The impact of fossils and taxon sampling on ancient molecular dating analyses
Open accessAbstract
The number and complexity of molecular dating studies has increased over the past decade. Along with a broadening acceptance of their utility has come significant controversy over the methods and models that are appropriate, as well as the accuracy of the estimates yielded by molecular clock analyses. Radically different age estimates have been published for the same divergences from analyses of different datasets with different fossil constraints obtained with different methods, and the underlying explanation for these differences is often unclear. Here we utilize two previously published datasets to examine the effect of fossil calibrations and taxon sampling on the age estimates for two deep eukaryote divergences in an attempt to discern the relative impact of these factors. Penalized likelihood, non-parametric rate smoothing, and Bayesian methods were utilized to generate age estimates for the origin of the Metazoa from a 7-gene dataset and for the divergence of Eukaryotes from a 129-gene dataset. From these analyses, it is clear that the fossil calibrations chosen and the method for applying constraints to these nodes have a large impact on age estimates, while the degree of taxon sampling within a dataset is less important in terms of the resulting age estimates. Concerns and recommendations for addressing these two factors when initiating a dating analysis are discussed.
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
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?
Few studies have considered the cumulative impact of uncertainties on the precision of evolutionary timescales.
“Yet, few studies have considered the cumulative impact of these uncertainties on the precision of evolutionary timescales (e.g., [45, 46]).”
From Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales (2015) · cites this paper as [45]
The Introduction (p. 1) says that few studies examine how fossil constraints affect age estimates and that the error from those constraints is generally ignored or unreported. The paper also examines fossil calibrations and taxon sampling together, but it does not establish the broader claim that few studies have considered the cumulative impact of uncertainties on the precision of evolutionary timescales. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463 · see citing works
PAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,344 · see citing works
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
Schmidt, H. A., Strimmer, K., Vingron, M., & von Haeseler, A. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.3.502 · Cited by 2,512 · see citing works
Sanderson, M. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003974 · Cited by 1,977 · see citing works
A molecular timescale for vertebrate evolution
Kumar, S., & Hedges, S. B. (1998) · Nature · doi:10.1038/31927 · Cited by 1,936 · see citing works
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906 · see citing works
Molecules as documents of evolutionary history
Zuckerkandl, E., & Pauling, L. C. (1965) · Journal of Theoretical Biology · doi:10.1016/0022-5193(65)90083-4 · Cited by 1,359 · see citing works
Phylogenomics and the reconstruction of the tree of life
Delsuc, F., Brinkmann, H., & Philippe, H. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1603 · Cited by 1,228 · see citing works
A nonparametric approach to estimating divergence times in the absence of rate constancy.
Sanderson, M. J. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025731 · Cited by 1,156 · see citing works
Computational Molecular Evolution
Yang, Z. (2006) · doi:10.1093/acprof:oso/9780198567028.001.0001 · Cited by 1,143 · see citing works
Divergence time and evolutionary rate estimation with multilocus data.
Thorne, J. L., & Kishino, H. (2002) · Systematic Biology · doi:10.1080/10635150290102456 · Cited by 962 · see citing works
Yang, Z., & Rannala, B. H. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj024 · Cited by 916 · see citing works
Paleontological Evidence to Date the Tree of Life
Benton, M. J., & Donoghue, P. C. J. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl150 · Cited by 916 · see citing works
Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision
Graur, D., & Martin, W. (2004) · Trends in Genetics · doi:10.1016/j.tig.2003.12.003 · Cited by 669 · see citing works
The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
Douzery, E. J. P., Snell, E. A., Bapteste, E., Delsuc, F., & Philippe, H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403984101 · Cited by 638 · see citing works
Performance of a divergence time estimation method under a probabilistic model of rate evolution.
