title: How clonal are Neisseria species? The epidemic clonality model revisited.
abstract: The three species Neisseria meningitidis, Neisseria gonorrheae, and Neisseria lactamica are often regarded as highly recombining bacteria. N. meningitidis has been considered a paradigmatic case of the "semiclonal model" or of "epidemic clonality," demonstrating occasional bouts of clonal propagation in an otherwise recombining species. In this model, occasional clonality generates linkage disequilibrium in the short term. In the long run, however, the effects of clonality are countered by recombination. We show that many data are at odds with this proposal and that N. meningitidis fits the criteria that we have proposed for predominant clonal evolution (PCE). We point out that (i) the proposed way to distinguish epidemic clonality from PCE may be faulty and (ii) the evidence of deep phylogenies by microarrays and whole-genome sequencing is at odds with the predictions of the semiclonal model. Last, we revisit the species status of N. meningitidis, N. gonorrheae, and N. lactamica in the light of the PCE model.
authors.affiliation: Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control, Institute of Research for Development 224, CNRS 5290, Universities of Montpellier 1 and 2, 34394 Montpellier Cedex 5, France; and michel.tibayrenc@ird.fr.
authors.forename: Michel
authors.initials: M
authors.lastname: Tibayrenc
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Ayala
mesh_terms: D060965:Clonal Evolution; D002999:Clone Cells; D008954:Models, Biological; D009343:Neisseria / Q000502:physiology*; D012660:Semantics; D013045:Species Specificity
keywords: deep phylogeny; linkage disequilibrium; molecular epidemiology; near-clade; predominant clonal evolution