The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
Abstract
We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.
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Cites
A new look at the statistical model identification
Akaike, H. (1974) · IEEE Transactions on Automatic Control · doi:10.1109/tac.1974.1100705 · Cited by 51,879
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
The role of parenteral antischistosomal therapy in the spread of hepatitis C virus in Egypt
Frank, C., Mohamed, M. K., Strickland, G. T., Lavanchy, D., Arthur, R. R., Magder, L. S., Khoby, T. E., Abdel-Wahab, Y., Ohn, E. S. A., Anwar, W., et al. (2000) · The Lancet · doi:10.1016/s0140-6736(99)06527-7 · Cited by 1,131
Drummond, A. J., Nicholls, G. K., Rodrigo, A. G., & Solomon, W. (2002) · Genetics · doi:10.1093/genetics/161.3.1307 · Cited by 1,059
Self-citationPybus, O. G. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg043 · Cited by 246
Cited by
Posterior summarization in Bayesian phylogenetics using tracer 1.7
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy032 · Cited by 11,159
“2002), and the non-parametric Bayesian skyline (Drummond et al. 2005; Heled and Drummond 2008), skyride (Minin et al.”
BackgroundSelf-citationRelaxed 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
“For example, the coalescent prior [56,57] is a commonly used prior for population-level data and has been extended to include various forms of demographic functions [58,59], sub-divided populations [60], and other complexities.”
BackgroundSelf-citationBEAST 2: a software platform for Bayesian evolutionary analysis
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003537 · Cited by 6,527
Self-citationGutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906
“, [4–6,16,17], but also see [10,18]).”
Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity
Hortal, J., de Bello, F., Diniz-Filho, J. A. F., Lewinsohn, T. M., Lobo, J. M., & Ladle, R. J. (2015) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-112414-054400 · Cited by 1,743
Metadata
- Authors
- Drummond, A. J.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-02-09
- Volume
- 22
- Issue
- 5
- Pages
- 1185-1192
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2153432740
- Cited by
- 3,143
- References
- 5
- FWCI
- 25.21
- Type
- journal article
- Language
- en
- Open access
- closed
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