title: Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study.
abstract: Phylogenetic reconstructions of bacterial species from DNA sequences are hampered by the existence of horizontal gene transfer. One possible way to overcome the confounding influence of such movement of genes is to identify and remove sequences which are responsible for significant character incongruence when compared to a reference dataset free of horizontal transfer (e.g., multilocus enzyme electrophoresis, restriction fragment length polymorphism, or random amplified polymorphic DNA) using the incongruence length difference (ILD) test of Farris et al. [Cladistics 10 (1995) 315]. As obtaining this "whole genome dataset" prior to the reconstruction of a phylogeny is clearly troublesome, we have tested alternative approaches allowing the release from such reference dataset, designed for a species with modest level of horizontal gene transfer, i.e., Escherichia coli. Eleven different genes available or sequenced in this work were studied in a set of 30 E. coli reference (ECOR) strains. Either using ILD to test incongruence between each gene against the all remaining (in this case 10) genes in order to remove sequences responsible for significant incongruence, or using just a simultaneous analysis without removals, gave robust phylogenies with slight topological differences. The use of the ILD test remains a suitable method for estimating the level of horizontal gene transfer in bacterial species. Supertrees also had suitable properties to extract the phylogeny of strains, because the way they summarize taxonomic congruence clearly limits the impact of individual gene transfers on the global topology. Furthermore, this work allowed a significant improvement of the accuracy of the phylogeny within E. coli.
authors.affiliation: INSERM E0339, IFR 02, Faculté de Médecine Xavier Bichat, 16 rue Henri Huchard, Paris 75018, France.
authors.forename: Patricia
authors.initials: P
authors.lastname: Escobar-Páramo
authors.forename: Audrey
authors.initials: A
authors.lastname: Sabbagh
authors.forename: Pierre
authors.initials: P
authors.lastname: Darlu
authors.forename: Olivier
authors.initials: O
authors.lastname: Pradillon
authors.forename: Christelle
authors.initials: C
authors.lastname: Vaury
authors.forename: Erick
authors.initials: E
authors.lastname: Denamur
authors.forename: Guillaume
authors.initials: G
authors.lastname: Lecointre
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics*; D019143:Evolution, Molecular; D018014:Gene Transfer Techniques; D010802:Phylogeny; D015203:Reproducibility of Results
chemical_list: D004269:DNA, Bacterial