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.
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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).”
BackgroundInfluential
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
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