1993; Bromham and Penny, 2003) and methods have been developed to cope with data that do not evolve in a clocklike fashion (e.g., Sanderson, 1997, 2003; Thorne et al., 1998).”
MethodDating Phylogenies with Hybrid Local Molecular Clocks
Aris‐Brosou, S. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000879 · Cited by 42
“For this specific data set, it was found [33] that the penalized likelihood approach [9] seemed to perform better than both nonparametric rate smoothing [8] and a Bayesian approach [11].”
BackgroundMethodInfluentialMast, A., Olde, P. M., Makinson, R. O., Jones, E., Kubes, A., Miller, E. T., & Weston, P. H. (2015) · American Journal of Botany · doi:10.3732/ajb.1500195 · Cited by 42
Angelis, K., Álvarez-Carretero, S., dos Reis, M., & Yang, Z. (2017) · Systematic Biology · doi:10.1093/sysbio/syx061 · Cited by 46
Modeling HIV-1 Drug Resistance as Episodic Directional Selection
Murrell, B., de Oliveira, T., Seebregts, C. J., Pond, S. L. K., & Scheffler, K. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002507 · Cited by 44
“Several authors have studied models that allow evolutionary rates to change over time, including models in which the selective pressure is different on different branches [11–14] as well as various models [15–17] in which the rate of evolution at any site may change at any point in time.”
BackgroundWhat can DNA Tell us About the Cambrian Explosion?
Bromham, L. D. (2003) · Integrative and Comparative Biology · doi:10.1093/icb/43.1.148 · Cited by 42
“For example, Aris-Brosou and Yang (2002) used a Bayesian approach (Thorne et al., 1998; Kishino et al., 2001) to allow rates of substitution of the 18S rRNA gene to vary across the phylogeny of 39 species of metazoan.”
MethodGuindon, S. (2012) · Systematic Biology · doi:10.1093/sysbio/sys063 · Cited by 41
Vargas‐Ramírez, M., Maran, J., & Fritz, U. (2010) · Organisms Diversity & Evolution · doi:10.1007/s13127-010-0016-0 · Cited by 41
“Molecular dating Divergence times of the known-locality clades of C. carbonaria were estimated by a Bayesian relaxed molecular clock approach (MULTIDISTRIBUTE package; Thorne et al. 1998; Thorne and Kishino 2002).”
MethodAccelerated Evolutionary Rate of Housekeeping Genes in Tunicates
Tsagkogeorga, G., Turón, X., Galtier, N., Douzery, E., & Delsuc, F. (2010) · Journal of Molecular Evolution · doi:10.1007/s00239-010-9372-9 · Cited by 43
“Because of practical constraints in using the program MULTIDIVTIME (Thorne et al. 1998), all amino-acid alignments for the 35 orthologous markers were slightly modified in order to ensure the presence of one non-bilaterian outgroup taxa in each gene data set.”
MethodInfluentialHerman, J. L., Challis, C. J., Novák, Á., Hein, J., & Schmidler, S. C. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu184 · Cited by 42
“Following the approach of Thorne et al. (1998) and Aris-Brosou and Yang (2002) with respect to variable rates of sequence evolution, we allow 2 to vary by branch, which provides additional flexibility while allowing important properties such as infinite divisibility and reversibility to be…”
BackgroundMethodGenPhyloData: realistic simulation of gene family evolution
Sjöstrand, J., Arvestad, L., Lagergren, J., & Sennblad, B. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-209 · Cited by 41
“In the second variant, autocorrelated models [22-26], a gradual rate evolution of the tree is modeled from the root to the leaves, so that rates are autocorrelated over paths in the tree.”
BackgroundMethodESTIMATING DIVERSIFICATION RATES: HOW USEFUL ARE DIVERGENCE TIMES?
Wertheim, J. O., & Sanderson, M. J. (2010) · Evolution · doi:10.1111/j.1558-5646.2010.01159.x · Cited by 41
“Most sequence datasets show evidence for nonclocklike evolution, which has prompted the widespread use of “relaxed clock” methods for inferring divergence times (Sanderson 1997, 2002; Thorne et al. 1998; Drummond et al. 2006).”
BackgroundSaslis‐Lagoudakis, C. H., Chase, M. W., Robinson, D. N., Russell, S. J., & Klitgaard, B. B. (2008) · American Journal of Botany · doi:10.3732/ajb.0800101 · Cited by 41
Gradients Do Grow on Trees: A Linear-Time O ( N )-Dimensional Gradient for Statistical Phylogenetics
Ji, X., Zhang, Z., Holbrook, A. J., Nishimura, A., Baele, G., Rambaut, A., Lemey, P., & Suchard, M. A. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa130 · Cited by 41
“Autocorrelated relaxed clock models assume that evolutionary rate undergoes a diffusion process from the root node to successive branches (Thorne et al. 1998; Kishino et al. 2001; Aris-Brosou and Yang 2002), whereas uncorrelated clock models make no assumption of rate correlation among branches…”
BackgroundRadiation of the ,,Drosophila“ subgenus (Drosophilidae, Diptera) in the Neotropics
Robe, L. J., Loreto, É. L. S., & Valente, V. L. D. S. (2010) · Journal of Zoological Systematics & Evolutionary Research · doi:10.1111/j.1439-0469.2009.00563.x · Cited by 41
Birth-death prior on phylogeny and speed dating
Åkerborg, Ö., Sennblad, B., & Lagergren, J. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-77 · Cited by 40
“[14], is to model rates as evolving over the tree, such that there is an auto-correlation between rates at adjacent nodes.”
