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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]
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“In the autocorrelated relaxed-clock models that have been described, including the commonly used lognormal model [ 15, 17, 55], it is also necessary to specify the degree of autocorrelation as a prior.”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [15]
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“Thorne, Kishino, and Painter (1998) and Aris-Brosou and Yang (2002) implemented parametric models in which the rate in a given branch (the descendant rate) is a priori related to the rate in the branch immediately ancestral to it (the parent rate).”
From Accuracy of Rate Estimation Using Relaxed-Clock Models with a Critical Focus on the Early Metazoan Radiation (2005) · cites this paper as Thorne, Kishino, and Painter 1998
In the citing paper
“Moreover, the relaxed clock approach retrieves the true divergence times (Table 1) when substitution rates are distributed according to the autocorrelated-rate model developed by Thorne et al. (32).”
From The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? (2004) · cites this paper as [32]
In the citing paper
“However, protein evolution is not homogeneous.”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [68]
In the citing paper
“Different sites and lineages accumulate substitutions at different rates (e.g., [67-69])”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [68]
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Items 101–200 of 998
Estimating Divergence Times in Large Phylogenetic Trees
Britton, T., Anderson, C. L., Jacquet, D., Lundqvist, S., & Bremer, K. (2007) · Systematic Biology · doi:10.1080/10635150701613783 · Cited by 295
“Thorne et al. (1998) , further developed by Kishino et al. (2001) and Thorne and Kishino (2002), produced a model for the rate variation, which is analyzed using Bayesian methods.”
BackgroundMethodInfluentialNabholz, B., Glémin, S., & Galtier, N. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-54 · Cited by 295
“Users of mtDNA as a tools for inferring divergence dates should imperatively use statistical phylogenetic methods accounting for substitution rate variation across lineages, the so-called clock-relaxed methods [44,48-50].”
MethodInfluentialPochon, X., Montoya‐Burgos, J. I., Stadelmann, B., & Pawlowski, J. W. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2005.04.028 · Cited by 299
“We estimated the divergence times by using the Bayesian relaxed molecular clock approach implemented in MULTIDISTRIBUTE (Kishino et al., 2001; Thorne and Kishino, 2002; Thorne et al., 1998).”
MethodToward an Integrative Historical Biogeography
Donoghue, M. J. (2003) · Integrative and Comparative Biology · doi:10.1093/icb/43.2.261 · Cited by 291
“Fortunately, confidence in temporal information is rapidly increasing, owing especially to the development of methods that better integrate fossil and molecular data (e.g., Sanderson, 1997, 2002; Rambaut and Bromham, 1998; Thorne et al., 1998; Culter, 2000; Huelsenbeck et al., 2000b; Kishino et al., 2001; Aris-Brosou…”
BackgroundThe colonization of land by animals: molecular phylogeny and divergence times among arthropods
Pisani, D., Poling, L. L., Lyons‐Weiler, M. A., & Hedges, S. B. (2004) · BMC Biology · doi:10.1186/1741-7007-2-1 · Cited by 297
Bayesian Analysis of Molecular Evolution Using MrBayes
Huelsenbeck, J. P., & Ronquist, F. (2005) · Springer eBooks · doi:10.1007/0-387-27733-1_7 · Cited by 292
“To date, two different models have been proposed for allowing rates to vary across the tree (Thorne et al., 1998; Huelsenbeck et al., 2000), and in both cases, a Bayesian MCMC approach was taken to estimate parameters.”
MethodMegaphylogeny resolves global patterns of mushroom evolution
Varga, T., Krizsán, K., Földi, C., Dima, B., Sánchez‐García, M., Ramirez, S. S., Szöllősi, G. J., Szarkándi, J. G., Papp, V., Albert, L., et al. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0834-1 · Cited by 294
“The independent-rates clock model, a WAG substitution model and approximate likelihood calculation 72 were used.”
