Key Points
-
The number of model organisms has grown in concert with the increasing number of genome-sequencing projects.
-
As a result, the 'tree of life', which was previously based on a ribosomal RNA gene sequence, has been replaced by one that is based on genome-wide sequence data.
-
Eukaryotes are no longer considered to be close relatives of Archaebacteria, but rather genomic hybrids of Archaebacteria and Eubacteria.
-
Large numbers of genes were transferred from prokaryotes to the eukaryote nucleus during symbiotic events.
-
Owing to recent analyses of genomic sequences, phylogenetic support for the presence of hyperthermophiles — species that live at high temperatures — at the base of the tree of life has been weakened.
-
Molecular-clock analyses have supported a more recent origin of Cyanobacteria than indicated by the fossil record. The date is now estimated to be closer to the time at which oxygen levels began to rise in the Earth's atmosphere, as indicated by geological evidence.
-
Some cytological and genomic evidence support the existence of a premitochondrial period in the history of eukaryotes, although this topic has been debated.
-
Whether the ancestors of some amitochondriate eukaryotes once had mitochondria also remains controversial.
-
The basal position of liverworts among land plants has been uprooted, although an alternative phylogeny has not yet been established.
-
Molecular-clock analyses indicate that the main groups of fungi diverged hundreds of millions of years earlier than indicated by the fossil record.
-
The relationships between humans, nematodes and fruitflies continue to be debated, despite the knowledge of their complete genomes.
Abstract
The phylogeny and timescale of life are becoming better understood as the analysis of genomic data from model organisms continues to grow. As a result, discoveries are being made about the early history of life and the origin and development of complex multicellular life. This emerging comparative framework and the emphasis on historical patterns is helping to bridge barriers among organism-based research communities.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Brenner, S. et al. Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 366, 265–268 (1993).
Pagel, M. Inferring the historical patterns of biological evolution. Nature 401, 877–884 (1999).Reviews how comparative biology methods that use phylogenies and molecular clocks can lead to remarkable insights into the evolution of life.
Enard, W. et al. Intra- and interspecific variation in primate gene expression patterns. Science 296, 340–343 (2002).
Ingman, M., Kaessmann, H., Pääbo, S. & Gyllensten, U. Mitochondrial genome variation and the origin of modern humans. Nature 408, 708–713 (2000).
Hedges, S. B. & Kumar, S. Vertebrate genomes compared. Science 297, 1283–1285 (2002).
Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl Acad. Sci. USA 87, 4576–4579 (1990).
Knoll, A. H. The early evolution of eukaryotes: a geological perspective. Science 256, 622–627 (1992).
Schopf, J. W. Microfossils of the early Archean Apex chert: new evidence of the antiquity of life. Science 260, 640–646 (1993).
Doolittle, W. F. Phylogenetic classification and the universal tree. Science 284, 2124–2128 (1999).Describes how the finding of large amounts of horizontal gene transfer, as inferred from phylogenetic analyses of sequence data, has reshaped our view of the 'tree of life'.
Philippe, H. & Forterre, P. The rooting of the universal tree of life is not reliable. J. Mol. Evol. 49, 509–523 (1999).
Margulis, L. Archael–eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proc. Natl Acad. Sci. USA 93, 1071–1076 (1996).
Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734–740 (1997).
Woese, C. R. & Fox, G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl Acad. Sci. USA 74, 5088–5090 (1977).
Hansmann, S. & Martin, W. 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. Int. J. Syst. Evol. Microbiol. 50, 1655–1663 (2000).
Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E. & Stanhope, M. J. Universal trees based on large combined protein data sets. Nature Genet. 28, 281–285 (2001).
Hedges, S. B. et al. A genomic timescale for the origin of eukaryotes. BMC Evol. Biol. 1, 4 (2001).
Wolf, Y. I., Rogozin, I. B., Grishin, N. V., Tatusov, R. L. & Koonin, E. V. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1, 8 (2001).
Brochier, C., Babteste, E., Moreira, D. & Philippe, H. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 18, 1–5 (2002).
