2013/10/29 by Joseph M. Chan, Gunnar Carlsson, Raúl Rabadán · 286 citations
Biochemistry, Genetics and Molecular Biology · Mathematics · #Evolution and Genetic Dynamics #Genomics and Phylogenetic Studies #RNA and protein synthesis mechanisms #Phylogenetic tree #Reassortment #Reticulate evolution #Evolutionary biology #Horizontal gene transfer #Biology #Tree (set theory) #Representation (politics) #Rate of evolution #Molecular evolution #Parallel evolution #Phylogenetics #Topology (electrical circuits) #Genome evolution #Genetics #Mathematics #Genome #Combinatorics #Coronavirus disease 2019 (COVID-19) #Gene
paper · pdf · doi:10.1073/pnas.1313480110
published in Proceedings of the National Academy of Sciences 110(46), 18566-18571 (National Academy of Sciences)
openalex publication_date 2013/10/29 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06
The tree structure is currently the accepted paradigm to represent evolutionary relationships between organisms, species or other taxa. However, horizontal, or reticulate, genomic exchanges are pervasive in nature and confound characterization of phylogenetic trees. Drawing from algebraic topology, we present a unique evolutionary framework that comprehensively captures both clonal and reticulate evolution. We show that whereas clonal evolution can be summarized as a tree, reticulate evolution exhibits nontrivial topology of dimension greater than zero. Our method effectively characterizes clonal evolution, reassortment, and recombination in RNA viruses. Beyond detecting reticulate evolution, we succinctly recapitulate the history of complex genetic exchanges involving more than two parental strains, such as the triple reassortment of H7N9 avian influenza and the formation of circulating HIV-1 recombinants. In addition, we identify recurrent, large-scale patterns of reticulate evolution, including frequent PB2-PB1-PA-NP cosegregation during avian influenza reassortment. Finally, we bound the rate of reticulate events (i.e., 20 reassortments per year in avian influenza). Our method provides an evolutionary perspective that not only captures reticulate events precluding phylogeny, but also indicates the evolutionary scales where phylogenetic inference could be accurate.