ArticlePLoS genetics2015
New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers, 1 of them a synthesis that pooled it.
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Who cites it
168 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Are Food Animals Responsible for Transfer of Antimicrobial-Resistant Escherichia coli or Their Resistance Determinants to Human Populations? A Systematic Review.Foodborne pathogens and disease · 2018Pooled it
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- PhyloCNN: Improving Tree Representation and Neural Network Architecture for Deep Learning from Trees in Phylodynamics and Diversification Studies.Systematic biology · 2026Article
- Inferring Sexual Network Bridging Using Genomics: A Simulation Study.medRxiv : the preprint server for health sciences · 2026Article
- SAASI: Sampling Aware Ancestral State Inference.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
- Genomic epidemiology ofMicrobial genomics · 2026Article
- Dispersal, adaptation and persistence of H5N1 in the sub-Antarctic and Antarctica.bioRxiv : the preprint server for biology · 2026Article
- SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements.Bioinformatics (Oxford, England) · 2026Article
- Global Distribution and Dispersal Pathways of Riparian Invasives: Perspectives Using Alligator Weed (Plants (Basel, Switzerland) · 2026Review
- Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes.Genetics · 2026Article
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- Introduction and inter-species transmission dynamics of high pathogenicity avian influenza H5N1 viruses in Japan 2021-25.Virus evolution · 2026Article
- Inferring epidemiological parameters under an infectious phylogeography model with visitor dynamics.medRxiv : the preprint server for health sciences · 2025Article
- Navigating Sampling Bias in Discrete Phylogeographic Analysis: Assessing the Performance of an Adjusted Bayes Factor.Molecular biology and evolution · 2025Article
- Evidence of latency reshapes our understanding of Ebola virus reservoir dynamics.bioRxiv : the preprint server for biology · 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
108 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Phylogeographic methods aim to infer migration trends and the history of sampled lineages from genetic data. Applications of phylogeography are broad, and in the context of pathogens include the reconstruction of transmission histories and the origin and emergence of outbreaks. Phylogeographic inference based on bottom-up population genetics models is computationally expensive, and as a result faster alternatives based on the evolution of discrete traits have become popular. In this paper, we show that inference of migration rates and root locations based on discrete trait models is extremely unreliable and sensitive to biased sampling. To address this problem, we introduce BASTA (BAyesian STructured coalescent Approximation), a new approach implemented in BEAST2 that combines the accuracy of methods based on the structured coalescent with the computational efficiency required to handle more than just few populations. We illustrate the potentially severe implications of poor model choice for phylogeographic analyses by investigating the zoonotic transmission of Ebola virus. Whereas the structured coalescent analysis correctly infers that successive human Ebola outbreaks have been seeded by a large unsampled non-human reservoir population, the discrete trait analysis implausibly concludes that undetected human-to-human transmission has allowed the virus to persist over the past four decades. As genomics takes on an increasingly prominent role informing the control and prevention of infectious diseases, it will be vital that phylogeographic inference provides robust insights into transmission history.
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