Genome-wide molecular clock and horizontal gene transfer in bacterial evolution

Pavel S. Novichkov, Marina V. Omelchenko, Mikhail S. Gelfand, Andrei A. Mironov, Yuri I. Wolf, Eugene V. Koonin

Research output: Contribution to journalArticlepeer-review

71 Citations (Scopus)

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 α-Proteobacteria, the γ-Proteobacteria, and the Bacillus-Clostridium group, the clock-like null hypothesis could not be rejected for ∼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.

Original languageEnglish
Pages (from-to)6575-6585
Number of pages11
JournalJournal of Bacteriology
Volume186
Issue number19
DOIs
Publication statusPublished - Oct 2004
Externally publishedYes

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