Gilbert, C., Ropiquet, A., & Hassanin, A. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.02.017 · Cited by 300
Single origin of Malagasy Carnivora from an African ancestor
Yoder, A. D., Burns, M. M., Zehr, S. M., Delefosse, T., Veron, G., Goodman, S. M., & Flynn, J. J. (2003) · Nature · doi:10.1038/nature01303 · Cited by 287
On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks
Eme, L., Sharpe, S. C., Brown, M. W., & Roger, A. J. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016139 · Cited by 287
“…drawn a priori from a parametric distribution whose mean is a function of the rate on the parent branch (e.g., the log-normal [LogN] distribution) (Thorne et al. 1998; Kishino et al. 2001), in which the evolutionary rate varies according to a lognormal distribution; or the Cox–Ingersoll–Rand…”
BackgroundTriassic origin and early radiation of multicellular volvocine algae
Herron, M. D., Hackett, J. D., Aylward, F. O., & Michod, R. E. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811205106 · Cited by 285
Bees diversified in the age of eudicots
Cardinal, S., & Danforth, B. N. (2013) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2012.2686 · Cited by 285
Time Tree of Rubiaceae: Phylogeny and Dating the Family, Subfamilies, and Tribes
Bremer, B., & Eriksson, T. (2009) · International Journal of Plant Sciences · doi:10.1086/599077 · Cited by 284
Single-copy nuclear genes resolve the phylogeny of the holometabolous insects
Wiegmann, B. M., Trautwein, M., Kim, J., Cassel, B. K., Bertone, M. A., Winterton, S. L., & Yeates, D. K. (2009) · BMC Biology · doi:10.1186/1741-7007-7-34 · Cited by 283
Gibb, G. C., Condamine, F. L., Kuch, M., Enk, J. M., Moraes‐Barros, N., Superina, M., Poinar, H. N., & Delsuc, F. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv250 · Cited by 283
“However, it has been shown that autocorrelated rate models, such as the autocorrelated log-normal model (LN; Thorne et al. 1998), generally offer a better fit, especially with large data sets above the species level (Lepage et al. 2007; Rehm et al. 2011).”
BackgroundInfluentialExploring the Demographic History of DNA Sequences Using the Generalized Skyline Plot
Strimmer, K., & Pybus, O. G. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003776 · Cited by 276
Yang, Z. (2014) · doi:10.1093/acprof:oso/9780199602605.001.0001 · Cited by 282
Taxon sampling effects in molecular clock dating: An example from the African Restionaceae
Linder, H. P., Hardy, C. R., & Rutschmann, F. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.12.006 · Cited by 273
“, the local clocks approach of Yoder and Yang, 2000), using nonparametric rate smoothing to constrain between internode rate variation (Sanderson, 1997), and searching for the optimal rates using Bayesian methods (Thorne et al., 1998) and penalized likelihood (Sanderson, 2002a).”
MethodInfluentialNear, T. J., Meylan, P. A., & Shaffer, H. B. (2005) · The American Naturalist · doi:10.1086/427734 · Cited by 270
“1995; Cooper and Penny 1997), to methods that include all of the data and attempt to estimate local rates for branches and lineages in the phylogeny using nonparametric, semiparametric, and Bayesian methodologies (Sanderson 1997, 2002; Thorne et al. 1998).”
MethodCutter, A. D. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn024 · Cited by 266
“Explicit incorporation of local or relaxed molecular clock models that accommodate rate variation provide one valuable avenue for inferring divergence times for taxa with evidence of rate differences among them (Thorne et al. 1998; Huelsenbeck et al. 2000; Sanderson 2002; Drummond et al. 2006).”
BackgroundModel-based multi-locus estimation of decapod phylogeny and divergence times
Porter, M. L., Pérez‐Losada, M., & Crandall, K. A. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2005.06.021 · Cited by 266
“Moreover, both methods make use of the rateevolution model of Thorne et al. (1998) and Kishino et al. (2001), but the TK approach averages over the rates in the MCMC procedure while the AHRS approach optimizes rates together with divergence times.”
