Current Overview

The prokaryotes are presently divided into two distinct groups or Domains named Archaea and Bacteria. However, how these two groups of prokaryotes are related to each other and how different molecular characteristics that distinguish them have evolved is presently not understood. Bacteria comprise the vast majority (>90%) of prokaryotes and an important aspect of understanding prokaryotic phylogeny is to understand the evolutionary relationships among them. Based on the 16S rRNA trees, the Bacterial domain is presently divided into 25 main groups (or phyla). However, this division is arbitrary as there are no objective criteria for identifying the main groups within Bacteria.

16s rRNA Tree

The different main groups within Bacteria are presently identified solely on the basis their branching pattern in the trees. For most of them no distinctive biochemical or molecular characteristics are known which distinguish them from all others. The branching order and hierarchical relationships among different main groups, which are central issues in elucidating bacterial phylogeny, are also presently not understood. The resolution of these issues should also clarify when, and in which group of prokaryotes, photosynthesis first evolved. It is important to determine whether these central issues in bacterial phylogeny are basically insolvable as suggested by 16S rRNA and other phylogenetic trees, or can be they be reliably resolved using other novel molecular sequence based approaches. It is also important to critically evaluate the extant of lateral gene transfer (LGT) among prokaryotes and its impact on understanding bacterial phylogeny.

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Phylogenetic tree based on signature sequences.

Similar to Bacteria, the evolutionary relationships among Archaea are also unresolved. For example, the methanogens which comprise the largest group among Archaea and are unique among prokaryotes in deriving all of their metabolic energy via reduction of carbon dioxide to methane (via hydrogen), do not form a monophyletic group in various phylogenetic trees. Thus, it is unclear how this important form of metabolism evloved or spread among archaeal lineage. Because prokaryotic organisms are ancestral to the eukaryotes, a reliable understanding of evolutionary relationships among them will also prove very helpful in understanding the origin of the eukaryotic cell.


This website details a number of new and powerful approaches that are proving very helpful in understanding a number of the above issues in bacterial phylogeny. These approaches make use of rare genomic changes (RGC’s) such as conserved inserts or deletions in protein sequences (i.e. signature sequences), or whole new proteins that are uniquely shared by organisms at different phylogenetic depths. Based upon the presence or absence of these RGC’s, a detailed understanding of the prokaryotic phylogeny has begun to emerge.


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Selected References:

Boone,D.R., Castenholz,R.W., & Garrity,G.M. (2001). Bergey's Manual of Systematic Bacteriology. New York: Springer.

Cavalier-Smith, T. (2002) The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int.J.Syst.Evol.Microbiol . 52: 7-76.

Doolittle,W.F. (1999). Phylogenetic classification and the universal tree. Science, 284, 2124-2128. [Abstract]

Dworkin. M, Falkow. S, Rosenberg. E., Schleifer. K.-H. & Stackebrandt. E (2007): The Prokaryotes: A Handbook on the Biology of Bacteria, vols. 1-7, 3rd ed. Springer.

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

Gribaldo, S. & Brochier-Armanet, C. (2006)The origin and evolution of Archaea: a state of the art. Philos Trans R Soc Lond B Biol Sci, 361: 1007-1022.

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. [PDF]

Gupta,R.S. & Griffiths,E. (2002). Critical Issues in Bacterial Phylogenies. Theor.Popul.Biol., 61, 423-434. [PDF]

Gupta,R.S. (2004) Evolutionary Relationship Among Photosynthetic Bacteria. Int. Congress of Photobiology, Jeju, Korea. [PDF of the Power Point presentation]

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. (2006) Phylogeny of Bacteria- Is it a tangled web or can this be reliably resolved? [PDF of the Power Point presentation]

Ludwig,W. & Klenk,H.-P. (2001). Overview: A phylogenetic backbone and taxonomic framework for prokaryotic systamatics. InD.R.Boone & R.W.Castenholz (Eds.), Bergey's Manual of Systematic Bacteriology (pp. 49-65). Berlin: Springer-Verlag.[PDF]

Oren, A. (2004) Prokaryote diversity and taxonomy: current status and future challenges. Philos.Trans.R.Soc.Lond B Biol.Sci. 359: 623-638.

Sapp,J. (2005). Microbial Phylogeny and Evolution: Concepts and Controversies. New York: Oxford University Press. [Link to Contents]

Shatalkin, A. I. (2004) Highest level of division in classification of Organisms. 3. Monodermata and Didermata. Zh.Obshch.Biol. 65: 195-210 .

Stackebrandt,E. (2000). Defining Taxonomic Ranks. InM.Dworkin & et al (Eds.), The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community New York: Springer-Verlag. [Link]

Tree of Life Web Project. 2006. Version 10 March 2006.

Yang,S., Doolittle,R.F., & Bourne,P.E. (2005). Phylogeny determined by protein domain content. Proc.Natl.Acad.Sci.U.S.A, 102(2), 373-378 .

Woese,C.R. (2003). How we do, Don't and should look at Bacteria and Bacteriology. (Ed.), The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community New York: Springer-Verlag. [Link]

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Citation for this webpage:
Bacterial (Prokaryotic) Phylogeny Webpage (March 2006).