Matte-Tailliez, O., Brochier, C., Forterre, P. & Philippe, H. Archael phylogeny based on ribosomal proteins. Mol. Biol. Evol. 19, 631–639 (2002).
Snel, B., Bork, P. & Huynen, M. A. Genome phylogeny based on gene content. Nature Genet. 21, 108–110 (1999).
House, C. H. & Fitz-Gibbon, S. T. Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J. Mol. Evol. 54, 539–547 (2002).
Tekaia, F., Lazcano, A. & Dujon, B. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9, 550–557 (1999).
Daubin, V., Gouy, M. & Perriere, G. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res. 12, 1080–1090 (2002).
Ragan, M. A. Detection of lateral gene transfer among microbial genomes. Curr. Opin. Genet. Dev. 11, 620–626 (2001).
Rivera, M. C. & Lake, J. A. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257, 74–76 (1992).
Cammarano, P., Creti, R., Sanangelantoni, A. M. & Palm, P. The Archaea monophyly issue: a phylogeny of translational elongation factor G(2) sequences inferred from an optimized selection of alignment positions. J. Mol. Evol. 49, 524–537 (1999).
Faguy, D. M. & Doolittle, W. F. Genomics: lessons from the Aeropyrum pernix genome. Curr. Biol. 9, R883–R886 (1999).
Tourasse, N. J. & Gouy, M. Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes. Mol. Phylogenet. Evol. 13, 159–168 (1999).
Katoh, K., Kuma, K. I. & Miyata, T. Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny. J. Mol. Evol. 53, 477–484 (2001).
Nisbet, E. G. & Sleep, N. H. The habitat and nature of early life. Nature 409, 1083–1091 (2001).
Galtier, N., Tourasse, N. & Gouy, M. A nonhyperthermophilic common ancestor to extant life forms. Science 283, 220–221 (1999).
Brochier, C. & Philippe, H. A non-hyperthermophilic ancestor for Bacteria. Nature 417, 244 (2002).
Daubin, V., Gouy, M. & Perrière, G. Bacterial phylogeny using supertree approach. Genome Informatics 12, 155–164 (2001).
Mojzsis, S. J. et al. Evidence for life on Earth before 3,800 million years ago. Nature 384, 55–59 (1996).
Fedo, C. M. & Whitehouse, M. J. Metasomatic origin of quartz-pyroxene rock, Akilia, Greenland, and implications for Earth's earliest life. Science 296, 1448–1452 (2002).
Schopf, J. W., Kudryavtsev, A. B., Agresti, D. G., Wdowiak, T. J. & Czaja, A. D. Laser-Raman imagery of Earth's earliest fossils. Nature 416, 73–76 (2002).
Brasier, M. D. et al. Questioning the evidence for Earth's earliest fossils. Nature 416, 76–81 (2002).Questions whether the 3.5-Gyr-old microfossils that were found in the Apex Chert rocks, in Australia (reference 8 ) are life forms. Reference 36 is a rebuttal to this paper and provides additional scrutiny of the same microfossils. These authors concur with one conclusion of reference 37 , that the fossils are not of Cyanobacteria, but maintain that they are, nonetheless, fossils of microbes.
Kollman, J. M. & Doolittle, R. F. Determining the relative rates of change for prokaryotic and eukaryotic proteins with anciently duplicated paralogs. J. Mol. Evol. 51, 173–181 (2000).
Feng, D.-F., Cho, G. & Doolittle, R. F. Determining divergence times with a protein clock: update and reevaluation. Proc. Natl Acad. Sci. USA 94, 13028–13033 (1997).An update of the influential 1996 Science paper from the laboratory of Russell Doolittle, one of the first to use large numbers of genes or proteins to date early events in the history of life.
Summons, R. E., Jahnke, L. L., Hope, J. M. & Logan, G. A. 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. Nature 400, 554–557 (1999).
Corliss, J. O. in Nature and Human Society: the Quest for a Sustainable World (ed. Raven, P. H.) 130–155 (The National Academy of Sciences, Washington DC, 2000).
Margulis, L. Origin of Eukaryotic Cells (Yale University Press, New Haven, Connecticut, 1970).
