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Estimating the rate of evolution of the rate of molecular evolution
Open accessAbstract
A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.
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“To convert this tree from units of time to molecular evolutionary units, the rates are either assigned to branches [ 15, 17] or to nodes [ 53, 54].”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
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Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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“Assigning an age to a particular node is only possible when the tree itself is assumed to be known and fixed, a limitation of previous relaxed-clock implementations [ 15, 17, 54].”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Such a model permits independent gain and loss of conservation on multiple lineages and also encourages nearby branches to have the same state and substitution rate, which is reasonable for closely related species and branches in a phylogeny and is also a common assumption in phylogenetics”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Thorne et al. 1998
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Recently, it has been realized that less drastic alternatives to the unrooted model of phylogeny may exist. Instead of dispensing with the molecular clock entirely, attempts have been made to relax the molecular clock assumption by allowing the rate to vary across the tree [ 13– 15].”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
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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“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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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.
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van Tuinen, M. (2004) · Journal of Heredity · doi:10.1093/jhered/esh045 · Cited by 25
“This result is consistent despite sometimes large variation in molecular divergence time estimation with different calibration points, methods, or datasets (Bromham et al. 1999; Smith and Peterson 2002).”
BackgroundResultGenomic, phylogenetic, and cell biological insights into metazoan origins
Nichols, S. A., Dayel, M. J., & King, N. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0003 · Cited by 24
Bahram, M., Vanderpool, D., Pent, M., Hiltunen, M., & Ryberg, M. K. (2018) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12612 · Cited by 24
The age of insects and the revival of the minimum age tree
Klopfstein, S. (2020) · Austral Entomology · doi:10.1111/aen.12478 · Cited by 26
“It has since been appreciated that the hypothesis of a strict molecular clock (i.e. rate constancy over time and across different organism groups) only holds very rarely (Britten 1986; Thorne et al. 1998): the clock ticks very unevenly across the tree of life.”
BackgroundMethodInfluentialBayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent
Flouri, T., Huang, J., Jiao, X., Kapli, P., Rannala, B. H., & Yang, Z. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac161 · Cited by 23
“This was originally proposed by Thorne et al. (1998) in the phylogenetic dating context and recently implemented in the context of MSC with relaxed clocks by Douglas et al. (2022) in STARBEAST3.”
MethodMitochondrial diversity in human head louse populations across the Americas
Ascunce, M. S., Fane, J., Kassu, G., Toloza, A. C., Picollo, M. I., González‐Oliver, A., & Reed, D. L. (2013) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22336 · Cited by 24
“It is to be noticed that in Light and Reed (2004) besides using sequences from different areas of the world, divergence times were estimated using Bayesian approaches implemented in multidivtime (Thorne et al., 1998; Kishino et al., 2001) and in a previous version of BEAST (v1.”
MethodEastern Beringian biogeography: historical and spatial genetic structure of singing voles in Alaska
Weksler, M., Lanier, H. C., & Olson, L. E. (2010) · Journal of Biogeography · doi:10.1111/j.1365-2699.2010.02310.x · Cited by 24
“Both speciation and coalescent analyses employed the GTR+C(4) nucleotide substitution model and a relaxed molecular-clock model (Thorne et al., 1998) that assumed uncorrelated (lognormal) distribution of rates among branches.”
MethodPhylogenetically vetted and stratigraphically constrained fossil calibrations within Aves
Ksepka, D. T., & Clarke, J. A. (2015) · Palaeontologia Electronica · doi:10.26879/373 · Cited by 25
“Although early analyses often treated calibrations as point constraints or hard minima, many current divergence dating methods allow implementation of prior age distributions (e.g., Thorne et al., 1998; Yang and Rannala, 2006; Yang, 2007; Drummond et al., 2006; Drummond and Rambaut, 2007).”
