title: Genome-wide molecular clock and horizontal gene transfer in bacterial evolution.
abstract: We describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. The approach used is based on comparing the evolutionary distances within a set of orthologs to a standard intergenomic distance, which was defined as the median of the distribution of the distances between all one-to-one orthologs. Under the clock-like model, the points on a plot of intergenic distances versus intergenomic distances are expected to fit a straight line. A statistical technique to identify significant deviations from the clock-like behavior is described. For several hundred analyzed orthologous sets representing three well-defined bacterial lineages, the alpha-Proteobacteria, the gamma-Proteobacteria, and the Bacillus-Clostridium group, the clock-like null hypothesis could not be rejected for approximately 70% of the sets, whereas the rest showed substantial anomalies. Subsequent detailed phylogenetic analysis of the genes with the strongest deviations indicated that over one-half of these genes probably underwent a distinct form of horizontal gene transfer, xenologous gene displacement, in which a gene is displaced by an ortholog from a different lineage. The remaining deviations from the clock-like model could be explained by lineage-specific acceleration of evolution. The results indicate that although xenologous gene displacement is a major force in bacterial evolution, a significant majority of orthologous gene sets in three major bacterial lineages evolved in accordance with the clock-like model. The approach described here allows rapid detection of deviations from this mode of evolution on the genome scale.
authors.affiliation: Department of Bioengineering and Bioinformatics, Moscow State University, Russia.
authors.forename: Pavel S
authors.initials: PS
authors.lastname: Novichkov
authors.forename: Marina V
authors.initials: MV
authors.lastname: Omelchenko
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
authors.forename: Andrei A
authors.initials: AA
authors.lastname: Mironov
authors.forename: Yuri I
authors.initials: YI
authors.lastname: Wolf
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D008957:Models, Genetic; D010802:Phylogeny