Gupta, R. S. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and eukaryotes. Microbiol. Mol. Biol. Rev. 62, 1435–1491 (1998).Provides a detailed and often overlooked critique of the evidence bearing on the origin of mitochondria and on the number of symbiotic events (and gene transfers) that occurred in the origin of eukaryotes.
Sogin, M. L., Gunderson, J. H., Elwood, H. J., Alonso, R. A. & Peattie, D. A. Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science 243, 75–77 (1989).
Roger, A. Reconstructing early events in eukaryotic evolution. Am. Nat. 154, S146–S163 (1999).
Horner, D. S. & Embley, T. M. Chaperonin 60 phylogeny provides further evidence for secondary loss of mitochondria among putative early-branching eukaryotes. Mol. Biol. Evol. 18, 1970–1975 (2001).
Silberman, J. D. et al. Retortamonad flagellates are closely related to diplomonads: implications for the history of mitochondrial function in eukaryote evolution. Mol. Biol. Evol. 19, 777–786 (2002).
Williams, B. A., Hirt, R. P., Lucocq, J. M. & Embley, T. M. A mitochondrial remnant in the microsporidian Trachipleistophora hominis. Nature 418, 865–869 (2002).
Katinka, M. D. et al. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414, 450–453 (2001).
Keeling, P. J., Luker, M. A. & Palmer, J. D. Evidence from β-tubulin phylogeny that microsporidia evolved from within the fungi. Mol. Biol. Evol. 17, 23–31 (2000).
Wang, D. Y.-C., Kumar, S. & Hedges, S. B. Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc. R. Soc. Lond. B Biol. Sci. 266, 163–171 (1999).
Baldauf, S. L., Roger, A. J., Wenk-Siefert, I. & Doolittle, W. F. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972–977 (2000).
Stechmann, A. & Cavalier-Smith, T. Rooting the eukaryote tree by using gene fusion. Science 297, 89–91 (2002).
Moreira, D., LeGuyader, H. & Philippe, H. The origin of red algae and the evolution of chloroplasts. Nature 405, 69–72 (2000).Provides strong evidence from several proteins that red algae and glaucocystophytes (glaucophytes) belong to the plant lineage, supporting a single origin of plastids.
Bapteste, E. et al. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba and Mastigamoeba. Proc. Natl Acad. Sci. USA 99, 1414–1419 (2002).
King, N. & Carroll, S. B. A receptor tyrosine kinase from choanoflagellates: molecular insights into early animal evolution. Proc. Natl Acad. Sci. USA 98, 15032–15037 (2001).
Stillier, J. W., Riley, J. & Hall, B. D. Are red algae plants? A critical evaluation of three key molecular data sets. J. Mol. Evol. 52, 527–539 (2001).
Nickrent, D. L., Parkinson, C. L., Palmer, J. D. & Duff, R. J. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Mol. Biol. Evol. 17, 1885–1895 (2000).
Chaw, S. M., Parkinson, C. L., Cheng, Y., Vincent, T. M. & Palmer, J. D. Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc. Natl Acad. Sci. USA 97, 4086–4091 (2000).
Qiu, Y.-L., Cho, Y., Cox, J. C. & Palmer, J. D. The gain of three mitochondrial introns identifies liverworts as the earliest land plants. Nature 394, 671–674 (1998).
Kumar, S. & Hedges, S. B. A molecular timescale for vertebrate evolution. Nature 392, 917–920 (1998).
Takezaki, N., Rzhetsky, A. & Nei, M. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12, 823–833 (1995).
Sanderson, M. J. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14, 1218–1231 (1997).
Thorne, J. L., Kishino, H. & Painter, I. S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15, 1647–1657 (1998).
Kishino, H., Thorne, J. L. & Bruno, W. J . Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18, 352–361 (2001).
Sanderson, M. J. & Doyle, J. A. Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data. Am. J. Bot. 88, 1499–1516 (2001).
Heckman, D. S. et al. Molecular evidence for the early colonization of land by fungi and plants. Science 293, 1129–1133 (2001).