Kishino, H., Thorne, J. L., & Bruno, W. J. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003811 · Cited by 633 · see citing works
A molecular timescale of eukaryote evolution and the rise of complex multicellular life
Hedges, S. B., Blair, J. E., Venturi, M. L., & Shoe, J. L. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-2 · Cited by 578 · see citing works
Estimating metazoan divergence times with a molecular clock
Peterson, K. J., Lyons, J. B., Nowak, K. S., Takacs, C. M., Wargo, M. J., & McPeek, M. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401670101 · Cited by 461 · see citing works
Peterson, K. J., & Butterfield, N. J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503660102 · Cited by 361 · see citing works
Yang, Z., & Yoder, A. D. (2003) · Systematic Biology · doi:10.1080/10635150390235557 · Cited by 357 · see citing works
Ancient Phylogenetic Relationships
Gribaldo, S., & Philippe, H. (2002) · Theoretical Population Biology · doi:10.1006/tpbi.2002.1593 · Cited by 314 · see citing works
Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling
Hedtke, S. M., Townsend, T. M., & Hillis, D. M. (2006) · Systematic Biology · doi:10.1080/10635150600697358 · Cited by 303 · see citing works
Precision of molecular time estimates
Hedges, S. B., & Kumar, S. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.03.004 · Cited by 289 · see citing works
Near, T. J., Meylan, P. A., & Shaffer, H. B. (2005) · The American Naturalist · doi:10.1086/427734 · Cited by 270 · see citing works
Benton, M. J., & Ayala, F. J. (2003) · Science · doi:10.1126/science.1077795 · Cited by 252 · see citing works
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 227 · see citing works
A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record
Berney, C., & Pawlowski, J. (2006) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2006.3537 · Cited by 212 · see citing works
Precision of molecular time estimates
BLAIRHEDGES, S. (2004) · Trends in Genetics · doi:10.1016/s0168-9525(04)00072-1 · Cited by 186 · see citing works
Roger, A. J., & Hug, L. A. (2006) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2006.1845 · Cited by 180 · see citing works
Self-citationNear, T. J., & Sanderson, M. J. (2004) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2004.1523 · Cited by 180 · see citing works
Aris-Brosou, S. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg226 · Cited by 164 · see citing works
IQPNNI: Moving Fast Through Tree Space and Stopping in Time
Le, V. S. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh176 · Cited by 162 · see citing works
Molecular Clocks Do Not Support the Cambrian Explosion
Blair, J. E., & Hedges, S. B. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi039 · Cited by 73 · see citing works
Near, Meylan, & Shaffer (2005) · The American Naturalist · doi:10.2307/3473141 · Cited by 62 · see citing works
van Tuinen, M., & Hadly, E. A. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-004-2624-9 · Cited by 57 · see citing works
Molecular dating: ape bones agree with chicken entrails
Glazko, G. V., Koonin, E. V., & Rogozin, I. B. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.12.006 · Cited by 35 · see citing works
The comparative method for evaluating fossil calibration dates: a reply to Hedges and Kumar
Reisz, R. R., & Müller, J. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.09.004 · Cited by 9 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Estimating the timing of early eukaryotic diversification with multigene molecular clocks
Parfrey, L. W., Lahr, D. J. G., Knoll, A. H., & Katz, L. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110633108 · Cited by 899 · see citing works
Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times
