The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time
Open accessAbstract
Research aimed at understanding the geographic context of evolutionary histories is burgeoning across biological disciplines. Recent endeavors attempt to interpret contemporaneous genetic variation in the light of increasingly detailed geographical and environmental observations. Such interest has promoted the development of phylogeographic inference techniques that explicitly aim to integrate such heterogeneous data. One promising development involves reconstructing phylogeographic history on a continuous landscape. Here, we present a Bayesian statistical approach to infer continuous phylogeographic diffusion using random walk models while simultaneously reconstructing the evolutionary history in time from molecular sequence data. Moreover, by accommodating branch-specific variation in dispersal rates, we relax the most restrictive assumption of the standard Brownian diffusion process and demonstrate increased statistical efficiency in spatial reconstructions of overdispersed random walks by analyzing both simulated and real viral genetic data. We further illustrate how drawing inference about summary statistics from a fully specified stochastic process over both sequence evolution and spatial movement reveals important characteristics of a rabies epidemic. Together with recent advances in discrete phylogeographic inference, the continuous model developments furnish a flexible statistical framework for biogeographical reconstructions that is easily expanded upon to accommodate various landscape genetic features.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793
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 5×
“More specifically, we propose a relaxed random walk (RRW) by integrating a model in which a diffusion rate scalar on each branch of the rooted phylogeny is drawn independently and identically from an underlying discretized rate distribution (Drummond et al. 2006).”
BackgroundMethodInfluentialSelf-citationStabilizing selection and the comparative analysis of adaptation
Hansen, T. F. (1997) · Evolution · doi:10.1111/j.1558-5646.1997.tb01457.x · Cited by 1,361
Estimating 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 2×
“Autocorrelated relaxed clock models preceded uncorrelated relaxed clocks (Thorne et al. 1998) and are also available in BEAST.”
MethodDrummond, A. J., Nicholls, G. K., Rodrigo, A. G., & Solomon, W. (2002) · Genetics · doi:10.1093/genetics/161.3.1307 · Cited by 1,059
Bayesian Selection of Continuous-Time Markov Chain Evolutionary Models
Suchard, M. A., Weiss, R. E., & Sinsheimer, J. S. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003872 · Cited by 791
Self-citation
Cited by
BEAST 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-citationBEAST 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-citationDetection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2020) · doi:10.1101/2020.12.21.20248640 · Cited by 2,535
“To model phylogenetic diffusion of the new cluster across the country, we used a flexible relaxed random walk (RRW) diffusion model that accommodates branch-specific variation in rates of dispersal with a Cauchy distribution 23 .”
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Tegally, H., Moir, M., Everatt, J., Giovanetti, M., Scheepers, C., Wilkinson, E., Subramoney, K., Makatini, Z., Moyo, S., Amoako, D. G., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01911-2 · Cited by 707
Self-citation
Metadata
- Authors
- Lemey, P., Rambaut, A., Welch, J. J., & Suchard, M. A.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-03-04
- Volume
- 27
- Issue
- 8
- Pages
- 1877-1885
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2139166200
- Cited by
- 685
- References
- 8
- FWCI
- 15.59
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