Magallon, S. & Sanderson, M. J. Absolute diversification rates in angiosperm clades. Evolution 55, 1762–1780 (2001).
Martin, W., Gierl, A. & Saedler, H. Molecular evidence for pre-Cretaceous angiosperm origins. Nature 339, 46–48 (1989).
Crane, P. R., Friis, E. M. & Pedersen, K. R. The origin and early diversification of angiosperms. Nature 374, 27–33 (1995).
Smith, A. B. Systematics and the Fossil Record (Blackwell Scientific, London, 1994).
Kenrick, P. & Crane, P. R. The origin and early evolution of plants on land. Nature 389, 33–39 (1997).
Kirk, P. M., Cannon, P. F., David, J. C. & Stalpers, J. A. Dictionary of Fungi (CAB International, Surrey, UK, 2001).
Redecker, D., Kodner, R. & Graham, L. E. Glomalean fungi from the Ordovician. Science 289, 1920–1921 (2000).
Berbee, M. L. & Taylor, J. W. in The Mycota. VIIB. Systematics and Evolution (eds McLaughlin, D. J. & McLaughlin, E.) 229–246 (Springer, New York, 2001).
Goffeau, A. et al. Life with 6000 genes. Science 274, 546–567 (1996).
Wood, V. et al. The genome sequence of Schizosaccharomyces pombe. Nature 415, 871–880 (2002).
Butterfield, N. J. Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 26, 386–404 (2000).Describes the oldest taxonomically resolved eukaryotic group (red algae): it arose 1.2 Gyr ago, and therefore has helped to constrain molecular clocks. The article also discusses the significance of this ancient group for understanding the origin of sex and multicellularity.
Forsburg, S. L. The art and design of genetic screens: yeast. Nature Rev. Genet. 2, 659–668 (2001).
Schulte, U., Becker, I., Mewes, H. W. & Mannhaupt, G. Large scale analysis of sequences from Neurospora crassa. J. Biotechnol. 94, 3–13 (2002).
Berbee, M. L. The phylogeny of plant and animal pathogens in the Ascomycota. Physiol. Mol. Plant Pathol. 59, 165–187 (2001).
May, R. M. in Nature and Human Society: the Quest for a Sustainable World (ed. Raven, P. H.) 30–45 (The National Academy of Sciences, Washington DC, 2000).
Li, W.-H., Gouy, M., Sharp, P. M., Ohuigin, C. & Yang, Y.-W. Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora and molecular clocks. Proc. Natl Acad. Sci. USA 87, 6703–6707 (1990).
Murphy, W. J. et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294, 2348–2351 (2001).Presents a phylogenetic analysis of the most taxonomically diverse sequence data set for placental mammals.
Rosenberg, M. S. & Kumar, S. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl Acad. Sci. USA 98, 10751–10756 (2001).
Aguinaldo, A. M. et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387, 489–493 (1997).An influential paper that describes an analysis of sequences from the small subunit ribosomal RNA gene of animals. As a result, nematodes are placed together with arthropods in a controversial grouping dubbed 'Ecdysozoa' (see also reference 93).
Adoutte, A. et al. The new animal phylogeny: reliability and implications. Proc. Natl Acad. Sci. USA 97, 4453–4456 (2000).
deRosa, R. et al. Hox genes in brachiopods and priapulids and protostome evolution. Nature 399, 772–776 (1999).
Manual, M., Kruse, M., Muller, W. E. G. & Parco, Y. L. The comparison of β-thymosin homologues among Metazoa supports an arthropod–nematode clade. J. Mol. Evol. 51, 378–381 (2000).
Carroll, S. B., Grenier, J. K. & Weatherbee, S. D. From DNA to Diversity (Blackwell Science, Malden, Massachusetts, 2001).
Davidson, E. H. Genomic Regulatory Systems (Academic, San Diego, 2001).
Hausdorf, B. Early evolution of the bilateria. Syst. Biol. 49, 130–142 (2000).
Blair, J. E., Ikeo, K., Gojobori, T. & Hedges, S. B. The evolutionary position of nematodes. BMC Evol. Biol. 2, 7 (2002).