Ho, S. Y. W., & Phillips, M. J. (2009) · Systematic Biology · doi:10.1093/sysbio/syp035 · Cited by 893 · see citing works
Estimating divergence times in large molecular phylogenies
Tamura, K., Battistuzzi, F. U., Billing-Ross, P., Murillo, O. D., Filipski, A., & Kumar, S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1213199109 · Cited by 660 · see citing works
Taxon sampling and the accuracy of phylogenetic analyses
(2008) · Journal of Systematics and Evolution · doi:10.3724/sp.j.1002.2008.08016 · Cited by 553 · see citing works
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales
dos Reis, M., Thawornwattana, Y., Angelis, K., Telford, M. J., Donoghue, P. C. J., & Yang, Z. (2015) · Current Biology · doi:10.1016/j.cub.2015.09.066 · Cited by 471 · see citing works
Vanneste, K., Baele, G., Maere, S., & de Peer, Y. V. (2014) · Genome Research · doi:10.1101/gr.168997.113 · Cited by 438 · see citing works
Sauquet, H., Ho, S. Y. W., Gandolfo, M. A., Jordan, G. J., Wilf, P., Cantrill, D. J., Bayly, M. J., Bromham, L. D., Brown, G. K., Carpenter, R. J., et al. (2011) · Systematic Biology · doi:10.1093/sysbio/syr116 · Cited by 425 · see citing works
Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia
Pyron, R. A. (2011) · Systematic Biology · doi:10.1093/sysbio/syr047 · Cited by 419 · see citing works
Koepfli, K., Deere, K. A., Slater, G. J., Begg, C. M., Begg, K. S., Grassman, L. I., Lucherini, M., Veron, G., & Wayne, R. K. (2008) · BMC Biology · doi:10.1186/1741-7007-6-10 · Cited by 397 · see citing works
Peterson, K. J., Cotton, J. A., Gehling, J. G., & Pisani, D. (2008) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2007.2233 · Cited by 313 · see citing works
BLANK, C. E., & SÁNCHEZ‐BARACALDO, P. (2010) · Geobiology · doi:10.1111/j.1472-4669.2009.00220.x · Cited by 298 · see citing works
A 4000-species dataset provides new insight into the evolution of ferns
Testo, W., & Sundue, M. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.09.003 · Cited by 292 · see citing works
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 · see citing works
Self-citationStrong 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 · see citing works
An online resource for marine fungi
Jones, E. B. G., Pang, K.-L., Abdel-Wahab, M. A., Scholz, B., Hyde, K. D., Boekhout, T., Ebel, R., Rateb, M. E., Henderson, L., Sakayaroj, J., et al. (2019) · Fungal Diversity · doi:10.1007/s13225-019-00426-5 · Cited by 229 · see citing works
Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts
Laenen, B., Shaw, B., Schneider, H., Goffinet, B., Paradis, E., Désamoré, A., Heinrichs, J., Villarreal, J. C., Gradstein, S. R., McDaniel, S. F., et al. (2014) · Nature Communications · doi:10.1038/ncomms6134 · Cited by 215 · see citing works
Lang, D., Weiche, B., Timmerhaus, G., Richardt, S., Riaño‐Pachón, D. M., Corrêa, L. G. G., Reski, R., Mueller‐Roeber, B., & Rensing, S. A. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq032 · Cited by 185 · see citing works
Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology
Hipsley, C. A., & Müller, J. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00138 · Cited by 176 · see citing works
Vanneste, K., Maere, S., & de Peer, Y. V. (2014) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0353 · Cited by 170 · see citing works
Molecular Dating, Evolutionary Rates, and the Age of the Grasses
Christin, P., Spriggs, E. L., Osborne, C. P., Strömberg, C. A. E., Salamin, N., & Edwards, E. J. (2013) · Systematic Biology · doi:10.1093/sysbio/syt072 · Cited by 166 · see citing works
The impact of calibration and clock-model choice on molecular estimates of divergence times
Duchêne, S., Lanfear, R., & Ho, S. Y. W. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.05.032 · Cited by 156 · see citing works
