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Life on Earth

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taxon links [up-->]Archaea [up-->]Eubacteria [up-->]Viruses [up-->]Eukaryotes Not MonophyleticPhylogenetic position of group is uncertain and group is not monophyleticPhylogenetic position of group is uncertain and group is not monophyletic Interpreting the tree
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This tree diagram shows the relationships between several groups of organisms.

The root of the current tree connects the organisms featured in this tree to their containing group and the rest of the Tree of Life. The basal branching point in the tree represents the ancestor of the other groups in the tree. This ancestor diversified over time into several descendent subgroups, which are represented as internal nodes and terminal taxa to the right.

example of a tree diagram

You can click on the root to travel down the Tree of Life all the way to the root of all Life, and you can click on the names of descendent subgroups to travel up the Tree of Life all the way to individual species.

For more information on ToL tree formatting, please see Interpreting the Tree or Classification. To learn more about phylogenetic trees, please visit our Phylogenetic Biology pages.

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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


Aravind, L., R. L. Tatusov, Y. I. Wolf, D. R. Walker, and E. V. Koonin. 1998. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends in Genetics 14:442-444.

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.

Deeds, E. J., H. Hennessey, and E. I. Shakhnovich. 2005. Prokaryotic phylogenies inferred from protein structural domains. Gen. Res. 15:393-402.

Des Marais, D. J. 1999. Astrobiology: Exploring the origins, evolution, and distribution of life in the universe. Annual Review of Ecology and Systematics 30:397-420.

Doolittle, W. F. 1998. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends in Genetics 14:307-311.

Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2128.

Doolittle, W. F. 1999. Lateral genomics. Trends in Biochemical Sciences 24: M5-M8.

Doolittle, W. F. 2000. Uprooting the tree of life. Scientific American 282:90-95.

Doolittle, W. F. and J. R. Brown. 1994. Tempo, mode, the progenote, and the universal root. Proceedings of the National Academy of Sciences of the United States of America 91:6721-6728.

Embley, T. M., M. van der Giezen, D. S. Horner, P. L. Dyal, S. Bell, and P. G. Foster. 2003. Hydrogenosomes, mitochondria and early eukaryotic evolution. International Union of Biochemistry and Molecular Biology: Life 55(7):387-395.

Feng, D.-F., G. Cho, and R.F. Doolittle. 1997. Determining divergence times with a protein clock: Update and reevaluation. Proceedings of the National Academy of Sciences of the United States of America 94:13028-13033.

Forterre, P. 2001. Genomics and early cellular evolution. The origin of the DNA world. Comptes Rendus de l'Academie des Sciences Serie III-Sciences de la Vie 324:1067-1076.

Forterre, P. and H. Philippe. 1999. Where is the root or the universal tree of life? BioEssays 21:871-879.

Gogarten, J. P., E. Hilario, and L. Olendzenski. 1996. Gene duplications and horizontal gene transfer during early evolution. Pages 267-292 in Evolution of Microbial Life (D. McL. Roberts, P. Sharp, G. Alderson, and M. Collins, eds.) Symposium 54. Society for General Microbiology. Cambridge University Press, Cambridge.

Gogarten, J. P. and L. Taiz. 1992. Evolution of proton pumping ATPases: Rooting the tree of life. Photosynthesis Research 33:137-146.

Golding, G.B. and R.S. Gupta. 1995. Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Molecular Biology and Evolution 12:1-6.

Gouy, M. and W.-H. Li. 1989. Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree. Nature 339:145-147.

Gouy, M. and W.-H. Li. 1990. Archaebacterial or eocyte tree? Nature 343:419.

Gray, M. W., G. Burger, and B. F. Lang. 1999. Mitochondrial evolution. Science 283:1476-1481.

Gribaldo, S. and P. Cammarano. 1998. The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery. Journal of Molecular Evolution 47:508-516.

Gupta, R. S. 1998. Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiology and Molecular Biology Reviews 62:1435-1491.

Gupta, R. S. 1998. What are archaebacteria: Life's third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Molecular Microbiology 29:695-707.

