title: Evolutionary history and phylogeography of human viruses.
abstract: Understanding the evolutionary history of human viruses, along with the factors that have shaped their spatial distributions, is one of the most active areas of study in the field of microbial evolution. I give an overview of our current knowledge of the genetic diversity of human viruses using comparative studies of viral populations, particularly those with RNA genomes, to highlight important generalities in the patterns and processes of viral evolution. Special emphasis is given to the major dichotomy between RNA and DNA viruses in their epidemiological dynamics and the different types of phylogeographic pattern exhibited by human viruses. I also consider a central paradox in studies of viral evolution: Although epidemiological theory predicts that RNA viruses have ancestries dating back millennia, with major ecological transitions facilitating their emergence, the genetic diversity in currently circulating viral populations has a far more recent ancestry, indicative of continual lineage turnover.
authors.affiliation: Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA. ech15@psu.edu
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
mesh_terms: D000818:Animals; D004267:DNA Viruses / Q000145:classification / Q000235:genetics; D017753:Ecosystem; D019143:Evolution, Molecular; D014644:Genetic Variation; D006515:Hepatitis B virus / Q000145:classification / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D011157:Population Dynamics; D012328:RNA Viruses / Q000145:classification / Q000235:genetics; D014780:Viruses / Q000145:classification* / Q000235:genetics*