Hitchhiking and the Population Genetic Structure of Avian Influenza Virus

Rubing Chen, Edward C. Holmes

Research output: Contribution to journalArticlepeer-review

30 Scopus citations


Previous studies have revealed a major difference in the phylogenetic structure, extent of genetic diversity, and selection pressure between the surface glycoproteins and internal gene segments of avian influenza viruses (AIV) sampled from wild birds. However, what evolutionary processes are responsible for these strikingly different evolutionary patterns is unclear. To address this issue, we estimated the rate of evolutionary change and time of origin of each segment of AIV sampled globally. Strikingly, the internal segments of the sampled AIV strains possess common ancestors that existed less than 200 years ago. Similarly recent times of origin were observed for each of the individual subtypes within the HA, NA, and NS gene segments. Such a shallow history of genetic diversity suggests an evolutionary model in which the genetic structure of AIV is shaped by a combination of occasional selective sweeps in the HA and NA (and possibly NS) segments, coupled with transient genetic linkage to the internal gene segments.

Original languageEnglish (US)
Pages (from-to)98-105
Number of pages8
JournalJournal of Molecular Evolution
Issue number1
StatePublished - Jan 2010


  • Avian influenza virus
  • Hitchhiking
  • Natural selection
  • Phylogeny
  • Reassortment

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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