The DOI matches its Crossref record; 26 of the 26 references it cites were found in a registry or an index.
Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times
Abstract
The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000). At around the same time, Sanderson (1997) published his nonparametric rate-smoothing algorithm, which operates by minimizing the magnitude of rate changes between adjacent branches in the tree. A related method, penalized likelihood, was subsequently implemented in a maximum-likelihood framework (Sanderson 2002). In this approach, large rate changes between neighboring branches are penalized. The degree of penalization is determined by a smoothing parameter, the value of which is obtained objectively through a cross-validation procedure.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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 · cited 9×
“Rates among branches were assumed to follow a lognormal distribution (Drummond et al. 2006).”
BackgroundMethodInfluentialSelf-citationIntcal04 Terrestrial Radiocarbon Age Calibration, 0–26 Cal Kyr BP
(2004) · Radiocarbon · doi:10.1017/s0033822200032999 · Cited by 3,673
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
Sanderson, M. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003974 · Cited by 1,977
Estimating the rate of evolution of the rate of molecular evolution
Thorne, J. L., Kishino, H., & Painter, I. S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025892 · Cited by 1,317
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 · cited 5×
“Eventually, the minimum-age nature of fossil evidence was formalized in the nonparametric ratesmoothing method (Sanderson 1997).”
BackgroundMethodInfluentialDivergence time and evolutionary rate estimation with multilocus data.
Thorne, J. L., & Kishino, H. (2002) · Systematic Biology · doi:10.1080/10635150290102456 · Cited by 962 · cited 2×
“Hard bounds are now available in many divergence dating methods (Thorne et al. 1998; Thorne and Kishino 2002; Drummond et al. 2006; Yang and Rannala 2006; Britton et al. 2007).”
BackgroundPaleontological 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
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
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 · cited 4×
“…between branches, which can Downloaded from https://academic.oup.com/sysbio/article-abstract/58/3/367/1613552 by guest on 30 July 2018 be done by allowing the rate to change or “evolve” over time (Thorne et al. 1998; Kishino et al. 2001; Lepage et al. 2006; Rannala and Yang 2007; Ho 2009).”
BackgroundInfluentialDetermining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock
Doolittle, R. F., Feng, D.-F., Tsang, S., Cho, G., & Little, E. (1996) · Science · doi:10.1126/science.271.5248.470 · Cited by 581
A general comparison of relaxed molecular clock models
Lepage, T., Bryant, D., Philippe, H., & Lartillot, N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm193 · Cited by 546 · cited 3×
“The available relaxed-clock methods have been compared in several reviews (Magallón 2004; Welch and Bromham 2005; Lepage et al. 2006; Rutschmann 2006), and their performance has been assessed in a number of studies (e.g., Ho et al. 2005; Drummond et al. 2006; Lepage et al. 2007).”
BackgroundMethodEstimation of primate speciation dates using local molecular clocks.
Yoder, A. D., & Yang, Z. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026389 · Cited by 494
Inferring speciation times under an episodic molecular clock
Rannala, B., & Yang, Z. (2007) · Systematic Biology · doi:10.1080/10635150701420643 · Cited by 475
Mass survival of birds across the Cretaceous–Tertiary boundary: Molecular evidence.
Cooper, A., & Penny, D. (1997) · Science · doi:10.1126/science.275.5303.1109 · Cited by 472
Rocks and clocks: calibrating the Tree of Life using fossils and molecules
Donoghue, P. C. J., & Benton, M. J. (2007) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2007.05.005 · Cited by 413 · cited 3×
“When attempting to infer the timing of origination of a taxon, 2 common errors are associated with literal readings of the fossil record: local absences and taxonomic/taphonomic biases (Penny and Phillips 2004; Donoghue and Benton 2007).”
BackgroundMethodDefinitive fossil evidence for the extant avian radiation in the Cretaceous
Clarke, J. A., Tambussi, C. P., Noriega, J. I., Erickson, G. M., & Ketcham, R. A. (2005) · Nature · doi:10.1038/nature03150 · Cited by 342
Estimating divergence dates from molecular sequences.
Rambaut, A., & Bromham, L. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025940 · Cited by 298
Edwards, C. J., Bollongino, R., Scheu, A., Chamberlain, A., Tresset, A., Vigne, J.-D., Baird, J. F., Larson, G., Ho, S. Y. W., Heupink, T. H., et al. (2007) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2007.0020 · Cited by 266
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
Aris-Brosou, S., & Yang, Z. (2002) · Systematic Biology · doi:10.1080/10635150290102375 · Cited by 230 · cited 2×
“In one Bayesian dating method, developed by Aris-Brosou and Yang (2002, 2003), the posterior estimates appeared to be strongly influenced by the priors (Ho et al. 2005; Welch and Bromham 2005).”
MethodConfidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons
Marshall, C. R. (1997) · Paleobiology · doi:10.1017/s0094837300016766 · Cited by 196
Ho, S. Y. W. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi125 · Cited by 190 · cited 3×
“In one Bayesian dating method, developed by Aris-Brosou and Yang (2002, 2003), the posterior estimates appeared to be strongly influenced by the priors (Ho et al. 2005; Welch and Bromham 2005).”
BackgroundMethodSelf-citationAris-Brosou, S. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg226 · Cited by 164
The impact of fossils and taxon sampling on ancient molecular dating analyses
Hug, L. A., & Roger, A. J. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm115 · Cited by 144 · cited 3×
“—Hardmaximumbounds are probably the most controversial type of calibration, and the difficulty in choosing them has been well documented (Yang and Rannala 2006; Benton and Donoghue 2007; Hug and Roger 2007).”
BackgroundMolecular Clock Calibrations and Metazoan Divergence Dates
Lee, M. S. Y. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006562 · Cited by 142 · cited 1×
“A considerable number of date estimates have been obtained using single calibration points, with some prominent studies having relied exclusively on a calibration based on the bird–mammal divergence estimated at around 300 Ma ago (Lee, 1999; Hedges and Kumar, 2004).”
Background
Cited by
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
The fossilized birth-death process for coherent calibration of divergence-time estimates
Heath, T. A., Huelsenbeck, J. P., & Stadler, T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319091111 · Cited by 834
Best Practices for Justifying Fossil Calibrations
Parham, J. F., Donoghue, P. C. J., Bell, C. J., Calway, T. D., Head, J. J., Holroyd, P. A., Inoue, J. G., Irmis, R. B., Joyce, W. G., Ksepka, D. T., et al. (2012) · Systematic Biology · doi:10.1093/sysbio/syr107 · Cited by 780
Total-Evidence Dating under the Fossilized Birth–Death Process
Zhang, C., Stadler, T., Klopfstein, S., Heath, T. A., & Ronquist, F. (2016) · Systematic Biology · doi:10.1093/sysbio/syv080 · Cited by 419
Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins
Gavryushkina, A., Heath, T. A., Ksepka, D. T., Stadler, T., Welch, D., & Drummond, A. J. (2016) · Systematic Biology · doi:10.1093/sysbio/syw060 · Cited by 372
Metadata
- Authors
- Ho, S. Y. W., & Phillips, M. J.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-06
- Volume
- 58
- Issue
- 3
- Pages
- 367-380
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W1605705157
- Cited by
- 887
- References
- 26
- FWCI
- 19.68
- Type
- journal article
- Language
- en
- Open access
- closed
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
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