Mushegian, A. R., Garey, J. R., Martin, J. & Liu, L. X. Large-scale taxonomic profiling of eukaryotic model organisms: a comparison of orthologous proteins encoded by the human, fly, nematode, and yeast genomes. Genome Res. 8, 590–598 (1998).
Easteal, S. & Herbert, G. Molecular evidence from the nuclear genome for the time frame of human evolution. J. Mol. Evol. 44, S121–S132 (1997).
Arnason, U., Gullberg, A., Burgeuete, A. S. & Janke, A. Molecular estimates of primate divergences and new hypotheses for primate dispersal and the origin of modern humans. Hereditas 133, 217–228 (2001).
Stauffer, R. L., Walker, A., Ryder, O. A., Lyons-Weiler, M. & Hedges, S. B. Human and ape molecular clocks and constraints on paleontological hypotheses. J. Hered. 92, 469–474 (2001).
Chen, F.-C. & Li, W.-H. Genomic divergences between humans and other hominoids and effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68, 444–456 (2001).
Leakey, M. G., Feibel, C. S., McDougall, I. & Walker, A. New four-million-year-old hominid species from Kanapoi and Allia Bay, Kenya. Nature 376, 565–571 (1995).
Wood, B. Hominid revelations from Chad. Nature 418, 134–135 (2002).
Brunet, M. et al. A new hominid from the Upper Miocene of Chad, Central Africa. Nature 418, 145–151 (2002).
Adkins, R. M., Gelke, E. L., Rowe, D. & Honeycutt, R. L. Molecular phylogeny and divergence time estimates for major rodent groups: evidence frm multiple genes. Mol. Biol. Evol. 18, 777–791 (2001).
Kumar, S. & Subramanian, S. Mutation rates in mammalian genomes. Proc. Natl Acad. Sci. USA 99, 803–808 (2002).
Benton, M. J. Vertebrate Palaeontology 452 (Blackwell Science, Oxford, 2000).
Hedges, S. B., Parker, P. H., Sibley, C. G. & Kumar, S. Continental breakup and the ordinal diversification of birds and mammals. Nature 381, 226–229 (1996).
Archibald, J. D. Fossil evidence for a late Cretaceous origin of "hoofed" mammals. Science 272, 1150–1153 (1996).
Springer, M. S. et al. Endemic African mammals shake the phylogenetic tree. Nature 388, 61–63 (1997).Sequence analyses define a superorder of mammals, now termed 'Afrotheria', that includes elephants, sea cows, hyraxes, aardvarks, golden moles and elephant shrews. After publication of this paper, tenrecs have also been added to this group. Support for the superorder continues to remain strong.
Wray, G. A., Levinton, J. S. & Shapiro, L. H. Molecular evidence for deep Precambrian divergences among metazoan phyla. Science 274, 568–573 (1996).
Fortey, R. A., Briggs, D. E. G. & Wills, M. A. The Cambrian evolutionary 'explosion': decoupling cladogenesis from morphological disparity. Biol. J. Linn. Soc. Lon. 57, 13–33 (1996).
Valentine, J. W., Jablonski, D. & Erwin, D. H. Fossils, molecules and embryos: new perspectives on the Cambrian explosion. Development 126, 851–859 (1999).
Budd, G. E. & Jensen, S. A critical reappraisal of the fossil record of the bilaterian phyla. Biol. Rev. 75, 253–295 (2000).
Smith, A. B. & Peterson, K. J. Dating the time of origin of major clades: molecular clocks and the fossil record. Annu. Rev. Earth Planet. Sci. Lon. 30, 65–88 (2002).
Knoll, A. H. in Early Life on Earth (ed. Bengtson, S.) 439–449 (Columbia Univ. Press, New York, 1994).
Knoll, A. H. & Carroll, S. B. Early animal evolution: emerging views from comparative biology and geology. Science 284, 2129–2137 (1999).
Hoffman, P. F., Kaufman, A. J., Halverson, G. P. & Schrag, D. P. A Neoproterozoic snowball Earth. Science 281, 1342–1346 (1998).