BackgroundFan, D., Chen, J., Meng, Y., Wen, J., Huang, J., & Yang, Y. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.08.018 · Cited by 40
“Bayesian dating employs a probabilistic model to describe the change in evolutionary rates over time and uses the MCMC procedure to derive the posterior distribution of rates and time (Thorne et al., 1998; Thorne and Kishino, 2002).”
MethodTang, Q., Getahun, A., & Liu, H. (2009) · Hydrobiologia · doi:10.1007/s10750-009-9848-z · Cited by 40
“The software MULTIDIVTIME was used to estimate the posterior ages of branching events and their standard deviations via Markov chain Monte Carlo (MCMC) analyses.”
MethodSainz-Escudero, L., López‐Estrada, E. K., Rodríguez‐Flores, P. C., & Garcı́a-Parı́s, M. (2021) · PeerJ · doi:10.7717/peerj.10865 · Cited by 40
Galtier, N., Blier, P. U., & Nabholz, B. (2008) · Mitochondrion · doi:10.1016/j.mito.2008.11.006 · Cited by 39
“Here we used the MULTIDIVTIME software (Thorne et al., 1998).”
MethodPadhi, A., & Verghese, B. (2011) · Veterinary Microbiology · doi:10.1016/j.vetmic.2011.10.005 · Cited by 40
Lum, J., Nikaido, M., Shimamura, M., Shimodaira, H., Shedlock, A., Okada, N., & Hasegawa, M. (2000) · Molecular biology and evolution · doi:10.1093/oxfordjournals.molbev.a026242 · Cited by 40
“In contrast, molecular phylogenetics have described cetaceans as nested within the order Artiodactyla (Graur and Higgins 1994; Shimamura et al. 1997), often with whales and hippopotamuses as sister taxa (Sarich 1985; Gatesy et al. 1996; Ursing and Arnarson 1998; Nikaido, Rooney, and Okada 1999).”
BackgroundShemesh, E., Huchon, D., Simon‐Blecher, N., & Achituv, Y. (2009) · Zoologica Scripta · doi:10.1111/j.1463-6409.2008.00384.x · Cited by 39
“Journal compilation © 2009 The Norwegian Academy of Science and Letters Molecular dating analyses were performed according to the Bayesian relaxed molecular clock approach (Thorne et al. 1998; Kishino et al. 2001) as implemented in the”
MethodNunome, M., Yasuda, S. P., Sato, J. J., Vogel, P., & Suzuki, H. (2007) · Zoologica Scripta · doi:10.1111/j.1463-6409.2007.00296.x · Cited by 39
Mast, A., Milton, E. F., Jones, E. H., Barker, R. M., Barker, W. R., & Weston, P. H. (2012) · American Journal of Botany · doi:10.3732/ajb.1100420 · Cited by 39
Linder, M., Britton, T., & Sennblad, B. (2011) · Systematic Biology · doi:10.1093/sysbio/syr009 · Cited by 39
“Although other priors for divergence times have been proposed (Thorne et al. 1998; Kishino et al. 2001; Drummond et al. 2006; Lepage et al. 2007), the birth–death process is the classic model for branching processes both in mathematics and in biology and is the natural null model choice for analyses above population l…”
BackgroundMethodInfluentialSpringer, M. S., Emerling, C. A., Gatesy, J., Randall, J. G., Collin, M. A., Hecker, N., Hiller, M., & Delsuc, F. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1359-6 · Cited by 39
Multiple invasions of Europe by East Asian cobitid loaches (Teleostei: Cobitidae)
Tang, Q., Freyhof, J., Xiong, B., & Liu, H. (2008) · Hydrobiologia · doi:10.1007/s10750-008-9296-1 · Cited by 39
“MULTIDIVTIME is used to estimate the prior and posterior ages of branching events, their standard deviations, and the 95% credibility intervals via Markov chain Monte Carlo.”
MethodSoares, A. E. R., & Schrago, C. G. (2014) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.09.004 · Cited by 39
Meredith, R. W., Westerman, M., & Springer, M. S. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.01.002 · Cited by 39
“As a result we employed Multidivtime (version 9-25-03) (Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002) and BEAST v.”
MethodInfluentialOrigins of social parasitism: The importance of divergence ages in phylogenetic studies
Smith, J. A., Tierney, S. M., Park, Y. C., Fuller, S. J., & Schwarz, M. P. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.12.028 · Cited by 38
Model Selection and the Molecular Clock
Pybus, O. G. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040151 · Cited by 38
Knowledge discovery and data mining in biological databases
Brusić, V., & Zeleznikow, J. (1999) · The Knowledge Engineering Review · doi:10.1017/s0269888999003069 · Cited by 38
“Examples of such biological applications include the estimation of evolutionary dates from sequence data (Thorne et al., 1998); classification of protein sequence families (Qu et al., 1998); determination of evolutionary distances in aligned sequences (Agarwal and States, 1996); and finding…”
Background
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
