The branching patterns of species in phylogenetic trees are affected by a large number of factors (e.g., multiple changes at a given site, long-branch attraction effect, differences in evolutionary rates, etc.), which often results in contradictory results or failure of the trees to resolve certain relationships. This has led to search for other phylogenetic markers that are less affected by such factors. Rare Genetic Changes (RGCs), which are uniquely shared by species either from a given group or from more than one defined groups of organisms provide powerful phylogenetic markers to deduce evolutionary relationships. The two kinds of RGC’s that have proven of particular use for such analyses are::
- Conserved Inserts and Deletions in Protein Sequences
- Whole Proteins that are Specific for Different Phylogenetic Groups
Selected References:
Baldauf,S.L. & Palmer,J.D. (1993). Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proceedings of the National Academy of Sciences of the United States of America, 90, 11558-11562.
Danchin,A. (2003). Genomes and evolution. Curr.Issues Mol.Biol., 5(2), 37-42.
Daubin,V. & Ochman,H. (2004). Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Research, 14(6), 1036-1042.
Galperin MY & Koonin EV (2004) 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res. 32: 5452-5463.
Gao, B., Parmanathan, R. and Gupta, R.S. (2006) Signature Proteins that are Distinctive Characteristics of Actinobacteria and Their Subgroups . Antonie van Leeuwenhoek, 90: 69-91.[Abstract]
Gao, B. and Gupta, R. S. (2007). Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genomics 8, 86. [PDF]
Griffiths,E. & Gupta,R.S. (2004). Distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the Deinococcus-Thermus phylum. Journal of Bacteriology, 186, 3097-3107. [Abstract]
Griffiths,E. & Gupta,R.S. (2004). Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales. International Microbiol., 7, 41-52. [Abstract]
Griffiths,E., Petrich,A., & Gupta,R.S. (2005). Conserved Indels in Essential Proteins that are Distinctive Characteristics of Chlamydiales and Provide Novel Means for Their Identification. Microbiology, 151: 2647-2657. [Abstract]
Griffiths , E., Ventresca, M.S. and Gupta, R.S. (2006) BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species. BMC Genomics, 14:7. [Abstract]
Gupta,R.S. (1998). Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships Among Archaebacteria, Eubacteria, and Eukaryotes. Microbiol.Mol.Biol.Rev., 62, 1435-1491. [Abstract]
Gupta,R.S. (2001). The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Inter.Microbiol., 4, 187-202. [PDF]
Gupta,R.S. & Griffiths,E. (2002). Critical Issues in Bacterial Phylogenies. Theor.Popul.Biol., 61, 423-434. [PDF]
Gupta,R.S. (2002). Phylogeny of Bacteria: Are we now close to understanding it? ASM News, 68, 284-291.[PDF]
Gupta,R.S., Pereira,M., Chandrasekera,C., & Johari,V. (2003). Molecular signatures in protein sequences that are characteristic of Cyanobacteria and plastid homologues. Int. J. Syst. Evol. Microbiol., 53, 1833-1842.
Gupta,R.S. (2004). The Phylogeny and Signature Sequences characteristics of Fibrobacters, Chlorobi and Bacteroidetes. Critical Reviews in Microbiology, 30, 123-143.
Gupta,R.S. (2005). Protein signatures distinctive of Alpha proteobacteria and its subgroups and a model for Alpha proteobacterial evolution. Crit Rev.Microbiol., 31:101-135. [PDF]
Gupta,R.S. (2005). Molecular Sequences and the Early History of Life. In J.Sapp (Ed.), Microbial Phylogeny and Evolution: Concepts and Controversies (pp. 160-183). New York: Oxford University Press. [PDF]
Gupta, R. S. (2005) Protein Signatures distinctive of Alpha proteobacteria and its Subgroups and a Model for Alpha-proteobacterial Evolution. Crit. Rev. Microbiol. 31: 101-135.
Kainth,P. & Gupta,R.S. (2005). Signature Proteins that are Distinctive of Alpha Proteobacteria. BMC Genomics, 6:94. [PDF]
Karlin,S., Mrázek,J., & Gentles,A.J. (2003). Genome comparisons and analysis. Current Opinion in Structural Biology, 13(3), 344-352.
Kunisawa,T. (2001). Gene arrangements and phylogeny in the class Proteobacteria. Journal of Theoretical Biology, 213(1), 9-19.
Rivera,M.C. & Lake,J.A. (1992). Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science, 257(5066), 74-76.
Rokas,A. & Holland,P.W. (2000). Rare genomic changes as a tool for phylogenetics. Trends Ecol.Evol., 15(11), 454-459.
Roberts, R. J.(2004) Identifying protein function--a call for community action. PLoS.Biol., 2: E42.
Sutcliffe,I.C. & Harrington,D.J. (2002). Pattern searches for the identification of putative lipoprotein genes in Gram-positive bacterial genomes. Microbiology, 148(Pt 7), 2065-2077.
Citation for this webpage:
Bacterial (Prokaryotic) Phylogeny Webpage (March 2006). http://www.bacterialphylogeny.com/index.html