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
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BackgroundInfluential
Cited by
Estimating the timing of early eukaryotic diversification with multigene molecular clocks
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The fossilized birth-death process for coherent calibration of divergence-time estimates
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Best Practices for Justifying Fossil Calibrations
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Total-Evidence Dating under the Fossilized Birth–Death Process
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Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins
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A new time tree reveals Earth history’s imprint on the evolution of modern birds
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“Fossil recovery biases can be quantified and incorporated into age estimates (34, 35) but not without theoretical and practical difficulties (32, 33).”
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On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks
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Exploring uncertainty in the calibration of the molecular clock
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A biologist’s guide to Bayesian phylogenetic analysis
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Self-citationWheat, C. W., & Wahlberg, N. (2013) · Systematic Biology · doi:10.1093/sysbio/sys074 · Cited by 80
Wang, Z., Shen, X., Liu, B., Su, J., Yonezawa, T., Yu, Y., Guo, S., Ho, S. Y. W., Vilà, C., Hasegawa, M., et al. (2010) · Journal of Biogeography · doi:10.1111/j.1365-2699.2010.02379.x · Cited by 79
Self-citationMolecular 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
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
Molecular paleobiology — Progress and perspectives
Wörheide, G., Dohrmann, M., & Yang, Q. (2016) · Palaeoworld · doi:10.1016/j.palwor.2015.01.005 · Cited by 10
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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