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
Equation of State Calculations by Fast Computing Machines
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., & Teller, E. (1953) · The Journal of Chemical Physics · doi:10.1063/1.1699114 · Cited by 37,192
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
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 4×
“Drummond et al. (2005) and Opgen-Rhein et al.”
MethodInfluentialEstimating 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 · cited 1×
“…a time-aware GMRF prior based on midpoint distances between intercoalescent intervals, d k 5 u k þ u k þ 1 2 : ð9Þ Midpoint distances have been successfully used before in molecular evolution by Thorne et al. (1998) to construct an autocorrelated prior for evolutionary rates on genealogy branches.”
MethodThe 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
Shankarappa, R., Margolick, J. B., Gange, S. J., Rodrigo, A. G., Upchurch, D., Farzadegan, H., Gupta, P., Rinaldo, C. R., Learn, G. H., He, X., et al. (1999) · Journal of Virology · doi:10.1128/jvi.73.12.10489-10502.1999 · Cited by 926
Pybus, 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
“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
Self-citationHudjashov, G., Endicott, P., Post, H., Nagle, N., Ho, S. Y. W., Lawson, D. J., Reidla, M., Karmin, M., Rootsi, S., Metspalu, E., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-20026-8 · Cited by 72
An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics
Lan, S., Palacios, J. A., Karcher, M., Minin, V. N., & Shahbaba, B. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv378 · Cited by 38
Self-citationDemographic reconstruction from ancient DNA supports rapid extinction of the great auk
Thomas, J. E., Carvalho, G. R., Haile, J., Rawlence, N. J., Martin, M. D., Ho, S. Y., Sigfússon, A. Þ., Jósefsson, V. A., Frederiksen, M., Linnebjerg, J. F., et al. (2019) · eLife · doi:10.7554/elife.47509 · Cited by 29
Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong
Xie, R., Edwards, K. M., Adam, D. C., Leung, K. S. M., Tsang, T. K., Gurung, S., Xiong, W., Wei, X., Ng, D. Y. M., Liu, G. Y. Z., et al. (2022) · doi:10.21203/rs.3.rs-2107395/v1 · Cited by 31
(2026) · doi:10.1038/s41564-025-02254-7 · Cited by 1
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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