MethodCarr, L. M., McLenachan, P. A., Waddell, P. J., Gemmell, N. J., & Penny, D. (2015) · Journal of Biogeography · doi:10.1111/jbi.12482 · Cited by 24
“San Mauro et al. (2006) had similar problems using a quite different set of taxa and a nuclear gene, along with the model of Thorne et al. (1998), further supporting the view of Kitazoe et al. (2007) that it is the use of inadequate models of rate change that may be responsible for some of the…”
BackgroundMethodWarren, B. H., & Hawkins, J. A. (2006) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2006.3560 · Cited by 24
“(d) Bayesian relaxed-clock analysis Bayesian methods that relax a strict molecular clock were used to estimate divergence times as implemented in the software MULTIDIVTIME (Thorne et al. 1998; Thorne & Kishino 2002).”
MethodInfluentialWare, J. L., Ho, S. Y. W., & Kjer, K. M. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.10.008 · Cited by 24
Determination of a complete lemur mitochondrial genome from feces
Matsui, A., Rakotondraparany, F., Hasegawa, M., & Horai, S. (2007) · Mammal Study · doi:10.3106/1348-6160(2007)32[7:doaclm]2.0.co;2 · Cited by 24
“…the evolution of eutherian mtDNA has been noted by several authors (Cao et al. 2000; Hasegawa et al. 2003), and new methods for estimating divergence dates without assuming the constant rate of molecular evolution have been developed (Thorne et al. 1998; Kishino et al. 2001; Yang and Rannala 2006).”
BackgroundRidenhour, B. J., & Storfer, A. T. (2008) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2008.01537.x · Cited by 24
“To estimate relative divergence times of our isolates, we used MULTIDIVTIME MULTIDIVTIME v. 09.25.03 ( Thorne et al., 1998 ).”
MethodInfluentialBloor, P., Kemp, S. J., & BROWN, R. P. (2007) · Molecular Ecology · doi:10.1111/j.1365-294x.2007.03575.x · Cited by 24
“Posterior distributions of rates and node dates for this topology were generated using a Bayesian Markov chain Monte Carlo approach as implemented by the program multidivtime (Thorne et al. 1998) using the approach described by Rutschmann (2004) (see also Thorne & Kishino 2002; Yang & Yoder 2003).”
MethodTIMING DEEP DIVERGENCE EVENTS IN CALCAREOUS DINOFLAGELLATES1
Gottschling, M., Renner, S. S., Meier, K. J. S., Willems, H., & Keupp, H. (2008) · Journal of Phycology · doi:10.1111/j.1529-8817.2008.00479.x · Cited by 24
“We used Thorne’s Bayesian relaxed clock approach (Thorne et al. 1998, Thorne and Kishino 2002), implemented in the multidivtime software available from his Web page (http://statgen.ncsu.edu/thorne/ thorne.html).”
MethodFelsenstein Phylogenetic Likelihood
Posada, D., & Crandall, K. A. (2021) · Journal of Molecular Evolution · doi:10.1007/s00239-020-09982-w · Cited by 25
Calibrations from the Fossil Record
Nguyen, J. M. T., & Ho, S. Y. W. (2020) · Springer eBooks · doi:10.1007/978-3-030-60181-2_8 · Cited by 23
Hanisch, P. E., Sosa‐Calvo, J., & Schultz, T. R. (2022) · Insect Systematics and Diversity · doi:10.1093/isd/ixab029 · Cited by 23
Zhang, L., Simmons, M. P., & Renner, S. S. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.03.002 · Cited by 23
“Adding these genetically divergent groups, however, worsened the problem of rate heterogeneity, which we attempt to circumvent by using a ‘‘relaxed clock’’ approach (Thorne et al., 1998).”
