ArticleMolecular biology and evolution2019
A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 157 papers, 3 of them syntheses that pooled it.
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Who cites it
157 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Pooled it
- Machine learning enables prediction of metabolic system evolution in bacteria.Science advances · 2023Pooled it
- African Swine Fever Virus Circulation between Tanzania and Neighboring Countries: A Systematic Review and Meta-Analysis.Viruses · 2021Pooled it
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- Stability in flexibility: Shifting alliances stabilize the symbioses of marine animals over 150 million years.Science advances · 2026Article
- Molecular Epidemiology and Evolution of Swine Influenza A Viruses, Vietnam, 2020-2024.Emerging infectious diseases · 2026Article
- Encoded metabolic remodeling amplifies drug resistance in Mycobacterium tuberculosis.PLoS pathogens · 2026Article
- Bottom-up reconstruction of synthetic pyrenoids provides insights into the mechanisms and evolution of carbon concentration by EPYC1 proteins.Nature plants · 2026Article
- Phylogenomic analysis of a methicillin-resistantMicrobial genomics · 2026Article
- Phylogenetic investigation of the 100 kDa hexokinase enzyme family with the topiary ancestral sequence reconstruction pipeline.Protein science : a publication of the Protein Society · 2026Article
- High-precision binary trait association on phylogenetic trees.Microbial genomics · 2026Article
- Summarizing Evolutionary Trajectories from Phylogenetic Character Maps of Discrete Traits.bioRxiv : the preprint server for biology · 2026Article
- Stepwise assembly of virulence-associated traits in the intracellular pathogenbioRxiv : the preprint server for biology · 2026Article
- Hospital Environment-Associated Sources of Mycobacterium abscessus Infection in Transplant Recipients.JAMA network open · 2026Article
- SAASI: Sampling Aware Ancestral State Inference.Nature communications · 2026Article
- Diversity and evolution of a phase-variable multi-locus antigen in Neisseria gonorrhoeae.PLoS pathogens · 2026Article
- Cooperation and the evolution of bacterial niche breadth.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Genomic features associated with sustained mammalian transmission of avian influenza A viruses.Nature microbiology · 2026Article
- Epistasis mediates the role of negative frequency-dependent selection in bacterial strain structure.PLoS computational biology · 2026Article
- Diversity and evolution of a phase-variable multi-locus antigen inbioRxiv : the preprint server for biology · 2026Article
97 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences. We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server. The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.
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