Gupta, R. S. and G. B. Golding. 1993. Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. Journal of Molecular Evolution 37:573-582.

Hilario, E. and J. P. Gogarten. 1993. Horizontal transfer of ATPase genes: The tree of life becomes a net of life. Biosystems 31:111-119.

Iwabe, N., K.-I. Kuma, M. Hagesawa, S. Osawa, T. Miyata. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proceedings of the Natural Academy of Sciences (USA) 86:9355-9359.

Jeffares, D. C., A. M. Poole, and D. Penny. 1998. Relics from the RNA world. Journal of Molecular Evolution 46:18-36.

Kandler, O. 1994. Cell wall biochemistry and three-domain concept of life. Systematic and Applied Microbiology 16:501-509.

Katz, L. A. 1998. Changing perspectives on the origin of eukaryotes. Trends in Ecology and Evolution 13:493-497.

Katz, L. A. 1999. The tangled web: gene genealogies and the origin of eukaryotes. Am. Nat. 154 (suppl.):S137-S145.

Koonin, E. V., A. R. Mushegian, M. Y. Galperin, and D. R. Walker. 1997. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Molecular Microbiology 25:619-637.

Kyrpides, N. C. and G. J. Olsen. 1999. Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry? Trends in Genetics 15:298-299.

Lake, J. A. 1990. Archaebacterial or eocyte tree? Nature 343:418-419.

Lake, J. A., M. W. Clark, E. Hendeson, S. P. Fay, M. Oakes, A. Scheinman, J. P. Thornber and R. A. Mah. 1985. Eubacteria, halobacteria and the origin of photosynthesis: The photocytes. Proceedings of the National Academy of Sciences (USA) 82:3716-3720.

Lake, J.A., E. Henderson, M. Oakes, M.W. Clark. 1984. Eocytes: a new ribosome structure indicates a kingdom with close relationship to eukaryotes. Proceedings of the National Academy of Sciences (USA) 81:3786-3790.

Lake, J. A. and M. C. Rivera. 1996. The prokaryotic ancestry of eukaryotes. Pages 87-108 in Evolution of Microbial Life (D. McL. Roberts, P. Sharp, G. Alderson, and M. Collins, eds.) Symposium 54. Society for General Microbiology. Cambridge University Press, Cambridge.

Lawson, F. S., R. L. Charlebois, and J.-A. R. Dillon. 1996. Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the Tree of Life. Molecular Biology and Evolution 13:970-977.

Liao, D. and P. P. Dennis. 1994. Molecular phylogenies based on ribosomal protein L11, L1, L10, and L12 sequences. Journal of Molecular Evolution 38:405-419.

Lopez, P., P. Forterre, and H. Philippe. 1999. The root of the tree of life in the light of the covarian model. Journal of Molecular Evolution 49:496-508.

Margulis, L. 1996. Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proceedings of the Natural Academy of Sciences (USA) 92:1071-1076.

Martin, W. 1999. Mosaic bacterial chromosomes: a challenge on route to a tree of genomes. BioEssays 21:99-104.

Martin W. and M. Müller. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392:37-41.

McClendon, J. H. 1999. The origin of life. Earth-Science Reviews 47:71-93.

Moreira, D. and P. Lopez-Garcia. 1998. Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. Journal of Molecular Evolution 47:517-530.

Nealson, K. H. and P. G. Conrad. 1999. Life: past, present and future. Philosophical Transactions of the Royal Society of London Series B 354:1923-1939.

Pennisi, E. 1998. Genome data shake the tree of life. Science 280:672-674.

Pennisi, E. 1999. Is it time to uproot the tree of life? Science 284:1305-1307.

Penny, D. and A. Poole. 1999. The nature of the last universal common ancestor. Current Opinion in Genetics and Development 9:672-677.

Philippe, H. and P. Forterre. 1999. The rooting of the universal tree of life is not reliable. Journal of Molecular Evolution 49:509-523.

Poole, A., D. Jeffares, and D. Penny. Early evolution: prokaryotes, the new kids on the block. BioEssays 21:880-889.