Inoue, J. G., Donoghue, P. C. J., & Yang, Z. (2009) · Systematic Biology · doi:10.1093/sysbio/syp078 · Cited by 269
Genomic clocks and evolutionary timescales
Hedges, S. B., & Kumar, S. (2003) · Trends in Genetics · doi:10.1016/s0168-9525(03)00053-2 · Cited by 257
Nikaido, M., Matsuno, F., Hamilton, H., Brownell, R. L., Cao, Y., Ding, W., Zuoyan, Z., Shedlock, A. M., Fordyce, R. E., Hasegawa, M., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.121139198 · Cited by 260
Tamura, K., Tao, Q., & Kumar, S. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy044 · Cited by 250
“This is, however, different from the autocorrelation rate model of Thorne et al. (1998) in which ancestral and descendant branch rates are autocorrelated throughout the tree.”
BackgroundMethodInfluentialLeys, R., WATTS, C. H. S., Cooper, S. J., & Humphreys, W. F. (2003) · Evolution · doi:10.1111/j.0014-3820.2003.tb01523.x · Cited by 259
“However, recent methods that incorporate models of change of molecular rates in and among branches (Sanderson 1997, 2002a; Thorne et al. 1998; Huelsenbeck et al. 2000a; Kishino et al. 2001) make it possible to calculate ultrametric trees and estimate divergence times when the age of one or more…”
MethodEizirik, E., Murphy, W. J., Koepfli, K., Johnson, W. E., Dragoo, J. W., Wayne, R. K., & O’Brien, S. J. (2010) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2010.01.033 · Cited by 256
“Considering the results from these two studies , more congruence with respect to Pinnipedia is ob - served with our Divtime analysis than with BEAST , suggesting that the latter may have underestimated the age of this node ( see Table 6 ) .”
MethodInfluentialPark, E., Hwang, D., Lee, J., Song, J., Seo, T., & Won, Y. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.10.008 · Cited by 266
“Rate heterogeneity among lineages was further investigated and modeled using a log-normal distribution under a Bayesian framework (Thorne et al., 1998).”
MethodMolecular Phylogenetic Dating of Asterid Flowering Plants Shows Early Cretaceous Diversification
Bremer, K., Friis, E. M., & Bremer, B. (2004) · Systematic Biology · doi:10.1080/10635150490445913 · Cited by 250
“There are now many methods available for phylogenetic dating (e.g., Takezaki et al., 1995; Sanderson, 1997, 2002a; Rambaut and Bromham, 1998; Thorne et al., 1998; Huelsenbeck et al., 2000; Yoder and Yang, 2000; Kishino et al., 2001; Britton et al., 2002; Thorne and Kishino, 2002; Yang and Yoder, 2003; for reviews see…”
MethodMolecular and Morphological Phylogenies of Ruminantia and the Alternative Position of the Moschidae
Hassanin, A., & Douzery, E. (2003) · Systematic Biology · doi:10.1080/10635150390192726 · Cited by 255
“The Bayesian relaxed molecular clock approach of continuous autocorrelation of evolutionary rates along branches developed by Thorne et al. (1998) and Kishino et al. (2001) was used.”
MethodRevealing the demographic histories of species using DNA sequences
Emerson, B. C., Paradis, E., & Thébaud, C. (2001) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(01)02305-9 · Cited by 254
Relaxed Molecular Clock Provides Evidence for Long-Distance Dispersal of Nothofagus (Southern Beech)
Knapp, M., Stöckler, K., Havell, D., Delsuc, F., Sebastiani, F., & Lockhart, P. J. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0030014 · Cited by 249
“Divergence times for the nodes in this tree (Figure 2) were estimated using the penalized likelihood (PL) method [27] and BRMC method [29,30,31].”
MethodZakharov, E. V., Caterino, M. S., & Sperling, F. A. H. (2004) · Systematic Biology · doi:10.1080/10635150490423403 · Cited by 246
Eick, G. N., Jacobs, D. S., & Matthee, C. A. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi180 · Cited by 247
“The relaxed Bayesian clock method (Thorne, Kishino, and Painter 1998; Thorne and Kishino 2002) following the methodology outlined in Matthee et al. (2004) was used to date the evolution of the various chiropteran lineages.”
