title: Directional gene flow and ecological separation inYersinia enterocolitica.
abstract: Yersinia enterocoliticais a common cause of food-borne gastroenteritis worldwide. Recent work defining the phylogeny of the genusYersiniasubdividedY. enterocoliticainto six distinct phylogroups. Here, we provide detailed analyses of the evolutionary processes leading to the emergence of these phylogroups. The dominant phylogroups isolated from human infections, PG3-5, show very little diversity at the sequence level, but do present marked patterns of gain and loss of functions, including those involved in pathogenicity and metabolism, including the acquisition of phylogroup-specific O-antigen loci. We tracked gene flow across the species in the core and accessory genome, and show that the non-pathogenic PG1 strains act as a reservoir for diversity, frequently acting as donors in recombination events. Analysis of the core and accessory genome also suggested that the differentY. enterocoliticaphylogroups may be ecologically separated, in contrast to the long-held belief of common shared ecological niches across theY. enterocoliticaspecies.
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.|Pathogen Research Group, Nottingham Trent University, Nottingham NG11 8NS, UK.
authors.forename: Sandra
authors.initials: S
authors.lastname: Reuter
authors.affiliation: Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
authors.affiliation: Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, Netherlands.
authors.forename: Mark
authors.initials: M
authors.lastname: de Been
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Simon
authors.initials: S
authors.lastname: Harris
authors.affiliation: Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
authors.forename: Lu
authors.initials: L
authors.lastname: Cheng
authors.affiliation: Pathogen Research Group, Nottingham Trent University, Nottingham NG11 8NS, UK.
authors.forename: Miquette
authors.initials: M
authors.lastname: Hall
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.|Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
authors.affiliation: Pathogen Research Group, Nottingham Trent University, Nottingham NG11 8NS, UK.
authors.forename: Alan
authors.initials: A
authors.lastname: McNally
keywords: Yersinia; accessory genome; ecology; recombination