MethodGlobal Rate Variation in Bony Vertebrates
Takezaki, N. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy125 · Cited by 21
Patterns and Processes of Speciation in Ancient Lakes
Wilke, T., Väinölä, R., & Riedel, F. (2009) · Springer eBooks · doi:10.1007/978-1-4020-9582-5 · Cited by 22
“Especially, those methods that relax the assumption of amolecular clock (e.g., Thorne et al., 1998; Kishino et al., 2001; Sanderson, 2002; Britton, 2005) and combine molecular data with time constraints (upper and lower bounds), usually derived from fossils or geological data, have become…”
MethodPacheco, M. A., Ceríaco, L. M. P., Matta, N. E., Vargas‐Ramírez, M., Bauer, A. M., & Escalante, A. A. (2020) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2020.104576 · Cited by 22
Dating Microbial Evolution with MCMCtree
dos Reis, M. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2691-7_1 · Cited by 20
Modeling the Evolution of Rates of Continuous Trait Evolution
Martin, B. S., Bradburd, G. S., Harmon, L. J., & Weber, M. G. (2022) · Systematic Biology · doi:10.1093/sysbio/syac068 · Cited by 20
“…matches the distribution of branchwise rates obtained via fine-grained simulations of GBM on phylogenies under plausible parameter values and is negligibly different from other computationally efficient approximations (e.g., Thorne et al., 1998; Lartillot and Poujol, 2011; Revell, 2021; Figs.”
MethodSnir, S., Wolf, Y. I., & Koonin, E. V. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu091 · Cited by 22
The Implications of Lineage-Specific Rates for Divergence Time Estimation
Carruthers, T., Sanderson, M. J., & Scotland, R. W. (2019) · Systematic Biology · doi:10.1093/sysbio/syz080 · Cited by 22
“This is because the number of substitutions along any particular branch—the parameter directly inferred from molecular sequence data—is a product of the rate of molecular evolution and the branch’s temporal duration (Gillespie 1991; Sanderson 1997, 2002; Thorne et al. 1998; Britton 2005).”
BackgroundThe Molecular Determinants of Thermoadaptation:Methanococcalesas a Case Study
Lecocq, M., Groussin, M., Gouy, M., & Brochier‐Armanet, C. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa312 · Cited by 21
“1 (Blanquart and Lartillot 2006) using the supermatrix gathering the 538 methanomada core protein families, with the autocorrelated relaxed clock model (Thorne et al. 1998), a gamma prior (mean1⁄4 2,000 and standard deviation1⁄4 2,000) on the age of the root, 10,000 points sampling, and a burn-in of 1,000.”
MethodLos pastos naturales de Canarias
Méndez, P., de Nascimiento, L., & Reyes-Betancort, J. A. (2014) · Vieraea Folia scientiarum biologicarum canariensium · doi:10.31939/vieraea.2013.41.10 · Cited by 21
Molecular evolution of the VP1, VP2 and VP3 genes in human rhinovirus species C
Kuroda, M., Niwa, S., Sekizuka, T., Tsukagoshi, H., Yokoyama, M., Ryo, A., Sato, H., Kiyota, N., Noda, M., Kozawa, K., et al. (2015) · Scientific Reports · doi:10.1038/srep08185 · Cited by 21
Nazziwa, J., Faria, N. R., Chaplin, B., Rawizza, H. E., Kanki, P. J., Dakum, P., Abimiku, A., Charurat, M. E., Ndembi, N., & Esbjörnsson, J. (2020) · Scientific Reports · doi:10.1038/s41598-020-59944-x · Cited by 21
Probing the genomic limits of de-extinction in the Christmas Island rat
Lin, J., Duchêne, D. A., Carøe, C., Smith, O., Ciucani, M. M., Niemann, J., Richmond, D. J., Greenwood, A. D., MacPhee, R. D. E., Zhang, G., et al. (2022) · Current Biology · doi:10.1016/j.cub.2022.02.027 · Cited by 23
Ancient Divergence in the Trans-Oceanic Deep-Sea Shark Centroscymnus crepidater
da Cunha, R. L., Coscia, I., Madeira, C., Mariani, S., Stefanni, S. S., & Castilho, R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049196 · Cited by 21
“In order to date lineage-splitting events within C. crepidater, we used MULTIDIVTIME [81,82] a Bayesian relaxed molecular-clock approach that incorporates variation of rates of evolution among lineages.”
MethodInfluentialMultigene Phylogenetics Reveals Temporal Diversification of Major African Malaria Vectors
Kamali, M., Marek, P. E., Peery, A., Antonio‐Nkondjio, C., Ndo, C., Tu, Z. J., Simard, F., & Sharakhov, I. V. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093580 · Cited by 23
“3 was then used to estimate node divergence times under a relaxed clock log normal model [40,41].”
