The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics
Open accessAbstract
Kingman's coalescent process opens the door for estimation of population genetics model parameters from molecular sequences. One paramount parameter of interest is the effective population size. Temporal variation of this quantity characterizes the demographic history of a population. Because researchers are rarely able to choose a priori a deterministic model describing effective population size dynamics for data at hand, nonparametric curve-fitting methods based on multiple change-point (MCP) models have been developed. We propose an alternative to change-point modeling that exploits Gaussian Markov random fields to achieve temporal smoothing of the effective population size in a Bayesian framework. The main advantage of our approach is that, in contrast to MCP models, the explicit temporal smoothing does not require strong prior decisions. To approximate the posterior distribution of the population dynamics, we use efficient, fast mixing Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. In a simulation study, we demonstrate that the proposed temporal smoothing method, named Bayesian skyride, successfully recovers "true" population size trajectories in all simulation scenarios and competes well with the MCP approaches without evoking strong prior assumptions. We apply our Bayesian skyride method to 2 real data sets. We analyze sequences of hepatitis C virus contemporaneously sampled in Egypt, reproducing all key known aspects of the viral population dynamics. Next, we estimate the demographic histories of human influenza A hemagglutinin sequences, serially sampled throughout 3 flu seasons.
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Cites
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MethodThe role of parenteral antischistosomal therapy in the spread of hepatitis C virus in Egypt
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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
“2005; Heled and Drummond 2008), skyride (Minin et al. 2008), and skygrid (Gill et al.”
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-citationSpecies-specific responses of Late Quaternary megafauna to climate and humans
Lorenzen, E. D., Nogués-Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K. A., Ugan, A., Borregaard, M. K., Gilbert, M. T. P., Nielsen, R., et al. (2011) · Nature · doi:10.1038/nature10574 · Cited by 638
Self-citationHIV persists throughout deep tissues with repopulation from multiple anatomical sources
Chaillon, A., Gianella, S., Dellicour, S., Rawlings, S. A., Schlub, T. E., De Oliveira, M. F., Ignacio, C., Porrachia, M., Vrancken, B., & Smith, D. M. (2020) · Journal of Clinical Investigation · doi:10.1172/jci134815 · Cited by 250
Campos, P. F., Willerslev, E., Sher, A., Orlando, L., Axelsson, E., Tikhonov, A., Aaris-Sørensen, K., Greenwood, A. D., Kahlke, R.-D., Kosintsev, P., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907189107 · Cited by 239
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Metadata
- Authors
- Minin, V. N., Bloomquist, E. W., & Suchard, M. A.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-04-03
- Volume
- 25
- Issue
- 7
- Pages
- 1459-1471
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2156358357
- Cited by
- 697
- References
- 8
- FWCI
- 10.72
- Type
- journal article
- Language
- en
- Open access
- bronze
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