Phylogeny of γ‐proteobacteria: resolution of one branch of the universal tree?

The reconstruction of bacterial evolutionary relationships has proven to be a daunting task because variable mutation rates and horizontal gene transfer (HGT) among species can cause grave incongruities between phylogenetic trees based on single genes. Recently, a highly robust phylogenetic tree was constructed for 13 γ-proteobacteria using the combined alignments of 205 conserved orthologous proteins.1 Only two proteins had incongruent tree topologies, which were attributed to HGT between Pseudomonas species and Vibrio cholerae or enterics. While the evolutionary relationships among these species appears to be resolved, further analysis suggests that HGT events with other bacterial partners likely occurred; this alters the implicit assumption of γ-proteobacteria monophyly. Thus, any thorough reconstruction of bacterial evolution must not only choose a suitable set of molecular markers but also strive to reduce potential bias in the selection of species. BioEssays 26:463–468, 2004. © 2004 Wiley Periodicals, Inc.

[1]  S. Salzberg,et al.  Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima , 1999, Nature.

[2]  C. Bauer,et al.  Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[4]  Doolittle Wf.  Phylogenetic Classification and the Universal Tree , 1999 .

[5]  L. Koski,et al.  The Closest BLAST Hit Is Often Not the Nearest Neighbor , 2001, Journal of Molecular Evolution.

[6]  S. Fitz-Gibbon,et al.  Whole genome-based phylogenetic analysis of free-living microorganisms. , 1999, Nucleic acids research.

[7]  John M. Logsdon,et al.  Evolutionary genomics: Thermotoga heats up lateral gene transfer , 1999, Current Biology.

[8]  J. Lawrence,et al.  Gene transfer in bacteria: speciation without species? , 2002, Theoretical population biology.

[9]  C R Woese,et al.  Classification of methanogenic bacteria by 16S ribosomal RNA characterization. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[10]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[11]  W. Martin,et al.  Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis. , 2000, International journal of systematic and evolutionary microbiology.

[12]  B A Stocker,et al.  A Salmonella typhimurium virulence gene linked to flg , 1989, Infection and immunity.

[13]  W. Doolittle,et al.  A kingdom-level phylogeny of eukaryotes based on combined protein data. , 2000, Science.

[14]  Y. Nakamura,et al.  Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. , 2000, DNA research : an international journal for rapid publication of reports on genes and genomes.

[15]  E. Koonin,et al.  The Impact of Comparative Genomics on Our Understanding of Evolution , 2000, Cell.

[16]  C. Ronson,et al.  The bio operon on the acquired symbiosis island of Mesorhizobium sp. strain R7A includes a novel gene involved in pimeloyl-CoA synthesis. , 2001, Microbiology.

[17]  C. V. Dohlen,et al.  Mealybug β-proteobacterial endosymbionts contain γ-proteobacterial symbionts , 2001, Nature.

[18]  James R. Brown,et al.  Horizontal transfer of drug‐resistant aminoacyl‐transfer‐RNA synthetases of anthrax and Gram‐positive pathogens , 2003, EMBO reports.

[19]  Michael J. Stanhope,et al.  Universal trees based on large combined protein sequence data sets , 2001, Nature Genetics.

[20]  R F Doolittle,et al.  Evolution by acquisition: the case for horizontal gene transfers. , 1992, Trends in biochemical sciences.

[21]  B. Snel,et al.  Genome phylogeny based on gene content , 1999, Nature Genetics.

[22]  G. B. Golding,et al.  The origin of the eukaryotic cell. , 1996, Trends in biochemical sciences.

[23]  James R. Brown,et al.  Archaea and the prokaryote-to-eukaryote transition. , 1997, Microbiology and molecular biology reviews : MMBR.

[24]  S. Carroll,et al.  Genome-scale approaches to resolving incongruence in molecular phylogenies , 2003, Nature.

[25]  R. Sockett,et al.  A novel assay to monitor predator-prey interactions for Bdellovibrio bacteriovorus 109 J reveals a role for methyl-accepting chemotaxis proteins in predation. , 2003, Environmental microbiology.

[26]  J. Handelsman,et al.  Mutants of Rhizobium tropici strain CIAT899 that do not induce chlorosis in plants. , 1998, Microbiology.

[27]  D. Dykhuizen,et al.  Recombination in Escherichia coli and the definition of biological species , 1991, Journal of bacteriology.

[28]  Peer Bork,et al.  Lateral Gene Transfer, Genome Surveys, and the Phylogeny of Prokaryotes , 1999 .

[29]  Hidetoshi Shimodaira,et al.  Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference , 1999, Molecular Biology and Evolution.

[30]  Gary J. Olsen,et al.  Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process , 2000, Microbiology and Molecular Biology Reviews.

[31]  H. Ochman,et al.  Molecular archaeology of the Escherichia coli genome. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[32]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[33]  N. Moran,et al.  From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria , 2003, PLoS biology.