MethodGarzón‐Orduña, I. J., Menchaca-Armenta, I., Contreras‐Ramos, A., Liu, X., & Winterton, S. L. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0746-5 · Cited by 21
“Therefore, in PhyloBayes we used two relaxed clock models that differ in their assumption regarding the heritability of substitution rates: an uncorrelated gamma multipliers model (UGAM) that assumes no heritability of substitution rates [29], and a log normal autocorrelated model (LN) [30] that assumes that the subst…”
MethodEkwanzala, M. D., Abia, A. L. K., Ubomba‐Jaswa, E., Keshri, J., & Momba, M. N. B. (2017) · AMB Express · doi:10.1186/s13568-016-0319-4 · Cited by 21
“2004) as sediments represent a beneficial environment for nutrient, food assimilation and protection from environmental stress such as contaminants and predation.”
BackgroundAncient balancing selection on heterocyst function in a cosmopolitan cyanobacterium
Sano, E. B., Wall, C. A., Hutchins, P. R., & Miller, S. R. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0435-9 · Cited by 21
Local and relaxed clocks: the best of both worlds
Fourment, M., & Darling, A. E. (2018) · PeerJ · doi:10.7717/peerj.5140 · Cited by 22
Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora
da Cunha, R. L., Forsman, Z. H., Belderok, R., Knapp, I. S. S., Castilho, R., & Toonen, R. J. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1476-2 · Cited by 21
“BEAST (rate homogeneity) showed more recent age estimates at the tips and an older root (Additional file 4: S4) when compared with MULTIDIVTIME (rate heterogeneity; Fig.”
MethodInfluentialEcological Specialization and Evolutionary Reticulation in Extant Hyaenidae
Westbury, M. V., Duc, D. L., Duchêne, D. A., Krishnan, A., Prost, S., Rutschmann, S., Grau, J. H., Dalén, L., Weyrich, A., Norén, K., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab055 · Cited by 23
“8 (Yang 2007), with improved efficiency by implementing approximate likelihood computation (Thorne et al. 1998).”
Hirase, S., & Ikeda, M. (2013) · Marine Biology · doi:10.1007/s00227-013-2359-5 · Cited by 21
Berry, I. M., Athreya, G. S., Kothari, M., Daniels, M., Bruno, W., Korber, B., KUIKEN, C. L., Ribeiro, R. M., & Leitner, T. (2009) · Epidemics · doi:10.1016/j.epidem.2009.10.003 · Cited by 21
“molecular clock was estimated as a constant accumulation of substitutions over time (Kimura, 1980; Zuckerkandl and Pauling, 1965), but that simplifying assumption may not always be appropriate (Gillespie, 1984, 1988; Takahata, 1987) and more recently several Bayesian methods have been suggested on how to relax the str…”
BackgroundYan, H., Hu, Z., Thomas, G. W. C., Edwards, S. V., Sackton, T. B., & Liu, J. S. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad195 · Cited by 28
“Earlier works also exist for estimating a per branch evolutionary rate, while not accounting for ILS (Thorne et al. 1998; Kishino et al. 2001).”
BackgroundInfluentialMarxen, J. C., Pick, C., Kwiatkowski, M., & Burmester, T. (2013) · Journal of Comparative Physiology B · doi:10.1007/s00360-013-0740-9 · Cited by 20
“We assumed the log-normal auto-correlated model (Thorne et al. 1998).”
García–R, J. C., & Hayman, D. T. S. (2016) · Parasitology · doi:10.1017/s0031182016001323 · Cited by 22
“A relaxed clock model can account the variation in substitution rates among lineages (Thorne et al. 1998) while a lognormal distribution accommodates greater flexibility regarding a cladogenetic event (Ho and Phillips, 2009).”
