Predicting evolution from the shape of genealogical trees

• Published in: eLife Vol. 3
• Main Authors: Neher, Richard A, Russell, Colin A, Shraiman, Boris I
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 11.11.2014; eLife Sciences Publications, Ltd
• Subjects: Adaptation; adaptive evolution; Algorithms; Base Sequence; Evolution; Evolution & development; Evolution, Molecular; Forecasting; Gene Flow; Genetic Fitness; Genetic Variation; Genomes; Genomics and Evolutionary Biology; Humans; Influenza; Influenza A; Influenza A Virus, H3N2 Subtype - classification; Influenza A Virus, H3N2 Subtype - genetics; Influenza, Human - epidemiology; Influenza, Human - virology; Inheritance Patterns; Models, Genetic; Mutation; Phylogeny; Population; population genetics; Quantitative genetics; Reproductive fitness; Seasons; Sequence Analysis, DNA; Trees; vaccine strain selection; Viruses; population genetics; genomics; viruses; vaccine strain selection; evolutionary biology; adaptive evolution
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.03568

Given a sample of genome sequences from an asexual population, can one predict its evolutionary future? Here we demonstrate that the branching patterns of reconstructed genealogical trees contains information about the relative fitness of the sampled sequences and that this information can be used to predict successful strains. Our approach is based on the assumption that evolution proceeds by accumulation of small effect mutations, does not require species specific input and can be applied to any asexual population under persistent selection pressure. We demonstrate its performance using historical data on seasonal influenza A/H3N2 virus. We predict the progenitor lineage of the upcoming influenza season with near optimal performance in 30% of cases and make informative predictions in 16 out of 19 years. Beyond providing a tool for prediction, our ability to make informative predictions implies persistent fitness variation among circulating influenza A/H3N2 viruses.