Toward Automatic Reconstruction of a Highly Resolved Tree of Life

We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of δ-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.

[1]  H. Philippe,et al.  Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. , 2005, Molecular biology and evolution.

[2]  J. McInerney,et al.  The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. , 2005, Molecular biology and evolution.

[3]  Derrick J. Zwickl,et al.  Is sparse taxon sampling a problem for phylogenetic inference? , 2003, Systematic biology.

[4]  N. Moran.  Accelerated evolution and Muller's rachet in endosymbiotic bacteria. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Derek E. Wildman,et al.  Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[6]  BMC Bioinformatics , 2005 .

[7]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[8]  E V Koonin,et al.  Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. , 1999, Genome research.

[9]  P. Bork,et al.  Vertebrate-Type Intron-Rich Genes in the Marine Annelid Platynereis dumerilii , 2005, Science.

[10]  David P. Kreil,et al.  Identification of thermophilic species by the amino acid compositions deduced from their genomes. , 2001, Nucleic acids research.

[11]  C. Kurland,et al.  Reductive evolution of resident genomes. , 1998, Trends in microbiology.

[12]  Philip Hugenholtz,et al.  Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity , 1998, Journal of bacteriology.

[13]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

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

[15]  Kenneth M. Halanych,et al.  The New View of Animal Phylogeny , 2004 .

[16]  J. Lake,et al.  Horizontal gene transfer among genomes: the complexity hypothesis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[17]  M. P. Cummings,et al.  PAUP* Phylogenetic analysis using parsimony (*and other methods) Version 4 , 2000 .

[18]  C. Kurland,et al.  Origin and Evolution of the Mitochondrial Proteome , 2000, Microbiology and Molecular Biology Reviews.

[19]  N. Moran,et al.  Phylogenetics and the Cohesion of Bacterial Genomes , 2003, Science.

[20]  F. Delsuc,et al.  Phylogenomics and the reconstruction of the tree of life , 2005, Nature Reviews Genetics.

[21]  Konstantinos T. Konstantinidis,et al.  Towards a Genome-Based Taxonomy for Prokaryotes , 2005, Journal of bacteriology.

[22]  P. Bork,et al.  Non-orthologous gene displacement. , 1996, Trends in genetics : TIG.

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

[24]  W. Doolittle,et al.  Prokaryotic evolution in light of gene transfer. , 2002, Molecular biology and evolution.

[25]  J. Felsenstein.  Cases in which Parsimony or Compatibility Methods will be Positively Misleading , 1978 .

[26]  Hervé Philippe,et al.  Horizontal gene transfer and phylogenetics. , 2003, Current opinion in microbiology.

[27]  A. L. Koch.  Were Gram-positive rods the first bacteria? , 2003, Trends in microbiology.

[28]  P. Forterre,et al.  Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? , 2005, Genome Biology.

[29]  J. Sugiyama,et al.  Detection of Seven Major Evolutionary Lineages in Cyanobacteria Based on the 16S rRNA Gene Sequence Analysis with New Sequences of Five Marine Synechococcus Strains , 1999, Journal of Molecular Evolution.

[30]  N. Lartillot,et al.  The new animal phylogeny: reliability and implications. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[31]  H Philippe,et al.  The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. , 2000, Trends in genetics : TIG.