BackgroundPereira, A. G., & Schrago, C. G. (2017) · PeerJ · doi:10.7717/peerj.3194 · Cited by 20
“To make the analyses feasible, we used an 205 approximate likelihood calculation modified from Thorne et al. (1998) and implemented in 206 mcmctree (Reis and Yang, 2011).”
MethodMitochondrial DNA Phylogenetic Definition of a Group of ‘Arid-Zone’ Carduelini Finches
Arnaiz‐Villena, A., Moscoso, J., Ruiz-del-Valle, V., González, J., Reguera, R., Ferri, A., Wink, M., & Serrano-Vela, J. I. (2008) · The Open Ornithology Journal · doi:10.2174/1874453200801010001 · Cited by 20
“The linearized ML dendrograms were calculated with PAUP* v. 4.0b10 [21] with the branch lengths estimated according to the model proposed by Thorne et al. [25] which assumes that the rates among the evolutionary lineages may not be constant.”
MethodPhylochronology of early metazoans: combined evidence from molecular and fossil data
Qun, Y., Ma, J., Xiaoyan, S., & Peiyun, C. (2007) · Geological Journal · doi:10.1002/gj.1074 · Cited by 20
“…method in calculating posterior probabilities of likelihood analyses under various evolutionary models and multiple fossil calibration points (Thorne et al. 1998; Kishino et al. 2001), and the use of non-parametric rate smoothing (NPRS) method in establishing variable molecular evolutionary…”
MethodTempo and Mode of Spliceosomal Intron Evolution in Actin of Foraminifera
Flakowski, J., Bolívar, I., Fahrni, J. F., & Pawlowski, J. W. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-005-0061-z · Cited by 20
“For dating analysis, we used a Bayesian relaxed molecular clock method implemented in the MULTIDIVTIME package (Thorne et al. 1998; Kishino et al. 2001; Thorne and Kishino 2002).”
MethodGenomic biodiversity, phylogenetics and coevolution in proteins.
Pollock, D. D. (2002) · PubMed · Cited by 20
Application of the Likelihood Function in Phylogenetic Analysis
Huelsenbeck, J. P., & Bollback, J. P. (2003) · Wiley eBooks · doi:10.1002/0470022620.bbc13 · Cited by 20
Data Integration in Bayesian Phylogenetics
Hassler, G. W., Magee, A. F., Zhang, Z., Baele, G., Lemey, P., Ji, X., Fourment, M., & Suchard, M. A. (2022) · Annual Review of Statistics and Its Application · doi:10.1146/annurev-statistics-033021-112532 · Cited by 23
A timeline of bacterial and archaeal diversification in the ocean
Martínez-Gutiérrez, C. A., Uyeda, J. C., & Aylward, F. O. (2023) · eLife · doi:10.7554/elife.88268 · Cited by 22
An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorilla
Galtier, N. (2024) · Peer Community Journal · doi:10.24072/pcjournal.359 · Cited by 19
Ortega‐Olivencia, A., & Catalán, P. (2009) · Taxon · doi:10.1002/tax.584018 · Cited by 19
Caldas, I. V., & Schrago, C. G. (2019) · Ecology and Evolution · doi:10.1002/ece3.4921 · Cited by 18
Model-Based Inference of Punctuated Molecular Evolution
Manceau, M., Marin, J., Morlon, H., & Lambert, A. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa144 · Cited by 23
Zhang, T., & Vďačný, P. (2021) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2021.107310 · Cited by 19
Liu, H., Yang, J.-Q., & Tang, Q. (2010) · Chinese Science Bulletin · doi:10.1007/s11434-010-3159-7 · Cited by 19
Omoto, K., Yonezawa, T., & Shinkawa, T. (2008) · Gene · doi:10.1016/j.gene.2008.10.030 · Cited by 19
Gaubert, P., & Begg, C. M. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.12.011 · Cited by 19
Markov Models in Molecular Evolution
Galtier, N., Gascuel, O., & Jean‐Marie, A. (2005) · Statistics in the health sciences · doi:10.1007/0-387-27733-1_1 · Cited by 19
“This can be achieved by assuming that transition rate µ is itself evolving according to some stochastic process upon which the process of sequence evolution is dependent ([ 36 ], [20]).”