Brown, J. W., & Sörhannus, U. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012759 · Cited by 148 · see citing works
Priors and Posteriors in Bayesian Timing of Divergence Analyses: The Age of Butterflies Revisited
Chazot, N., Wahlberg, N., Freitas, A. V. L., Mitter, C. W., Labandeira, C. C., Sohn, J., Sahoo, R. K., Seraphim, N., de Jong, R., & Heikkilä, M. (2019) · Systematic Biology · doi:10.1093/sysbio/syz002 · Cited by 141 · see citing works
Martín‐Bravo, S., Jiménez‐Mejías, P., Villaverde, T., Escudero, M., Hahn, M., Spalink, D., Roalson, E. H., Hipp, A. L., the Global Carex Group, Benítez‐Benítez, C., et al. (2019) · Journal of Systematics and Evolution · doi:10.1111/jse.12549 · Cited by 132 · see citing works
Gustafsson, A. L. S., Verola, C. F., & Antonelli, A. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-177 · Cited by 126 · see citing works
Molecular phylogenetics of ponerine ants (Hymenoptera: Formicidae: Ponerinae)
Schmidt, C. A. (2013) · Zootaxa · doi:10.11646/zootaxa.3647.2.1 · Cited by 108 · see citing works
Roquet, C., Sanmartín, I., Garcia‐Jacas, N., Sáez, L., Susanna, A., Wikström, N., & Aldasoro, J. J. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.05.014 · Cited by 102 · see citing works
Saitoh, K., Sado, T., Doosey, M. H., BART, H. L. J., Inoue, J. G., Nishida, M., Mayden, R. L., & Miya, M. U. (2011) · Zoological Journal of the Linnean Society · doi:10.1111/j.1096-3642.2010.00651.x · Cited by 98 · see citing works
A Hierarchical Bayesian Model for Calibrating Estimates of Species Divergence Times
Heath, T. A. (2012) · Systematic Biology · doi:10.1093/sysbio/sys032 · Cited by 97 · see citing works
Aguirre, J., Perfectti, F., & Braga, J. C. (2010) · Paleobiology · doi:10.1666/09041.1 · Cited by 96 · see citing works
Blank, C. E. (2013) · Journal of Phycology · doi:10.1111/jpy.12111 · Cited by 95 · see citing works
Aghová, T., Kimura, Y., Bryja, J., Dobigny, G., Granjon, L., & Kergoat, G. J. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.07.017 · Cited by 91 · see citing works
Battistuzzi, F. U., Filipski, A., Hedges, S. B., & Kumar, S. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq014 · Cited by 89 · see citing works
Ware, J. L., Grimaldi, D. A., & Engel, M. S. (2009) · Arthropod Structure & Development · doi:10.1016/j.asd.2009.11.003 · Cited by 83 · see citing works
Wheat, C. W., & Wahlberg, N. (2013) · Systematic Biology · doi:10.1093/sysbio/sys074 · Cited by 80 · see citing works
Arribas, P., Andújar, C., MORAZA, M. L., Linard, B., Emerson, B. C., & Vogler, A. P. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz255 · Cited by 82 · see citing works
Wang, Y., Cui, Y., Rédei, D., Baňař, P., Xie, Q., Štys, P., Damgaard, J., Chen, P., Yi, W., Wang, Y., et al. (2015) · Cladistics · doi:10.1111/cla.12137 · Cited by 82 · see citing works
Light, J. E., & Reed, D. L. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.10.023 · Cited by 78 · see citing works
Su, Y. C. F., & SAUNDERS, R. M. K. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-153 · Cited by 78 · see citing works
Pérez-Ortega, S. A., Garrido‐Benavent, I., Grube, M., Olmo, R., & Rı́os, A. D. L. (2016) · Fungal Diversity · doi:10.1007/s13225-016-0361-1 · Cited by 71 · see citing works
Geomolecular Dating and the Origin of Placental Mammals
Phillips, M. J. (2015) · Systematic Biology · doi:10.1093/sysbio/syv115 · Cited by 68 · see citing works
Arroyave, J., Denton, J. S. S., & Stiassny, M. L. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077269 · Cited by 69 · see citing works
Tripp, E. A., & McDade, L. A. (2014) · Systematic Biology · doi:10.1093/sysbio/syu029 · Cited by 69 · see citing works
A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth–Death Process