Rasmussen, B., Bengston, S., Fletcher, I. R. & McNaughton, N. J. Discoidal impressions and trace-like fossils more than 1200 million years old. Science 296, 1112–1115 (2002).
Nei, M. & Kumar, S. Molecular Evolution and Phylogenetics (Oxford Univ. Press, New York, 2000).
Rannala, B. & Yang, Z. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304–311 (1996).
Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791 (1985).
Zuckerkandl, E. & Pauling, L. in Horizons in Biochemistry (eds Marsha, M. & Pullman, B.) 189–225 (Academic, New York, 1962).
Sanderson, M. J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19, 101–109 (2002).
Brocks, J. J., Logan, G. A., Buick, R. & Summons, R. E. Archean molecular fossils and the early rise of eukaryotes. Science 285, 1033–1036 (1999).
Han, T.-M. & Runnegar, B. Megascopic eukaryotic algae from the 2.1 billion-year-old Negaunee iron-formation, Michigan. Science 257, 232–235 (1992).
Javaux, E. J., Knoll, A. H. & Walter, M. R. Morphological and ecological complexity in early eukaryotic ecosystems. Nature 412, 66–69 (2001).
Wikström, N. Savolainen, V. & Chase, M. W. Evolution of the angiosperms: calibrating the family tree. Proc. R. Soc. Lond. B Biol. Sci. 268, 2211–2220 (2001).
James, T. Y., Porter, D., Leander, C. A., Vilgalys, R. & Longcore, J. E. Molecular phylogenies of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Can. J. Bot. 78, 336–350 (2000).
Acknowledgements
I thank J. Blair, D. Geiser, S. Kumar, and D. Pisani for comments. I apologize to colleagues whose work could not be cited due to space constraints. Research in the author's laboratory is supported by the National Aeronautics and Space Administration (Astrobiology Institute) and National Science Foundation.
Author information
Authors and Affiliations
Related links
Related links
FURTHER INFORMATION
Deep hypha (phylogeny of Fungi)
Dictyostelium database (DictyBase)
DOE microbial genomics gateway
Generic model organism database
International geologic timescale
NASA evolutionary genomics web site
NIH model organism database report
NIH model organism initiatives
Glossary
- HORIZONTAL TRANSFER
-
The transfer of genetic material between the genomes of two organisms, which are usually different species.
- NEIGHBOUR JOINING
-
A method that selects the tree that has the shortest overall length (sum of all branch lengths).
- MAXIMUM LIKELIHOOD
-
A method that selects the tree that has the highest probability of explaining the sequence data, under a specific model of substitution (changes in the nucleotide or amino-acid sequence).
- BAYESIAN METHOD
-
A method that selects the tree that has the greatest posterior probability (probability that the tree is correct), under a specific model of substitution.
- MAXIMUM PARSIMONY
-
A method that selects the tree that requires the fewest number of substitutions.
- BOOTSTRAP METHOD
-
As applied to molecular phylogenies. Nucleotide or amino-acid sites are sampled randomly, with replacement, and a new tree is constructed. This is repeated many times and the frequency of appearance of a particular node among the bootstrap trees is viewed as a support (confidence) value for deciding on the significance of that node.
- RELATIVE RATE TESTS
-
Statistical tests that determine, at a given level of stringency, whether two or more branches in a tree have evolved at the same rate of sequence change.
- CYANOBACTERIA
-
A phylum of Eubacteria, formerly known as the “blue-green algae”. These prokaryotes are the only organisms known to be capable of oxygenic photosynthesis.
- SPIROCHAETES
-
A phylum of Eubacteria that has a spiral or corkscrew-like appearance and axial filaments (similar to flagella). These prokaryotes are responsible for human diseases, such as Lyme disease and syphilis.
- MONOPHYLETIC
-
Includes all the descendants of a single common ancestor.
- ELONGATION FACTOR 1
-
An enzyme that functions in the process of protein translation.
- PARAPHYLETIC
-
Includes some, but not all, of the descendants of a single common ancestor.