BackgroundEvolution of the Inner Light-Harvesting Antenna Protein Family of Cyanobacteria, Algae, and Plants
Zhang, Y., Chen, M., Zhou, B. B., Jermiin, L. S., & Larkum, A. W. D. (2007) · Journal of Molecular Evolution · doi:10.1007/s00239-006-0058-2 · Cited by 19
“BEAST uses a relaxed clock model, based on an approach described by Thorne et al. (2002) .”
MethodCano-Maqueda, J., Talavera, S., Arista, M., & Catalán, P. (2008) · Taxon · doi:10.1002/tax.574016 · Cited by 19
The lemur revolution starts now: The genomic coming of age for a non-model organism
Yoder, A. D. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.08.024 · Cited by 18
“Copious literature exists on the subject of rate/time interdependence (succinctly articulated in Thorne et al., 1998)), though it is beyond the scope of this review to summarize the relevant issues, which also include routine violations of a molecular clock, the necessity to incorporate realistic…”
Probabilistic Phylogenetic Inference in the Fossil Record: Current and Future Applications
Wagner, P. J., & Marcot, J. D. (2010) · The Paleontological Society Papers · doi:10.1017/s108933260000187x · Cited by 19
“Wagner (2000a) recommends treating θ as an evolving parameter the way that some analyses mentioned above treat δ as an evolving parameter (e.g., Thorne et al., 1998).”
MethodThe molecular clock and evolutionary timescales
Luo, A., & Ho, S. Y. W. (2018) · Biochemical Society Transactions · doi:10.1042/bst20180186 · Cited by 19
The temporal dynamics of evolutionary diversification in Ipomoea
Carruthers, T., Muñoz‐Rodríguez, P., Wood, J. R., & Scotland, R. W. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.106768 · Cited by 19
Villanova, F., Cui, S., Ai, X., & Leal, E. D. S. (2016) · Archives of Virology · doi:10.1007/s00705-015-2744-0 · Cited by 18
Dating the Bacterial Tree of Life Based on Ancient Symbiosis
Wang, S., & Luo, H. (2024) · Systematic Biology · doi:10.1093/sysbio/syae071 · Cited by 17
“The idea was originally proposed by Thorne et al. 1998 and later implemented in PAML-MCMCtree as the approximate likelihood method (dos Reis and Yang 2011).”
Barba‐Montoya, J., Tao, Q., & Kumar, S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa820 · Cited by 18
Genomic diversification of the specialized parasite of the fungus-growing ant symbiosis
Gotting, K., May, D. S., Sosa‐Calvo, J., Khadempour, L., Francoeur, C. B., Berasategui, A., Thairu, M. W., Sandstrom, S., Carlson, C. M., Chevrette, M. G., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2213096119 · Cited by 17
“We inferred divergence dates of Escovopsis and the fungus-growing ants using the Bayesian program MCMCTREE (100) implemented as part of the package PAML (46) which uses the approximate-likelihood approach of (101).”
MethodThe ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2
Barido‐Sottani, J., & Morlon, H. (2023) · Systematic Biology · doi:10.1093/sysbio/syad027 · Cited by 17
“This is similar in principle to a relaxed autocorrelated clock model (Thorne et al. 1998).”
The Permian–Triassic mass extinction forces the radiation of the modern marine phytoplankton
Medlin, L. K. (2011) · Phycologia · doi:10.2216/10-31.1 · Cited by 17
“With each dataset, divergence times were estimated using Bayesian methods (Thorne et al. 1998; Kishino et al. 2001; Thorne & Kishino 2002) in the program multidistribute 9/25/03 (Thorne & Kishino 2002) and PAML 3.15 (Yang 1997).”
MethodInfluentialSudarto, S., Lalu, X. C., Kosen, J. D., Tjakrawidjaja, A. H., Kusumah, R. V., Sadhotomo, B., Kadarusman, Pouyaud, L., Slembrouck, J., & Paradis, E. (2010) · Marine Biology · doi:10.1007/s00227-010-1492-7 · Cited by 17
“This is certainly due to the autocorrelation of rates as assumed in the Multidivtime model ( Thorne et al. 1998 ).”