MethodThe nature of the last universal common ancestor and its impact on the early Earth system
Moody, E. R. R., Álvarez-Carretero, S., Mahendrarajah, T., Clark, J., Betts, H. C., Dombrowski, N., Szánthó, L. L., Boyle, R. A., Daines, S. J., Chen, X., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02461-1 · Cited by 285
Initial Diversification of Living Amphibians Predated the Breakup of Pangaea
Mauro, D. S., Vences, M., Alcobendas, M., Zardoya, R., & Meyer, A. (2005) · The American Naturalist · doi:10.1086/429523 · Cited by 255
Lartillot, N., & Poujol, R. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msq244 · Cited by 243
“This has been first proposed in the context of molecular dating methods, using Brownian diffusion processes (Thorne et al. 1998; Kishino et al. 2001; Thorne and Kishino 2002; Yang and Rannala 2006; Lepage et al. 2007; Rannala and Yang 2007).”
MethodMatthee, C. A., van Vuuren, B. J., Bell, D., & Robinson, T. J. (2004) · Systematic Biology · doi:10.1080/10635150490445715 · Cited by 246
“Given the absence of a constant molecular clock for the leporids, we employed the recently developed relaxed Bayesian methods for multilocus data (Thorne et al. 1998; Thorne and Kishino, 2002).”
MethodRelaxed molecular clocks for dating historical plant dispersal events
Renner, S. S. (2005) · Trends in Plant Science · doi:10.1016/j.tplants.2005.09.010 · Cited by 241
Brown, J. M., Hedtke, S. M., Lemmon, A. R., & Lemmon, E. M. (2009) · Systematic Biology · doi:10.1093/sysbio/syp081 · Cited by 243
Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains
Polato, N. R., Gill, B. A., Shah, A. A., Gray, M. M., Casner, K. L., Barthelet, A., Messer, P. W., Simmons, M. P., Guayasamin, J. M., Encalada, A. C., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1809326115 · Cited by 254
Sanderson, M. J., & Doyle, J. A. (2001) · American Journal of Botany · doi:10.2307/3558458 · Cited by 240
Soltis, P. S., Soltis, P. S., Savolainen, V., Crane, P. R., & Barraclough, T. G. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032087199 · Cited by 238
Pereira, S. L., & Baker, A. J. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl038 · Cited by 238
“…present a new timescale for avian evolution derived from a Bayesian approach to molecular dating that accounts for uncertainties in fossil data and in branch lengths in the higher level phylogeny and allows for change in rates of evolution through time (Thorne et al. 1998; Thorne and Kishino 2002).”
BackgroundMethodMueller, R. L. (2006) · Systematic Biology · doi:10.1080/10635150500541672 · Cited by 239
“Bayesian framework using the multidivtime software package, which allows partitioning of the dataset into separate genes or subsets (Thorne and Kishino, 2002; Thorne et al., 1998 ).”
MethodTristan, L., Douady, C. J., Gouy, M., Trontelj, P., Briolay, J., & Gibert, J. (2006) · Molecular Ecology · doi:10.1111/j.1365-294x.2006.02888.x · Cited by 238
Aris-Brosou, S., & Yang, Z. (2002) · Systematic Biology · doi:10.1080/10635150290102375 · Cited by 230
Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages
Brown, J. W., Rest, J. S., García-Moreno, J., Sorenson, M. D., & Mindell, D. P. (2008) · BMC Biology · doi:10.1186/1741-7007-6-6 · Cited by 236
Arrival and Diversification of Caviomorph Rodents and Platyrrhine Primates in South America
Poux, C., Chevret, P., Huchon, D., JONG, W. W. D., & Douzery, E. (2006) · Systematic Biology · doi:10.1080/10635150500481390 · Cited by 240
“, 2001) and a Bayesian relaxed molecular clock dating method (Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002), allows for the first time to compare simultaneously the phylogeny and the evolutionary history of primates and rodents in South America using the same orthologous markers.”
MethodWright, T. F., Schirtzinger, E. E., Matsumoto, T. E., Eberhard, J. R., Graves, G. R., Sánchez, J. J., Capelli, S., Müller, H., Scharpegge, J., Chambers, G. K., et al. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn160 · Cited by 240
“The second dating approach was a Bayesian relaxedclock method that allows for the incorporation of uncertainty in calibration dates and of variation in rates of evolution along different branches of the phylogenetic tree (Thorne et al. 1998; Drummond et al. 2006).”
Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages
Cassens, I., Vicario, S., Waddell, V. G., Balchowsky, H. A., Belle, D. V., Ding, W., Fan, C., Mohan, R. S. L., Simões‐Lopes, P. C., Bastida, R., et al. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.21.11343 · Cited by 232
Rutschmann, F. (2005) · Diversity and Distributions · doi:10.1111/j.1366-9516.2006.00210.x · Cited by 228
“Method 10: Bayesian implementation of rate autocorrelation in MULTIDIVTIME (Thorne et al., 1998; Kishino et al., 2001; Thorne & Kishino, 2002) The Bayesian dating method implemented in (Thorne et al., 1998; Kishino et al., 2001; Thorne & Kishino, 2002) uses a fully probabilistic and high parametric model to describe t…”
MethodInfluentialAmphibians as Indicators of Early Tertiary "Out-of-India" Dispersal of Vertebrates
Bossuyt, F., & Milinkovitch, M. C. (2001) · Science · doi:10.1126/science.1058875 · Cited by 234
Molecular dating when rates vary
Welch, J. J., & Bromham, L. D. (2005) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2005.02.007 · Cited by 228
“Finally, Thorne et al. [ 32 ,44] introduced a useful compromise between the approaches discussed above.”
BackgroundInfluentialA species-level timeline of mammal evolution integrating phylogenomic data
Álvarez-Carretero, S., Tamuri, A. U., Battini, M., do Nascimento, F. F., Carlisle, E. M., Asher, R. J., Yang, Z., Donoghue, P. C. J., & dos Reis, M. (2021) · Nature · doi:10.1038/s41586-021-04341-1 · Cited by 236
Independent Origins and Rapid Evolution of the Placenta in the Fish Genus Poeciliopsis
Reznick, D. N., Mateos, M., & Springer, M. S. (2002) · Science · doi:10.1126/science.1076018 · Cited by 226
Dating primate divergences through an integrated analysis of palaeontological and molecular data
Wilkinson, R. D., Steiper, M. E., Soligo, C., Martin, R. D., Yang, Z., & Tavaré, S. (2011) · Systematic Biology · doi:10.1093/sysbio/syq054 · Cited by 218
“This progressed to introducing uncertainty by specifying a range of possible values with hard bounds representing the limits of the uncertainty (Thorne et al., 1998), with zero probability assigned to ages outside of this range.”
BackgroundStadelmann, B., Lin, L. ‐., Kunz, T., & Rüedi, M. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.06.019 · Cited by 224
“Divergence age of selected nodes was estimated by the Bayesian relaxed molecular-clock approach implemented in the program MULTIDISTRIBUTE, developed by Thorne et al. (1998), Kishino et al. (2001), and Thorne and Kishino (2002).”
MethodHIV evolutionary dynamics within and among hosts.
Lemey, P., Rambaut, A., & Pybus, O. G. (2006) · PubMed · Cited by 222
The evolution of tribospheny and the antiquity of mammalian clades
Woodburne, M. O., Rich, T. H., & Springer, M. S. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00113-1 · Cited by 223
Jansa, S. A., Barker, F. K., & Heaney, L. R. (2006) · Systematic Biology · doi:10.1080/10635150500431254 · Cited by 217
“These methods differ in whether they require an explicit model of sequence evolution (Thorne et al., 1998; Thorne and Kishino, 2002; Yoder and Yang, 2000), are nonparametric (Sanderson, 1997), or combine parametric and nonparametric methods through a semiparametric approach (Sanderson, 2002).”
BackgroundMethodJones, M. E. H., Anderson, C. L., Hipsley, C. A., Müller, J., Evans, S. E., & Schoch, R. R. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-208 · Cited by 227
Remarkable species diversity in Malagasy mouse lemurs (primates, Microcebus )
Yoder, A. D., Rasoloarison, R. M., Goodman, S. M., Irwin, J. A., Atsalis, S., Ravosa, M. J., & Ganzhorn, J. U. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.200121897 · Cited by 217
A phylogenomic framework and timescale for comparative studies of tunicates
Delsuc, F., Philippe, H., Tsagkogeorga, G., Simion, P., Tilak, M., Turón, X., López‐Legentil, S., Piette, J., Lemaire, P., & Douzery, E. (2018) · BMC Biology · doi:10.1186/s12915-018-0499-2 · Cited by 223
“In order to select the best-fitting clock model, we compared the autocorrelated log-normal (LN) relaxed clock model [52] with the uncorrelated gamma (UGAM) model [53] and a strict molecular clock (CL) model.”