- ADAPTIVE RADIATION
-
The rapid diversification of a group of species into various habitats over a relatively short period of geological time. However, the term is often used as a synonym for any large monophyletic group of taxa.
- GLAUCOCYSTOPHYTES
-
A small group of freshwater algae, also called 'glaucophytes'. Species in this group have plastids with a peptidoglycan cell wall (peptidoglycan is the main component of bacterial cell walls).
- BRYOPHYTES
-
A term that refers traditionally to non-vascular land plants, nearly all of which are quite small (1–2 cm high). Bryophytes include hornworts, liverworts and mosses; however, the term might also be used in a more restricted sense to refer to the mosses alone (Division: Bryophyta).
- HORNWORTS
-
A group of small, non-vascular plants (Division: Anthocerotophyta) that are distinguished by their tall horn-like sporophyte (diploid generation) that grows on the more flattened gametophyte (haploid generation). They usually have a single, large chloroplast in each cell.
- LIVERWORTS
-
A group of small, mat-like, non-vascular plants (Division: Marchantiophyta) that occur in diverse habitats but most commonly on the forest floor. Some species have lobe-shaped leaves that resemble a liver.
- MONOCOTS
-
(Monocotyledonous plants). Flowering plants with one cotyledon (or seed leaf).
- EUDICOTS
-
The largest clade of angiosperms, characterized by two cotyledons (seed leaves) and three symmetrically placed pollen apertures or aperture arrangements that are derived from this.
- ANGIOSPERMS
-
Flowering vascular plants that form seeds inside an ovary.
- GYMNOSPERMS
-
Non-flowering vascular plants with naked seeds that are not enclosed in an ovary (for example, pine).
- PRECAMBRIAN
-
An informal geological time period that spans from the time the Earth was born, ∼4,500 million years ago (Mya), until ∼545 Mya.
- LOCAL-CLOCK METHOD
-
A method for estimating divergence time by accounting for differences in the rate of substitution among lineages (branches) in a tree.
- CAMBRIAN EXPLOSION
-
The sudden appearance, ∼520 million years ago, of many major groups (phyla) of animals, as witnessed in the fossil record.
- ASCOMYCOTA
-
The largest phylum of fungi; also called ascomycetes or 'sac fungi'. They produce sexual spores in specialized sac-like cells called asci.
- PYRENOMYCETES
-
The largest subgroup of ascomycotan fungi, which are characterized by flask-shaped fruiting bodies.
- ARTIODACTYLS
-
Hoofed animals with an even number of digits. They belong to the mammalian Order Artiodactyla and include animals such as cattle, deer and pigs.
- TAXON SAMPLING
-
A term that indicates that the branching pattern of a tree might be influenced by the number or type of taxa (for example, species) included.
- PSEUDOCOELOM
-
Literally 'false cavity'; the body cavity of an animal, such as a nematode, that is not fully lined with mesodermal cells.
- COELOM
-
The body cavity of an animal, such as a vertebrate or insect, which is completely lined with mesodermal cells.
- CENOZOIC
-
The geological time period (era) that spans from 65 million years ago to the present day.
Rights and permissions
About this article
Cite this article
Hedges, S. The origin and evolution of model organisms. Nat Rev Genet 3, 838–849 (2002). https://doi.org/10.1038/nrg929
Issue Date:
DOI: https://doi.org/10.1038/nrg929
This article is cited by
-
Nuclear genome annotation of wheel animals and thorny-headed worms: inferences about the last common ancestor of Syndermata (Rotifera s.l.)
Hydrobiologia (2023)
-
Cell-type specific pallial circuits shape categorical tuning responses in the crow telencephalon
Communications Biology (2022)
-
Newly described anatomical opening on forelimb tendon in the artiodactyls and its relation to knee clicks
Scientific Reports (2022)
-
Phase separation driven by interchangeable properties in the intrinsically disordered regions of protein paralogs
Communications Biology (2022)
-
Naturally Fluorescent Field Mouse, Mus booduga (Gray, 1837) and Common House Gecko, Hemidactylus frenatus (Schlegel, 1836) as Model Organisms for Biomedical Studies
National Academy Science Letters (2022)