Rasmussen, B. 2000. Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit. Nature 405:676-679.

Reysenbach1, A. L. and E. Shock. 2002. Merging genomes with geochemistry in hydrothermal ecosystems. Science 296:1077-1082.

Ribeiro, S. and G. B. Golding. 1998. The mosaic nature of the eukaryotic nucleus. Molecular Biology and Evolution 15:779-788.

Rivera, M. C., R. Jain, J. E. Moore, and J. A. Lake. 1998. Genomic evidence for two functionally distinct gene classes. Proceedings of the National Academy of Sciences (USA) 95:6239-6244.

Rivera, M. C., and J. A. Lake. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152-155.

Robinson, R. 2005. Jump-starting a cellular world: Investigating the origin of life, from soup to networks. PLoS Biol 3(11): e396. http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030396

Skophammer, R. G., C. W. Herbold, M. C. Rivera, J. A. Servin, and J. A. Lake. 2006. Evidence that the Root of the Tree of Life Is Not within the Archaea. Molecular Biology and Evolution 23(9):1648-1651.

Syvanen, M. and C. I. Kado (eds.) 1998. Horizontal Gene Transfer. Chapman & Hall, London.

Tourasse, N. J. and M. Gouy. 1999. Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes. Molecular Phylogenetics and Evolution 13:159-168.

Vellai, T. and G. Vida. 1999. The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells. Proceedings of the Royal Society of London Series B 266:1571-1577.

Vishwanatha, P., P. Favaretto, H. Hartman, S. C. Mohr, and T. F. Smith. 2004. Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes. Molecular Phylogenetics and Evolution 33(3):615-625.

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Wolf, Y. I., I. B. Rogozin, N. V. Grishin, and E. V. Koonin. 2002. Genome trees and the tree of life. Trends Genet. 18:472-479.

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Information on the Internet

Title Illustrations
Click on an image to view larger version & data in a new window
Click on an image to view larger version & data in a new window
Scientific Name Fischerella
Copyright © 1995
Scientific Name Chrysina gloriosa
Location USA AZ Cochise Co.: Huachuca Mts, Miller Canyon 1810m. 31º24.7´N 110º16.8´W
Comments Riparian forest, collected at blacklight.
Source Chrysina gloriosa - Glorious Scarab
Copyright © Alex Wild
Scientific Name Sulfolobus and Sulfolobus tengchongensis spindle-shaped virus 1 (STSV1)
Location Yunnan Province, China
Comments Cell of the Archaean Sulfolobus infected by virus STSV1 observed under microscopy. Two spindle-shaped viruses were being released from the host cell. The strain of Sulfolobus and STSV1 were isolated by Xiaoyu Xiang and his colleagues in an acidic hot spring in Yunnan Province, China. At present, STSV1 is the largest archaeal virus that has been isolated and studied. Its genome sequence has been sequenced.
Creator Photo taken by Xiaoyu Xiang
Specimen Condition Dead Specimen
Source Image:RT8-4.jpg
Source Collection Wikimedia Commons
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Page: Tree of Life Life on Earth. The TEXT of this page is licensed under the Creative Commons Attribution-NonCommercial License - Version 3.0. Note that images and other media featured on this page are each governed by their own license, and they may or may not be available for reuse. Click on an image or a media link to access the media data window, which provides the relevant licensing information. For the general terms and conditions of ToL material reuse and redistribution, please see the Tree of Life Copyright Policies.

Citing this page:

Tree of Life Web Project. 1997. Life on Earth. Version 01 January 1997 (temporary). http://tolweb.org/Life_on_Earth/1/1997.01.01 in The Tree of Life Web Project, http://tolweb.org/

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This page is a Tree of Life Branch Page.

Each ToL branch page provides a synopsis of the characteristics of a group of organisms representing a branch of the Tree of Life. The major distinction between a branch and a leaf of the Tree of Life is that each branch can be further subdivided into descendent branches, that is, subgroups representing distinct genetic lineages.

For a more detailed explanation of the different ToL page types, have a look at the Structure of the Tree of Life page.

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