ArticleBioinformatics (Oxford, England)2014
Efficient Bayesian inference under the structured coalescent.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed.
- SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.Nature communications · 2026Article
- Parallel algorithms for phylogenetic inference under a structured coalescent approximation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection.Molecular biology and evolution · 2026Article
- Navigating Sampling Bias in Discrete Phylogeographic Analysis: Assessing the Performance of an Adjusted Bayes Factor.Molecular biology and evolution · 2025Article
- When migration leaves a clean trace: Decoupling migration from coalescence in the structured serial coalescent.bioRxiv : the preprint server for biology · 2025Article
- Parallel algorithms for phylogenetic inference under a structured coalescent approximation.bioRxiv : the preprint server for biology · 2025Article
- Robust phylodynamic inference and model specification for HIV transmission dynamics.Epidemics · 2025Article
- The contribution of integrated and non-integrated pig farms to epidemiological dynamics of porcine reproductive and respiratory syndrome virus in Italy.Scientific reports · 2025Article
- Evolution and transmission dynamics of wild poliovirus in Pakistan and Afghanistan (2012-2023).Nature communications · 2025Article
- Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data.Molecular biology and evolution · 2025Article
- Bayesian phylodynamic inference of population dynamics with dormancy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model.PLoS computational biology · 2025Article
- How does date-rounding affect phylodynamic inference for public health?PLoS computational biology · 2025Article
- The evolution and epidemiology of H3N2 canine influenza virus after 20 years in dogs.Epidemiology and infection · 2025Article
- Bayesian phylodynamic inference of population dynamics with dormancy.bioRxiv : the preprint server for biology · 2025Article
- Lost in the woods: shifting habitats can lead phylogeography astray.Virus evolution · 2025Article
- Eco-Evolutionary Drivers of Vibrio parahaemolyticus Sequence Type 3 Expansion: Retrospective Machine Learning Approach.JMIR bioinformatics and biotechnology · 2024Article
- Comparing Phylogeographies to Reveal Incompatible Geographical Histories within Genomes.Molecular biology and evolution · 2024Article
- Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong.Systematic biology · 2024Article
- D for dominant: porcine circovirus 2d (PCV-2d) prevalence over other genotypes in wild boars and higher viral flows from domestic pigs in Italy.Frontiers in microbiology · 2024Article
25 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationPopulation structure significantly affects evolutionary dynamics. Such structure may be due to spatial segregation, but may also reflect any other gene-flow-limiting aspect of a model. In combination with the structured coalescent, this fact can be used to inform phylogenetic tree reconstruction, as well as to infer parameters such as migration rates and subpopulation sizes from annotated sequence data. However, conducting Bayesian inference under the structured coalescent is impeded by the difficulty of constructing Markov Chain Monte Carlo (MCMC) sampling algorithms (samplers) capable of efficiently exploring the state space.
resultsIn this article, we present a new MCMC sampler capable of sampling from posterior distributions over structured trees: timed phylogenetic trees in which lineages are associated with the distinct subpopulation in which they lie. The sampler includes a set of MCMC proposal functions that offer significant mixing improvements over a previously published method. Furthermore, its implementation as a BEAST 2 package ensures maximum flexibility with respect to model and prior specification. We demonstrate the usefulness of this new sampler by using it to infer migration rates and effective population sizes of H3N2 influenza between New Zealand, New York and Hong Kong from publicly available hemagglutinin (HA) gene sequences under the structured coalescent. AVAILABILITY AND IMPLEMENTATION: The sampler has been implemented as a publicly available BEAST 2 package that is distributed under version 3 of the GNU General Public License at http://compevol.github.io/MultiTypeTree.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.