Luo, A., Duchêne, D. A., Zhang, C., Zhu, C., & Ho, S. Y. W. (2019) · Systematic Biology · doi:10.1093/sysbio/syz038 · Cited by 66 · see citing works
Meng, K., Chen, S., Xu, K., Zhou, R., Li, M., Dhamala, M. K., Liao, W., & Fan, Q. (2021) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2021.107083 · Cited by 62 · see citing works
Schenk, J. J., & Hufford, L. D. (2010) · Systematic Botany · doi:10.1600/036364410792495809 · Cited by 60 · see citing works
Phylogenomics and diversification of Sordariomycetes
Chen, Y., Su, P., Hyde, K., & Maharachchikumbura, S. S. N. (2023) · Mycosphere · doi:10.5943/mycosphere/14/1/5 · Cited by 58 · see citing works
Fossil record of stem groups employed in evaluating the chronogram of insects (Arthropoda: Hexapoda)
Wang, Y., Engel, M. S., Rafael, J. A., Wu, H., Rédei, D., Xie, Q., Wang, G., Liu, X., & Bu, W. (2016) · Scientific Reports · doi:10.1038/srep38939 · Cited by 58 · see citing works
Evolution of Xylariomycetidae (Ascomycota: Sordariomycetes)
Samarakoon, M. C. (2016) · Mycosphere · doi:10.5943/mycosphere/7/11/9 · Cited by 54 · see citing works
Not so old Archaea – the antiquity of biogeochemical processes in the archaeal domain of life
Blank, C. E. (2009) · Geobiology · doi:10.1111/j.1472-4669.2009.00219.x · Cited by 52 · see citing works
Molecular clocks and the early evolution of metazoan nervous systems
Wray, G. A. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0046 · Cited by 51 · see citing works
Condamine, F. L., Toussaint, E. F. A., Cotton, A. M., Genson, G., Sperling, F. A. H., & Kergoat, G. J. (2012) · Cladistics · doi:10.1111/j.1096-0031.2012.00412.x · Cited by 51 · see citing works
Ediacaran origin and Ediacaran-Cambrian diversification of Metazoa
Carlisle, E. M., Yin, Z., Pisani, D., & Donoghue, P. C. J. (2024) · Science Advances · doi:10.1126/sciadv.adp7161 · Cited by 54 · see citing works
Assembling 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 · see citing works
MicroRNAs 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 44 · see citing works
Sanders, K. L., Mumpuni, Hamidy, A., Head, J. J., & Gower, D. J. (2010) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2010.04.031 · Cited by 43 · see citing works
Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights
Lee, A. K., Gilman, I. S., Srivastav, M., Lerner, A. D., Donoghue, M. J., & Clement, W. L. (2021) · American Journal of Botany · doi:10.1002/ajb2.1695 · Cited by 42 · see citing works
Soares, A. E. R., & Schrago, C. G. (2014) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.09.004 · Cited by 39 · see citing works
Battistuzzi, F. U., Billing-Ross, P., Murillo, O., Filipski, A., & Kumar, S. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv075 · Cited by 34 · see citing works
Comment on “Whole-genome analyses resolve early branches in the tree of life of modern birds”
Mitchell, K. J., Cooper, A., & Phillips, M. J. (2015) · Science · doi:10.1126/science.aab1062 · Cited by 38 · see citing works
The mouth, the anus, and the blastopore—open questions about questionable openings
Hejnol, A., & Martindale, M. Q. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0004 · Cited by 37 · see citing works
The Emergence of Earliest Angiosperms May be Earlier than Fossil Evidence Indicates
Salomo, K., Smith, J. F., Feild, T. S., Samain, M., Bond, L., Davidson, C., Zimmers, J. C., Neinhuis, C., & Wanke, S. (2017) · Systematic Botany · doi:10.1600/036364417x696438 · Cited by 37 · see citing works
Björn Stelbrink, A., Richter, R., Köhler, F., Riedel, F., Strong, E. E., Bocxlaer, B. V., Albrecht, C., Hauffe, T., Page, T. J., Aldridge, D. C., et al. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa011 · Cited by 37 · see citing works
