title: Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis.
abstract: In this review, we synthesise current models and recent comparative genomic studies describing how bacterial species may emerge through adaptation to a new ecological niche and maintain themselves in the same niche over long time periods. We notably consider the impact of genetic exchange with phylogenetically close relatives living in sympatry and how this leads to the heterogeneous evolution of different genes within the bacterial genome. This heterogeneity provides landmarks to recognise genes that determine adaptation to the ecological niche, and we present reverse ecology strategies to unravel ecological properties of bacterial populations.
authors.affiliation: University College London, Gower Street, London, WC1E 6BT, United Kingdom. Electronic address: florent.lassalle@ucl.ac.uk.
authors.forename: Florent
authors.initials: F
authors.lastname: Lassalle
authors.affiliation: Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France. Electronic address: daniel.muller@univ-lyon1.fr.
authors.forename: Daniel
authors.initials: D
authors.lastname: Muller
authors.affiliation: Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, USC1364, Ecologie Microbienne, Villeurbanne, France. Electronic address: xavier.nesme@univ-lyon1.fr.
authors.forename: Xavier
authors.initials: X
authors.lastname: Nesme
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D005075:Biological Evolution; D017753:Ecosystem; D049810:Genetic Speciation; D016680:Genome, Bacterial; D023281:Genomics; D010802:Phylogeny; D013045:Species Specificity
keywords: Bacterial speciation; Core genome; Core niche; Ecological niche; Ecological speciation; Ecotype