BackgroundMethodPennington, R. T., Lewis, G. P., & Ratter, J. A. (2006) · CRC Press eBooks · doi:10.1201/9781420004496-1 · Cited by 218
Dates from the molecular clock: how wrong can we be?
Pulquério, M. J. F., & Nichols, R. A. (2007) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2006.11.013 · Cited by 267
Contrasted patterns of hyperdiversification in Mediterranean hotspots
Sauquet, H., Weston, P. H., Anderson, C. L., Barker, N. P., Cantrill, D. J., Mast, A., & Savolainen, V. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805607106 · Cited by 217
Miller, W., Hayes, V. M., Ratan, A., Petersen, D. C., Wittekindt, N. E., Miller, J. R., Walenz, B. P., Knight, J., Qi, J., Zhao, F., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102838108 · Cited by 217
Barba‐Montoya, J., dos Reis, M., Schneider, H., Donoghue, P. C. J., & Yang, Z. (2018) · New Phytologist · doi:10.1111/nph.15011 · Cited by 213
“The likelihood (or the probability of the sequence alignment given the tree and branch lengths) was calculated using the approximate method (Thorne et al., 1998; dos Reis & Yang, 2011), employing the SQRT transformation (dos Reis & Yang, 2011).”
MethodInfluentialEvolutionary and biogeographic history of weasel-like carnivorans (Musteloidea)
Sato, J. J., Wolsan, M., Prevosti, F. J., D’Elía, G., Begg, C. M., Begg, K. S., Hosoda, T., Campbell, K. L., & Suzuki, H. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.02.025 · Cited by 214
“The Multidivtime analysis was performed using the Bayesian relaxed-clock method first proposed by Thorne et al. (1998) and further developed in Kishino et al. (2001) and Thorne and Kishino (2002).”
MethodDelsuc, F., Vizcaíno, S. F., & Douzery, E. J. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-11 · Cited by 212
“Recent methodological advances in molecular dating have aimed at relaxing the assumption of the global molecular clock [30] by modelling the variation of the evolutionary rate along the phylogenetic tree [31-35].”
BackgroundMethodResultInfluentialA biologist’s guide to Bayesian phylogenetic analysis
Nascimento, F. F., Reis, M. D., & Yang, Z. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0280-x · Cited by 212
Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data
Silvestro, D., Schnitzler, J., Liow, L. H., Antonelli, A., & Salamin, N. (2014) · Systematic Biology · doi:10.1093/sysbio/syu006 · Cited by 217
“The resulting posterior distributions of the parameters are therefore comparable to those obtained by the standard (Bayesian) phylogenetic methods for molecular dating (Thorne et al. 1998; Drummond et al. 2006; Ronquist, Teslenko et al. 2012) and estimation of diversification rates (Ryberg et al.”
ResultPhylogeny and Temporal Diversification of Darters (Percidae: Etheostomatinae)
Near, T. J., Bossu, C. M., Bradburd, G. S., Carlson, R. L., Harrington, R. C., Hollingsworth, P. R., Keck, B. P., & Etnier, D. A. (2011) · Systematic Biology · doi:10.1093/sysbio/syr052 · Cited by 206
“The past decade has witnessed the development of several powerful strategies to correct for molecular evolutionary rate heterogeneity (e.g., Sanderson 1997, 2002; Thorne et al. 1998; Drummond et al. 2006), and, more recently, a thorough consideration of calibration methods has emerged (Near, Meylan, et al.”
