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The rooting of the Tree of Life, and the relationships of the major lineages, are controversial. The monophyly of Archaea is uncertain, and recent evidence for ancient lateral transfers of genes indicates that a highly complex model is needed to adequately represent the phylogenetic relationships among the major lineages of Life. We hope to provide a comprehensive discussion of these issues on this page soon. For the time being, please refer to the papers listed in the References section.

Discussion of Phylogenetic Relationships

Two alternative views on the relationship of the major lineages (omitting viruses) are shown below

• The "archaea tree":
• The "eocyte tree":

References

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Baldauf, S. L., J. D. Palmer, and W. F. Doolittle. 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proceedings of the National Academy of Sciences of the United States of America 93:7749-7754.

Becerra, A., L. Delaye, S. Islas, and A. Lazcano. 2007. The very early stages of biological evolution and the nature of the last common ancestor of the three major cell domains. Annual Review of Ecology, Evolution, and Systematics 38:361-379.

Benachenhou, L. N., P. Forterre and B. Labedan. 1993. Evolution of glutamate dehydrogenase genes: Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. Journal Of Molecular Evolution 36:335-346.

Brinkmann, H. and H. Phillippe. 1999. Archaea sister group of bacteria? Indications from Tree Reconstruction Artifacts from ancient Phylogenies. Molecular Biology and Evolution 16:817-825.

Brocks, J. J., G. A. Logan, R. Buick, and R. E. Summons. 1999. Archean molecular fossils and the early rise of eukaryotes. Science 285:1033-1036.

Brown, J. R. 2001. Genomic and phylogenetic perspectives on the evolution of prokaryotes. Systematic Biology 50:497-512.

Brown, J. R. and W. F. Doolittle. 1995. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proceedings of the National Academy of Sciences of the United States of America 92:2441-2445.

Brown, J. R. and W. F. Doolittle. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiology and Molecular Biology Reviews 61:456-502.

Caetano-Anolles, G. 2002. Evolved RNA secondary structure and the rooting of the universal tree of life. Journal of Molecular Evolution 54: 333-345.

Cammarano, P., P. Palm, R. Creti, E. Ceccarelli, A. M. Sanangelantoni, and O. Tiboni. 1992. Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: Phylogenetic coherence and structure of the Archaeal domain. Journal Of Molecular Evolution 34:396-405.

Cammarano, P., R. Creti, A. M. Sanangelantoni, and P. Palm. 1999. The archaean monophyly issue: a phylogeny of translational elongation factor G(2) sequences inferred from an optimized selection of alignment positions. Journal Of Molecular Evolution 49:524-537.

Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionay Microbiology 52:7-76.

Ciccarelli, F. D., T. Doerks, C. von Mering, C. J. Creevey, B. Snel, and P. Bork. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311(5765):1283-1287.

Creti, R., E. Ceccarelli, M. Bocchetta, A. M. Sanangelantoni, O. Tiboni, P. Palm and P. Cammarano. 1994. Evolution of translational elongation factor (EF) sequences: Reliability of global phylogenies inferred from EF-1-alpha(Tu) and EF-2(G) proteins. Proceedings of the National Academy of Sciences of the United States of America 91:3255-3259.

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Information on the Internet

• Tree of Life Turns Out to Have Complex Roots. New York Times, April 1998.
• Looking for LUCA (the Last Universal Common Ancestor). Patrick Forterre, Institut de Génétique et Microbiologie Université Paris-Sud, France.
• The Origins of The Nucleus and the Tree of Life . James Lake, UCLA.
• When did eukaryotic cells first evolve? What do we know about how they evolved from earlier life-forms? Scientific American, Ask the Experts.
• The Beginnings of Life on Earth. American Scientist, September-October 1995.
• From soup to cells — the origin of life. From the Understanding Evolution web site.
• Astrobiology: Environmental Genomes and the Evolution of Complex Systems in Simple Organisms. Marine Biological Laboratory, Woods Hole, USA.
• Astrobiology Web.
• NASA Astrobiology Institute.
• Origins: Galaxies, Stars, Planets . . . and Life. NASA's Origins Program.
• Astrobiology and the Origins of Life. Online lecture by Stanley Awramik. Access Excellence and the California Academy of Sciences BioForum for high school biology teachers.
• Origin of Life Research. University of Glasgow, UK.
• New York Center for Studies on the Origins of Life. Rensselaer Polytechnic Institute, Troy, NY, USA.
• The RNA World Website. Institut für Molekulare Biotechnologie Jena, Germany.
• Molecular "Fossils" Of Early Life. Yale University Press Release, June 1998.
• Is life just genes? BBC News, December 1999.
• Scientists call for life creation debate. BBC News, December 1999.
• Ancient Organisms Born in Undersea Inferno. San Francisco Chronicle, June 2000.
• The Search for Extreme Life. Scientific American, July 2000.
• Life at High Temperatures. Thomas D. Brock. Yellowstone Association for Natural Science, History & Education, Inc.
• DNA from the Beginning. Dolan DNA Learning Center, Cold Spring Harbor Laboratory Cold Spring Harbor, NY.
• Cell Biology. MIT Biology Hypertextbook.
• Cell Biology. The Biology Project. University of Arizona, USA.
• The Cell. A ThinkQuest high school student project.