title: Widespread genetic exchange among terrestrial bacteriophages.
abstract: Bacteriophages are the most numerous entities in the biosphere. Despite this numerical dominance, the genetic structure of bacteriophage populations is poorly understood. Here, we present a biogeography study involving 25 previously undescribed bacteriophages from the Cystoviridae clade, a group characterized by a dsRNA genome divided into three segments. Previous laboratory manipulation has shown that, when multiple Cystoviruses infect a single host cell, they undergo (i) rare intrasegment recombination events and (ii) frequent genetic reassortment between segments. Analyzing linkage disequilibrium (LD) within segments, we find no significant evidence of intrasegment recombination in wild populations, consistent with (i). An extensive analysis of LD between segments supports frequent reassortment, on a time scale similar to the genomic mutation rate. The absence of LD within this group of phages is consistent with expectations for a completely sexual population, despite the fact that some segments have >50% nucleotide divergence at 4-fold degenerate sites. This extraordinary rate of genetic exchange between highly unrelated individuals is unprecedented in any taxa. We discuss our results in light of the biological species concept applied to viruses.
authors.affiliation: Department of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Olin K
authors.initials: OK
authors.lastname: Silander
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Weinreich
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Wright
authors.forename: Kara J
authors.initials: KJ
authors.lastname: O'Keefe
authors.forename: Camilla U
authors.initials: CU
authors.lastname: Rang
authors.forename: Paul E
authors.initials: PE
authors.lastname: Turner
authors.forename: Lin
authors.initials: L
authors.lastname: Chao
mesh_terms: D001435:Bacteriophages / Q000235:genetics*; D017910:Cystoviridae / Q000235:genetics; D014644:Genetic Variation; D016679:Genome, Viral; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012313:RNA / Q000235:genetics; D012330:RNA, Double-Stranded / Q000737:chemistry; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014780:Viruses / Q000235:genetics
chemical_list: D012330:RNA, Double-Stranded; D012313:RNA