ArticleGenetics2004
Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations.
Article in Genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection.Molecular biology and evolution · 2026Article
- When migration leaves a clean trace: Decoupling migration from coalescence in the structured serial coalescent.bioRxiv : the preprint server for biology · 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
- Bayesian phylodynamic inference of population dynamics with dormancy.bioRxiv : the preprint server for biology · 2025Article
- Joint Inference of Migration and Reassortment Patterns for Viruses with Segmented Genomes.Molecular biology and evolution · 2022Article
- A brief history and popularity of methods and tools used to estimate micro-evolutionary forces.Ecology and evolution · 2021Review
- Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks.Frontiers in veterinary science · 2020Article
- MASCOT: parameter and state inference under the marginal structured coalescent approximation.Bioinformatics (Oxford, England) · 2018Article
- The Structured Coalescent and Its Approximations.Molecular biology and evolution · 2017Article
- Emerging Concepts of Data Integration in Pathogen Phylodynamics.Systematic biology · 2017Review
- Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.Molecular biology and evolution · 2016Article
- Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection.Genetics · 2016Article
- New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation.PLoS genetics · 2015Article
- Efficient Bayesian inference under the structured coalescent.Bioinformatics (Oxford, England) · 2014Article
- Phylogenetic and epidemic modeling of rapidly evolving infectious diseases.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2011Review
- Coalescent genealogy samplers: windows into population history.Trends in ecology & evolution · 2009Review
- Estimating population parameters using the structured serial coalescent with Bayesian MCMC inference when some demes are hidden.Evolutionary bioinformatics online · 2007Article
- Relaxed phylogenetics and dating with confidence.PLoS biology · 2006Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a Bayesian statistical inference approach for simultaneously estimating mutation rate, population sizes, and migration rates in an island-structured population, using temporal and spatial sequence data. Markov chain Monte Carlo is used to collect samples from the posterior probability distribution. We demonstrate that this chain implementation successfully reaches equilibrium and recovers truth for simulated data. A real HIV DNA sequence data set with two demes, semen and blood, is used as an example to demonstrate the method by fitting asymmetric migration rates and different population sizes. This data set exhibits a bimodal joint posterior distribution, with modes favoring different preferred migration directions. This full data set was subsequently split temporally for further analysis. Qualitative behavior of one subset was similar to the bimodal distribution observed with the full data set. The temporally split data showed significant differences in the posterior distributions and estimates of parameter values over time.
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Registered trials
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.