title: Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori.
abstract: Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipα) and hitherto unknown functional genes.
authors.affiliation: Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Austria Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
authors.forename: Valeria
authors.initials: V
authors.lastname: Montano
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Foll
authors.affiliation: Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16801 Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.
authors.forename: Bodo
authors.initials: B
authors.lastname: Linz
authors.affiliation: Max Planck Genome Centre Cologne, D-50829 Cologne, Germany Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany.
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.affiliation: Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Suerbaum
authors.affiliation: Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Austria Department of Zoology, University of Venda, Thohoyandou 0950, South Africa jeffrey.jensen@epfl.ch yoshan.moodley@univen.ac.za.
authors.forename: Yoshan
authors.initials: Y
authors.lastname: Moodley
authors.affiliation: School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland jeffrey.jensen@epfl.ch yoshan.moodley@univen.ac.za.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Jensen
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D016481:Helicobacter Infections / Q000382:microbiology*; D016480:Helicobacter pylori / Q000235:genetics* / Q000502:physiology; D006801:Humans; D058974:Phylogeography; D012641:Selection, Genetic
keywords: adaptation; human pathogens; neutral evolution