Weighted Genome Trees: Refinements and Applications

ABSTRACT There are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. Such groupings help us organize biological information and bear crucially on underlying processes of genome and organismal evolution. Genome trees make use of all comparable genes but can variously weight the contributions of these genes according to similarity, congruent patterns of similarity, or prevalence among genomes. Here we explore such possible weighting strategies, in an analysis of 142 prokaryotic and 5 eukaryotic genomes. We demonstrate that alternate weighting strategies have different advantages, and we propose that each may have its specific uses in systematic or evolutionary biology. Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution.

[1]  David M. Hillis,et al.  Faculty Opinions recommendation of From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. , 2003 .

[2]  W. Fitch,et al.  Construction of phylogenetic trees. , 1967, Science.

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

[4]  Michael Y. Galperin,et al.  Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. , 1999, Genome research.

[5]  M. Ragan,et al.  Inferring Genome Trees by Using a Filter To Eliminate Phylogenetically Discordant Sequences and a Distance Matrix Based on Mean Normalized BLASTP Scores , 2002, Journal of bacteriology.

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

[7]  Radhey S. Gupta,et al.  Critical issues in bacterial phylogeny. , 2002, Theoretical population biology.

[8]  Satoshi Fukuchi,et al.  Unique amino acid composition of proteins in halophilic bacteria. , 2003, Journal of molecular biology.

[9]  Hervé Philippe,et al.  Eubacterial phylogeny based on translational apparatus proteins. , 2002, Trends in genetics : TIG.

[10]  M. Gouy,et al.  A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. , 2002, Genome research.

[11]  J. Lake,et al.  Genomic evidence for two functionally distinct gene classes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[12]  G. Singer,et al.  Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. , 2000, Molecular biology and evolution.

[13]  R. L. Charlebois,et al.  Characterization of species-specific genes using a flexible, web-based querying system. , 2003, FEMS microbiology letters.

[14]  H. Philippe,et al.  Ancient phylogenetic relationships. , 2002, Theoretical population biology.

[15]  Dmitrij Frishman,et al.  The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum , 2000, Nature.

[16]  A. Halpern,et al.  Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. , 2000, Molecular biology and evolution.

[17]  N. Grishin,et al.  Genome trees constructed using five different approaches suggest new major bacterial clades , 2001, BMC Evolutionary Biology.

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

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

[20]  L. Aravind,et al.  Comparative Genome Analysis of the Pathogenic Spirochetes Borrelia burgdorferi and Treponema pallidum , 2000, Infection and Immunity.

[21]  Nikos Kyrpides,et al.  Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586 , 2002, Journal of bacteriology.

[22]  Gary J. Olsen,et al.  The history of life , 2001, Nature Genetics.

[23]  J. Felsenstein,et al.  A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. , 1994, Molecular biology and evolution.

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

[25]  C. Kurland,et al.  On the origin of mitochondria: a genomics perspective. , 2003, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[26]  E V Koonin,et al.  Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange. , 1999, Trends in genetics : TIG.

[27]  G. Singer,et al.  Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. , 2003, Gene.

[28]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

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

[30]  J. Felsenstein.  An alternating least squares approach to inferring phylogenies from pairwise distances. , 1997, Systematic biology.

[31]  Robert P. Hirt,et al.  Organelles, Genomes and Eukaryote Phylogeny : An Evolutionary Synthesis in the Age of Genomics , 2004 .

[32]  Hervé Philippe,et al.  Archaeal phylogeny based on ribosomal proteins. , 2002, Molecular biology and evolution.

[33]  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.

[34]  L. Hood,et al.  Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. , 2001, Genome research.

[35]  Elliott Sober,et al.  Testing the hypothesis of common ancestry. , 2002, Journal of theoretical biology.

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

[37]  Nick V Grishin,et al.  A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. , 2002, Nucleic acids research.

[38]  T. Cavalier-smith,et al.  The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. , 2002, International journal of systematic and evolutionary microbiology.

[39]  L. Orgel,et al.  Phylogenetic Classification and the Universal Tree , 1999 .