ArticleProceedings. Biological sciences2014
A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin.
Article in Proceedings. Biological sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Hierarchical genotype networks and incipient ecological speciation in Q[Formula: see text] phage quasispecies.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Pathogen diversity in meta-population networks.Chaos, solitons, and fractals · 2023Article
- Immunity-induced criticality of the genotype network of influenza A (H3N2) hemagglutinin.PNAS nexus · 2022Article
- Intra-Population Competition during Adaptation to Increased Temperature in an RNA Bacteriophage.International journal of molecular sciences · 2021Article
- Localization, epidemic transitions, and unpredictability of multistrain epidemics with an underlying genotype network.PLoS computational biology · 2021Article
- Microfluidic devices for the detection of viruses: aspects of emergency fabrication during the COVID-19 pandemic and other outbreaks.Proceedings. Mathematical, physical, and engineering sciences · 2020Review
- Article
- Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis.PLoS computational biology · 2020Article
- Recombinant GII.P16/GII.4 Sydney 2012 Was the Dominant Norovirus Identified in Australia and New Zealand in 2017.Viruses · 2018Article
- Evolutionary analysis of Porcine circovirus 3 (PCV3) indicates an ancient origin for its current strains and a worldwide dispersion.Virus genes · 2018Article
- Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology.Trends in microbiology · 2018Review
- Polymorphism analysis of the apxIA gene of Actinobacillus pleuropneumoniae serovar 5 isolated in swine herds from Brazil.PloS one · 2018Article
- Genonets server-a web server for the construction, analysis and visualization of genotype networks.Nucleic acids research · 2016Article
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Abstract
Networks of evolving genotypes can be constructed from the worldwide time-resolved genotyping of pathogens like influenza viruses. Such genotype networks are graphs where neighbouring vertices (viral strains) differ in a single nucleotide or amino acid. A rich trove of network analysis methods can help understand the evolutionary dynamics reflected in the structure of these networks. Here, I analyse a genotype network comprising hundreds of influenza A (H3N2) haemagglutinin genes. The network is rife with cycles that reflect non-random parallel or convergent (homoplastic) evolution. These cycles also show patterns of sequence change characteristic for strong and local evolutionary constraints, positive selection and mutation-limited evolution. Such cycles would not be visible on a phylogenetic tree, illustrating that genotype network analysis can complement phylogenetic analyses. The network also shows a distinct modular or community structure that reflects temporal more than spatial proximity of viral strains, where lowly connected bridge strains connect different modules. These and other organizational patterns illustrate that genotype networks can help us study evolution in action at an unprecedented level of resolution.
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