A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin.
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.
Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Building Y27, Winterthurerstrasse 190, Zurich 8057, Switzerland The Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne 1015, Switzerland The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA andreas.wagner@ieu.uzh.ch.
Andreas
A
Wagner
D019143:Evolution, Molecular; D005838:Genotype; D006388:Hemagglutinins / Q000235:genetics*; D053122:Influenza A Virus, H3N2 Subtype / Q000145:classification / Q000235:genetics*; D010802:Phylogeny
D006388:Hemagglutinins
cycles; evolution; homoplasy; influenza; networks