BackgroundNauheimer, L., Metzler, D., & Renner, S. S. (2012) · New Phytologist · doi:10.1111/j.1469-8137.2012.04220.x · Cited by 205
“…+49 89 17861250 Email: l.nauheimer@gmail.com Susanne Renner Tel: +49 89 17861250 Email: renner@lrz.uni-muenchen.de Received: 4 April 2012 Accepted: 23 May 2012 New Phytologist (2012) 195: 938–950 doi: 10.1111/j.1469-8137.2012.04220.x Key words: ancestral area reconstruction, calibration,…”
BackgroundInfluentialAs Time Goes by: A Simple Fool's Guide to Molecular Clock Approaches in Invertebrates *
Wilke, T., Schultheiß, R., & Albrecht, C. (2009) · American Malacological Bulletin · doi:10.4003/006.027.0203 · Cited by 204
“A similar approach was developed by Thorne et al. (1998) using a Bayesian framework (see also Kishino et al. 2001).”
MethodSmith, A. B., Pisani, D., Mackenzie‐Dodds, J. A., Stockley, B., Webster, B. L., & Littlewood, D. T. J. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl039 · Cited by 202
“Overall, for our data, log-PL was best at recovering known divergence times, although employing better substitution models to estimate branch lengths in the Bayesian approach of Thorne et al. (1998) might be expected to improve the success rate of this method.”
MethodInfluentialAlfaro, M. E., Santini, F., & Brock, C. D. (2007) · Evolution · doi:10.1111/j.1558-5646.2007.00182.x · Cited by 202
Dispersal and vicariance: The complex evolutionary history of boid snakes
Noonan, B. P., & Chippindale, P. T. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.03.010 · Cited by 201
“…utilizing a relaxed Bayesian molecular clock method, which allows for variability in the evolutionary rate over time, using the MULTIDISTRIBUTE package (http://statgen.ncsu.edu/ thorne/multidivtime.html, contents italicized below) developed by Thorne et al. (1998) and Thorne and Kishino (2002).”
MethodConsequences of Secondary Calibrations on Divergence Time Estimates
Schenk, J. J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0148228 · Cited by 201
“…advances include local molecular-clocks [6], the penalized-likelihood approach implemented in r8s [7,8], the multigene Bayesian-approach implemented in Multi-divtime [9 – 11], and the Bayesian approach that implements the uncorrelated lognormal (UCLN) model (among others) in Beast [12,13].”
Miller‐Butterworth, C. M., Murphy, W. J., O’Brien, S. J., Jacobs, D. S., Springer, M. S., & Teeling, E. C. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm076 · Cited by 201
“Branch lengths were estimated with ESTBRANCHES for the concatenated data set and for each data partition discussed above (Thorne et al. 1998).”
MethodThe Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference
Tarver, J. E., dos Reis, M., Mirarab, S., Moran, R. J., Parker, S., O’Reilly, J., King, B. L., O’Connell, M. J., Asher, R. J., Warnow, T. J., et al. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evv261 · Cited by 201
dos Reis, M., Gunnell, G. F., Barba‐Montoya, J., Wilkins, A., Yang, Z., & Yoder, A. D. (2018) · Systematic Biology · doi:10.1093/sysbio/syy001 · Cited by 190
“Arguments have been put forward in favour and against both of the two types of relaxed-clock models examined by our study (Thorne et al. 1998, Drummond et al. 2006, Ho 2009), and clearly further research is still needed to understand the merits of each clock model and how they relate to…”
BackgroundResultDating the Time of Origin of Major Clades: Molecular Clocks and the Fossil Record
Smith, A. B., & Peterson, K. J. (2002) · Annual Review of Earth and Planetary Sciences · doi:10.1146/annurev.earth.30.091201.140057 · Cited by 193
“Thorne et al. (1998) took a similar approach by assuming autocorrelation of rates but using a parametric model for relaxing the clock.”
MethodMinegishi, Y., Aoyama, J., Inoue, J. G., Miya, M. U., Nishida, M., & Tsukamoto, K. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.09.003 · Cited by 193
“, 2003), or the Bayesian approach (Kishino et al., 2001; Thorne et al., 1998; Thorne and Kishino, 2002) for the estimation of the divergence times (e.”
BackgroundBELL, C. (2005) · Organisms Diversity & Evolution · doi:10.1016/j.ode.2004.10.014 · Cited by 196
“Recent Bayesian methods (Thorne et al., 1998; Kishino et al., 2001) that relax the clock were also used to estimate divergence times, using the computer software MULTIDIVTIME (available from J. Thorne, North Carolina State University).”
