The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation
Open accessAbstract
The use of fossil evidence to calibrate divergence time estimation has a long history. More recently, Bayesian Markov chain Monte Carlo has become the dominant method of divergence time estimation, and fossil evidence has been reinterpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting hashave not been carefully investigated. Here, we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis.
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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 2×
“This is especially the case in Bayesian phylogenetic models that support “relaxed phylogenetics,” in which genetic distances are partitioned into divergence times and lineage-specific substitution rates using a relaxed molecular clock (Drummond et al. 2006).”
BackgroundSelf-citationDrummond, A. J., Nicholls, G. K., Rodrigo, A. G., & Solomon, W. (2002) · Genetics · doi:10.1093/genetics/161.3.1307 · Cited by 1,059
Self-citation
Cited by
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006650 · Cited by 4,556
Self-citationA comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2015) · Nature · doi:10.1038/nature15697 · Cited by 1,668
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
dos Reis, M., Inoue, J., Hasegawa, M., Asher, R. J., Donoghue, P. C. J., & Yang, Z. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.0683 · Cited by 526
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
Self-citationA new time tree reveals Earth history’s imprint on the evolution of modern birds
Claramunt, S., & Cracraft, J. (2015) · Science Advances · doi:10.1126/sciadv.1501005 · Cited by 383
“We ran analyses without sequence data to evaluate the behavior of calibration priors (115).”
MethodExploring uncertainty in the calibration of the molecular clock
Warnock, R. C. M., Yang, Z., & Donoghue, P. C. J. (2012) · Biology Letters · doi:10.1098/rsbl.2011.0710 · Cited by 238
The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci
Dos Reis, M., Zhu, T., & Yang, Z. (2014) · Systematic Biology · doi:10.1093/sysbio/syu020 · Cited by 93
Wheat, C. W., & Wahlberg, N. (2013) · Systematic Biology · doi:10.1093/sysbio/sys074 · Cited by 80
Budd, G. E., & Mann, R. P. (2020) · Interface Focus · doi:10.1098/rsfs.2019.0110 · Cited by 54
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
- Heled, J., & Drummond, A. J.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-08-18
- Volume
- 61
- Issue
- 1
- Pages
- 138-149
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2125241803
- Cited by
- 328
- References
- 2
- FWCI
- 9.29
- Type
- journal article
- Language
- en
- Open access
- hybrid
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