From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria

• DOI: 10.1371/journal.pbio.0000019
• Publication Date: 2003-09-15T22:06:52Z
• Authors: Emmanuelle Lerat; Vincent Daubin; Nancy A Moran
• Keywords: Horizontal Gene Transfer; Phylogenomics

The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on scale of entire genomes. However, extensive lateral gene transfer (LGT) may thwart this goal by preventing establishment organismal relationships based individual phylogenies. group which cases LGT are most frequently documented and greatest density complete genome is available γ-Proteobacteria, an ecologically diverse ancient including free-living species as well pathogens intracellular symbionts plants animals. We propose approach multigene phylogeny using genomes apply it case γ-Proteobacteria. applied stringent criteria identify a set likely orthologs then tested compatibilities resulting protein alignments with several phylogenetic hypotheses. Our results demonstrate concordance among virtually all (203 205) selected families, each exceptions consistent single event. concatenated concordant families yield fully resolved phylogeny. This topology also received strong support analyses aimed at excluding effects heterogeneity nucleotide base composition across lineages. analysis indicates that single-copy orthologous genes resistant horizontal transfer, even bacterial groups subject high rates LGT. can be identified used robust hypotheses phylogenies, thus establishing foundation reconstructing transitions, such underlie diversity content organization.