MethodBarker, N. P., Weston, P. H., Rutschmann, F., & Sauquet, H. (2007) · Journal of Biogeography · doi:10.1111/j.1365-2699.2007.01749.x · Cited by 195
“The Bayesian multidivtime dating method (Thorne et al., 1998; Thorne & Kishino, 2002) uses a probabilistic model to describe the change in evolutionary rate over time and uses the MCMC procedure to derive the posterior distribution of rates and time.”
MethodCombined Data, Bayesian Phylogenetics, and the Origin of the New Zealand Cicada Genera
Buckley, T. R., Arensburger, P., Simon, C., & Chambers, G. K. (2002) · Systematic Biology · doi:10.1080/106351502753475844 · Cited by 195
Pramuk, J. B., Robertson, T., Sites, J. W., & Noonan, B. P. (2007) · Global Ecology and Biogeography · doi:10.1111/j.1466-8238.2007.00348.x · Cited by 194
“ , Thorne et al. , 1998; Thorne & Kishino, 2002) may not be a realistic way to model rate evolution (Drummond et al ., 2006).”
MethodAdaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model
Douglas, J., Zhang, R., & Bouckaert, R. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008322 · Cited by 191
Ho, S. Y. W. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi125 · Cited by 190
Ecological Limits on Clade Diversification in Higher Taxa
Rabosky, D. L. (2009) · The American Naturalist · doi:10.1086/597378 · Cited by 189
Identifiability of Parameters in MCMC Bayesian Inference of Phylogeny
Rannala, B. (2002) · Systematic Biology · doi:10.1080/10635150290102429 · Cited by 190
Molecular phylogenetics reveal multiple tertiary vicariance origins of the African rain forest trees
Couvreur, T. L. P., Chatrou, L. W., Sosef, M. S. M., & Richardson, J. E. (2008) · BMC Biology · doi:10.1186/1741-7007-6-54 · Cited by 192
Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset
Higdon, J. W., Bininda‐Emonds, O. R. P., Beck, R. M. D., & Ferguson, S. H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-216 · Cited by 198
“Table 3: Divergence dates calculated using Bayesian relaxed molecular clock method implemented by multidivtime [122, 123 ] for all genes combined and for mtDNA genes only, each fitted to the preferred supertree topology (Fig. 1).”
Castoe, T. A., Daza, J. M., Smith, E. N., Sasa, M., Kuch, U., Campbell, J. A., Chippindale, P. T., & Parkinson, C. L. (2008) · Journal of Biogeography · doi:10.1111/j.1365-2699.2008.01991.x · Cited by 188
“…two relaxed clock methods to estimate divergence times across the pitviper phylogeny, the penalized likelihood (PL) method implemented in r8s (Sanderson, 1997, 2002, 2003) and the Bayesian relaxed clock method implemented in the program multidistribute (Thorne et al., 1998; Thorne & Kishino, 2002).”
MethodMarshall, C. R. (2008) · The American Naturalist · doi:10.1086/587523 · Cited by 189
“DOI: 10.1086/587523 signed to accommodate varying rates of evolution across molecular phylogenies (Takezaki et al. 1995; Cooper and Penny 1997; Sanderson 1997, 2002; Rambaut and Bromham 1998; Thorne et al. 1998; Cutler 2000; Aris-Brosou and Yang 2002; Drummond et al. 2006).”
BackgroundInfluentialDating the Diversification of the Major Lineages of Ascomycota (Fungi)
Prieto, M., & Wedin, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065576 · Cited by 189
“Different methods have been developed to handle rate heterogeneity [7], some of which attempt to relax the molecular clock assumption by allowing the rate to vary across the tree [8–11].”
MethodInda, L. A., Segarra‐Moragues, J. G., Müller, J., Peterson, P. M., & Catalán, P. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.11.022 · Cited by 186
THE AGE OF THE ANGIOSPERMS: A MOLECULAR TIMESCALE WITHOUT A CLOCK
Bell, C. D., Soltis, P. S., & Soltis, P. S. (2005) · Evolution · doi:10.1111/j.0014-3820.2005.tb01775.x · Cited by 189
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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