MethodPaleobotany, Evidence, and Molecular Dating: An Example from the Nymphaeales
Nixon, K. C. (2008) · Annals of the Missouri Botanical Garden · doi:10.3417/2007063 · Cited by 17
Log Transformation Improves Dating of Phylogenies
Mai, U., & Mirarab, S. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa222 · Cited by 19
“2000) or allow correlated rates across branches (Thorne et al. 1998; Kishino et al. 2001; Sanderson 2002; Lepage et al. 2007; Drummond and Suchard 2010; Snir et al. 2012; Tamura et al. 2012).”
BackgroundRitchie, A. M., Hua, X., & Bromham, L. D. (2022) · BMC Ecology and Evolution · doi:10.1186/s12862-022-02015-8 · Cited by 17
“92 Common variants include uncorrelated models, in which each branch-specific rate is an 93 independent draw from a distribution with a common mean (20); and autocorrelated models, 94 in which the mean of the distribution for each branch-specific rate depends on the rate drawn 95 for its parent branch (25, 26).”
BackgroundPaleozoic diversification of terrestrial chitin-degrading bacterial lineages
Gruen, D. S., Wolfe, J. M., & Fournier, G. P. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1357-8 · Cited by 19
“Conversely, autocorrelated clocks assume that more closely related branches on the tree should also have more similar rates [46, 56, 58, 59].”
BackgroundShafir, A., Azouri, D., Goldberg, E. E., & Mayrose, I. (2020) · Evolution · doi:10.1111/evo.14036 · Cited by 17
“…however, the constant clock hypothesis is violated and thus various alternative models have been developed to alleviate this assumption, including the widely used autocorrelated and uncorrelated relaxed clock models (Thorne et al. 1998; Sanderson 2002; Drummond et al. 2006; Rannala and Yang 2007).”
MethodNahum, L. A., Pereira, S. L., Fernandes, F. M. D. C., Matioli, S. R., & Wajntal, A. (2003) · Genetics and Molecular Biology · doi:10.1590/s1415-47572003000400003 · Cited by 16
“Some methods allow rates to differ among lineages (Sanderson, 1997; Thorne et al., 1998) and others accept rate variation at any point of the tree (Huelsenbeck et al., 2000).”
MEEROW, A. W., Noblick, L. R., Borrone, J. W., Couvreur, T. L. P., Mauro‐Herrera, M., Hahn, W. J., Kuhn, D. N., Nakamura, K., Oleas, N. H., & Schnell, R. J. (2009) · PLoS ONE · doi:10.1371/annotation/c59c150a-0412-490a-8e7d-ae5622fd4434 · Cited by 17
Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications
Kenney, T., & Gu, H. (2012) · Statistical Applications in Genetics and Molecular Biology · doi:10.1515/1544-6115.1779 · Cited by 16
Vargas‐Ramírez, M., Michels, J., Castaño-Mora, O. V., Cárdenas-Arévalo, G., Gallego‐García, N., & Fritz, U. (2012) · Amphibia-Reptilia · doi:10.1163/15685381-00002840 · Cited by 16
Carruthers, T., & Scotland, R. W. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz310 · Cited by 15
Westerman, M., Loke, S., & Springer, M. S. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2003.08.006 · Cited by 16
Extensive evolutionary rate variation in floral color determining genes in the genus Ipomoea
TOLENO, D. M., Durbin, M. L., Lundy, K. E., & Clegg, M. T. (2010) · Plant Species Biology · doi:10.1111/j.1442-1984.2009.00256.x · Cited by 16
A Method to Correct for the Effects of Purifying Selection on Genealogical Inference
O’Fallon, B. D. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq132 · Cited by 16
Gilbert, C., O’Brien, P. C., Bronner, G., Yang, F., Hassanin, A., Ferguson-Smith, M. A., & Robinson, T. J. (2006) · Chromosome Research · doi:10.1007/s10577-006-1091-0 · Cited by 16
Roycroft, E., Ford, F., Ramm, T., Schembri, R., Breed, W. G., Burns, P. A., Rowe, K. C., & Moritz, C. C. (2024) · Molecular Ecology · doi:10.1111/mec.17301 · Cited by 15
“Data were partitioned by codon position, with a GTR + Γ substitu-tion model, uncorrelated Γ relaxed clock, and using the approximate likelihood calculation (Thorne et al., 1998).”
MethodModeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock
Mello, B., & Schrago, C. G. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae199 · Cited by 16
“This method was implemented in Multidivtime, the first Bayesian relaxed clock software (Thorne et al. 1998; Kishino et al. 2001).”
BackgroundMethodInfluentialEvolution is coupled with branching across many granularities of life
Douglas, J., Bouckaert, R., Harris, S. C., Carter, C. W., & Wills, P. R. (2025) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2025.0182 · Cited by 18
Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation
Beavan, A. J. S., Donoghue, P. C. J., Beaumont, M., & Pisani, D. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa105 · Cited by 12
“The clock methods used were strict clock (-cl), lognormal-autocorrelated clock (-ln, Thorne et al. 1998), and uncorrelated gamma multipliers (-ugam, Drummond et al. 2006), implemented according to the default settings in PhyloBayes.”
Improvement of molecular phylogenetic inference and the phylogeny of Bilateria
Lartillot, N., & Philippe, H. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0012 · Cited by 15
Timing of a mtDNA gene rearrangement and intercontinental dispersal of varanid lizards
Amer, S. A. M., & Kumazawa, Y. (2008) · Genes & Genetic Systems · doi:10.1266/ggs.83.275 · Cited by 15
“The multidistribute package (Thorne et al., 1998) implements the Bayesian method for divergence time estimation without assuming the molecular clock (i.e., by allowing the rate variation along branches).”
MethodSilencing, Positive Selection and Parallel Evolution: Busy History of Primate Cytochromes c
Pierron, D., Opazo, J. C., Heiske, M., Papper, Z., Uddin, M., Chand, G., Wildman, D. E., Romero, R. J., Goodman, M., & Grossman, L. I. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026269 · Cited by 15
“We have estimated divergence times for the whole group using a Bayesian local molecular clock approach [40,41].”
MethodMonte Carlo algorithms for Brownian phylogenetic models
Horvilleur, B., & Lartillot, N. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu485 · Cited by 15
“Typically, the Brownian process is explicitly sampled only at the internal nodes of the phylogeny, corresponding to cladogenetic events (Thorne et al., 1998; Lepage et al., 2007) or at the midpoints along the branches (Rannala and Yang, 2007).”
BackgroundMethodMolecular clocks: Closing the gap between rocks and clocks
Cranston, K., & Rannala, B. H. (2005) · Heredity · doi:10.1038/sj.hdy.6800644 · Cited by 15
Li, S., Yu, F.-H., Yang, S.-F., Wang, Y.-X., Jiang, X.-L., McGuire, P., Feng, Q., & Yang, J.-X. (2008) · Zoologica Scripta · doi:10.1111/j.1463-6409.2008.00335.x · Cited by 16
“A Bayesian dating approach (Thorne et al. 1998) was conducted to estimate the divergence times, based on the Bayesian topology, with PAML v3.”
MethodHimmelmann, L., & Metzler, D. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp417 · Cited by 15
“In the uncorrelated exponential model (UEX) and the uncorrelated log-normal model (ULN) [ TKP98 , DHPR06] rate factors for all edges in the tree are independently drawn from an exponential and log-normal distribution, respectively.”
Molecular Timescale of Evolution in the Proterozoic
Hedges, S. B., Battistuzzi, F. U., & Blair, J. E. (2007) · Springer eBooks · doi:10.1007/1-4020-5202-2_7 · Cited by 15
“The latter contains a great diversity of methods (Hasegawa et al., 1989; Takezaki et al., 1995; Sanderson, 1997; Schubart et al., 1998; Thorne et al., 1998), some of which are referred to as “relaxed clock” methods.”
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
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