Tomiya, S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024146 · Cited by 35 · see citing works
Larabee, F. J., Fisher, B. L., Schmidt, C. A., Matos‐Maraví, P. F., Janda, M., & Suarez, A. V. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.07.024 · Cited by 35 · see citing works
Phylogenomics indicates the “living fossil” Isoetes diversified in the Cenozoic
Wood, D. P., Besnard, G., Beerling, D. J., Osborne, C. P., & Christin, P. (2020) · PLoS ONE · doi:10.1371/journal.pone.0227525 · Cited by 33 · see citing works
Recent progress in paleontological methods for dating the Tree of Life
Laurin, M. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00130 · Cited by 32 · see citing works
Quantifying the Error of Secondary vs. Distant Primary Calibrations in a Simulated Environment
Powell, C. L. E., Waskin, S., & Battistuzzi, F. U. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00252 · Cited by 29 · see citing works
Hodge, J. R., Read, C. I., Bellwood, D. R., & van Herwerden, L. (2013) · Journal of Biogeography · doi:10.1111/jbi.12124 · Cited by 27 · see citing works
Evolving Perceptions on the Antiquity of the Modern Avian Tree
Brown, J. W., & van Tuinen, M. (2011) · Wiley eBooks · doi:10.1002/9781119990475.ch12 · Cited by 27 · see citing works
Gamboa, M., Murányi, D., Kanmori, S., & Watanabe, K. (2019) · PLoS ONE · doi:10.1371/journal.pone.0210269 · Cited by 26 · see citing works
Salvi, D., Pinho, C., Mendes, J., & Harris, D. J. (2021) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2021.107169 · Cited by 26 · see citing works
Mello, B., & Schrago, C. G. (2014) · Evolutionary Bioinformatics · doi:10.4137/ebo.s13908 · Cited by 26 · see citing works
Siver, P. A., Wolfe, A. P., Rohlf, F. J., Shin, W., & Jo, B. Y. (2013) · Geobiology · doi:10.1111/gbi.12023 · Cited by 26 · see citing works
Bukontaite, R., Ranarilalatiana, T., Randriamihaja, J. H., & Bergsten, J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0120777 · Cited by 25 · see citing works
Soares, A. E. R., & Schrago, C. G. (2012) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s9677 · Cited by 25 · see citing works
Villaverde, T., Maguilla, E., Luceño, M., & Hipp, A. L. (2020) · Journal of Systematics and Evolution · doi:10.1111/jse.12724 · Cited by 25 · see citing works
Dating the origin of the major lineages of Branchiopoda
Sun, X., Xia, X., & Yang, Q. (2015) · Palaeoworld · doi:10.1016/j.palwor.2015.02.003 · Cited by 25 · see citing works
RelTime Relaxes the Strict Molecular Clock throughout the Phylogeny
Battistuzzi, F. U., Tao, Q., Jones, L., Tamura, K., & Kumar, S. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy118 · Cited by 25 · see citing works
Genomic, 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 · see citing works
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 · see citing works
A Comparative Study of Mammalian Diversification Pattern
Yu, W., Xu, J., Wu, Y., & Yang, G. (2012) · International Journal of Biological Sciences · doi:10.7150/ijbs.3982 · Cited by 23 · see citing works
Global Rate Variation in Bony Vertebrates
Takezaki, N. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy125 · Cited by 21 · see citing works
Genetic and Biochemical Diversity among Valeriana jatamansi Populations from Himachal Pradesh
Singh, S. K., Katoch, R., & Kapila, R. K. (2015) · The Scientific World JOURNAL · doi:10.1155/2015/863913 · Cited by 21 · see citing works
Hellen, E., & Brookfield, J. F. Y. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss206 · Cited by 20 · see citing works
Ksepka, D. T., Balanoff, A. M., Bell, M. A., & Houseman, M. (2013) · Palaeontology · doi:10.1111/pala.12040 · Cited by 18 · see citing works
Kartik, N., Ranjit Singh, H., Balagopalan, U., & A, K. S. (2010) · AFRICAN JOURNAL OF BIOTECHNOLOGY · doi:10.5897/ajb10.1745 · Cited by 17 · see citing works
