Phylogenomic approaches to bacterial phylogeny

Abstract Reconstructing the history of bacterial species is one of the most challenging question molecular phylogeneticists have to answer. Both the antiquity of bacteria and their mode of evolution constitute barriers to the elucidation of the relationships among phyla. Time, on one side, has eroded the phylogenetic signal that would allow reconstructing the deep branches of this several billion years old tree. In addition, because of frequent gene exchanges among distantly related bacteria, even an accurate gene phylogeny may no longer represent the species tree. Methods aimed at using complete genomes for phylogenetic inference may however help resolve this issue.