ArticlePLoS computational biology2015
Measuring Asymmetry in Time-Stamped Phylogenies.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- From sites to structure to serology: a roadmap for structure-aware molecular evolution of antigenically evolving viruses.Journal of virology · 2026Review
- Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2.Wellcome open research · 2024Article
- Model design for nonparametric phylodynamic inference and applications to pathogen surveillance.Virus evolution · 2023Article
- Bayesian Inference of Clonal Expansions in a Dated Phylogeny.Systematic biology · 2022Article
- Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.Virus evolution · 2022Article
- Employing phylogenetic tree shape statistics to resolve the underlying host population structure.BMC bioinformatics · 2021Article
- Model design for non-parametric phylodynamic inference and applications to pathogen surveillance.bioRxiv : the preprint server for biology · 2021Article
- Dispersal strategies shape persistence and evolution of human gut bacteria.Cell host & microbe · 2021Article
- A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Identification of Hidden Population Structure in Time-Scaled Phylogenies.Systematic biology · 2020Article
- Why is cancer not more common? A changing microenvironment may help to explain why, and suggests strategies for anti-cancer therapy.Open biology · 2020Article
- A balance index for phylogenetic trees based on rooted quartets.Journal of mathematical biology · 2019Article
- Tree shape-based approaches for the comparative study of cophylogeny.Ecology and evolution · 2019Article
- Biased phylodynamic inferences from analysing clusters of viral sequences.Virus evolution · 2017Article
- Inference of Transmission Network Structure from HIV Phylogenetic Trees.PLoS computational biology · 2017Article
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Authors and funding
2 authors.
Funding
Abstract
Previous work has shown that asymmetry in viral phylogenies may be indicative of heterogeneity in transmission, for example due to acute HIV infection or the presence of 'core groups' with higher contact rates. Hence, evidence of asymmetry may provide clues to underlying population structure, even when direct information on, for example, stage of infection or contact rates, are missing. However, current tests of phylogenetic asymmetry (a) suffer from false positives when the tips of the phylogeny are sampled at different times and (b) only test for global asymmetry, and hence suffer from false negatives when asymmetry is localised to part of a phylogeny. We present a simple permutation-based approach for testing for asymmetry in a phylogeny, where we compare the observed phylogeny with random phylogenies with the same sampling and coalescence times, to reduce the false positive rate. We also demonstrate how profiles of measures of asymmetry calculated over a range of evolutionary times in the phylogeny can be used to identify local asymmetry. In combination with different metrics of asymmetry, this combined approach offers detailed insights of how phylogenies reconstructed from real viral datasets may deviate from the simplistic assumptions of commonly used coalescent and birth-death process models.
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