Molecular technology in paleontology and paleobiology: Applications and limitations
Abdelhady, A. A., Seuß, B., Jain, S., Fathy, D., Sami, M., Ali, A., Elsheikh, A., Ahmed, M. S., Elewa, A. M. T., & Hussain, A. M. (2024) · Quaternary International · doi:10.1016/j.quaint.2024.01.006 · Cited by 16 · see citing works
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 · see citing works
Martín‐Bravo, S., & Daniel, T. F. (2016) · American Journal of Botany · doi:10.3732/ajb.1600083 · Cited by 15 · see citing works
Testing a time hypothesis in the biogeography of the arowana genus Scleropages (Osteoglossidae)
Lavoué, S. (2015) · Journal of Biogeography · doi:10.1111/jbi.12585 · Cited by 15 · see citing works
Analysis of Genetic Diversity of Persea bombycina “Som” Using RAPD-Based Molecular Markers
Bhau, B. S., Medhi, K., Das, A. P., Saikia, S. P., Neog, K., & Choudhury, S. N. (2009) · Biochemical Genetics · doi:10.1007/s10528-009-9242-6 · Cited by 13 · see citing works
Impact of the Partitioning Scheme on Divergence Times Inferred from Mammalian Genomic Data Sets
Voloch, C. M., & Schrago, C. G. (2012) · Evolutionary Bioinformatics · doi:10.4137/ebo.s9627 · Cited by 12 · see citing works
Deciphering deuterostome phylogeny: molecular, morphological, and palaeontological perspectives
Smith, A. B., & Swalla, B. J. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0009 · Cited by 13 · see citing works
The evolution of nervous system centralization
Arendt, D., Denes, A. S., Jékely, G., & Tessmar‐Raible, K. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0007 · Cited by 12 · see citing works
Peterson, K. J., Cotton, J. A., Gehlîng, J. G., & Pisani, D. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0002 · Cited by 12 · see citing works
A Simulation-Based Evaluation of Total-Evidence Dating Under the Fossilized Birth-Death ProcessPreprint
Luo, A., Duchêne, D. A., Zhang, C., Zhu, C., & Ho, S. Y. W. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/436303 · Cited by 11 · see citing works
Abramson, N. I., Skalon, E. K., Bondareva, O., Bodrov, S. Y., Petrova, T. V., & Dvoyashov, I. A. (2025) · Diversity · doi:10.3390/d17010061 · Cited by 10 · see citing works
Evolution: A Fixed-Nitrogen Fix in the Early Ocean?
Lyons, T. W., Reinhard, C. T., & Planavsky, N. J. (2014) · Current Biology · doi:10.1016/j.cub.2014.02.034 · Cited by 10 · see citing works
Zhang, R., Wang, L., Tian, S., Liu, Y., Jiang, Y., Zhou, X., Yang, D., Liu, X., & Wang, Y. (2025) · Systematic Entomology · doi:10.1111/syen.12684 · Cited by 9 · see citing works
- Authors
- Hug, L. A., & Roger, A. J.
- Affiliations
- Dalhousie University (CA)
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-06-07
- Volume
- 24
- Issue
- 8
- Pages
- 1889-1897
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2164727170
- Cited by
- 144
- References
- 37
- Citations by year
- 2025: 6 · 2024: 3 · 2023: 1 · 2022: 1 · 2021: 3 · 2020: 7 · 2019: 8 · 2018: 6 · 2017: 2 · 2016: 7 · 2015: 12 · 2014: 12 · 2013: 8 · 2012: 14
- FWCI
- 5.97
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Alfred P. Sloan Foundation
- Killam Trusts
- Canadian Institutes of Health Research (62809, MOP62809)
- Natural Sciences and Engineering Research Council of Canada (227085-2005)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- fossil calibration, taxon sampling, divergence time estimation, eukaryotic origin, penalized likelihood, Bayesian phylogenetics, molecular clock
- MeSH terms
- Animals, Bayes Theorem, Eukaryotic Cells, Fossils, Invertebrates, Models, Genetic, Phylogeny, Genetic Variation, Likelihood Functions, Sequence Analysis, DNA, 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
