Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Science 13 June 2003:
Vol. 300. no. 5626, pp. 1703 - 1706
DOI: 10.1126/science.1085544
Prev | Table of Contents | Next

Viewpoint

The Deep Roots of Eukaryotes

S. L. Baldauf

Most cultivated and characterized eukaryotes can be confidently assigned to one of eight major groups. After a few false starts, we are beginning to resolve relationships among these major groups as well. However, recent developments are radically revising this picture again, particularly (i)the discovery of the likely antiquity and taxonomic diversity of ultrasmall eukaryotes, and (ii)a fundamental rethinking of the position of the root. Together these data suggest major gaps in our understanding simply of what eukaryotes are or, when it comes to the tree, even which end is up.

Department of Biology, University of York, Box 373, Heslington, York YO10 5YW, UK. E-mail:slb14{at}york.ac.uk

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
A Contiguous Compartment Functions as Endoplasmic Reticulum and Endosome/Lysosome in Giardia lamblia.
M. Abodeely, K. N. DuBois, A. Hehl, S. Stefanic, M. Sajid, W. deSouza, M. Attias, J. C. Engel, I. Hsieh, R. D. Fetter, et al. (2009)
Eukaryot. Cell 8, 1665-1676
   Abstract »    Full Text »    PDF »
Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology.
D. A. Caron, P. D. Countway, P. Savai, R. J. Gast, A. Schnetzer, S. D. Moorthi, M. R. Dennett, D. M. Moran, and A. C. Jones (2009)
Appl. Envir. Microbiol. 75, 5797-5808
   Abstract »    Full Text »    PDF »
Photosystem II and Pigment Dynamics among Ecotypes of the Green Alga Ostreococcus.
C. Six, R. Sherrard, M. Lionard, S. Roy, and D. A. Campbell (2009)
Plant Physiology 151, 379-390
   Abstract »    Full Text »    PDF »
A Novel WRKY-like Protein Involved in Transcriptional Activation of Cyst Wall Protein Genes in Giardia lamblia.
Y.-J. Pan, C.-C. Cho, Y.-Y. Kao, and C.-H. Sun (2009)
J. Biol. Chem. 284, 17975-17988
   Abstract »    Full Text »    PDF »
The origins of apicomplexan sequence innovation.
J. Wasmuth, J. Daub, J. M. Peregrin-Alvarez, C. A.M. Finney, and J. Parkinson (2009)
Genome Res. 19, 1202-1213
   Abstract »    Full Text »    PDF »
Analysis of Rare Genomic Changes Does Not Support the Unikont-Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes.
I. B. Rogozin, M. K. Basu, M. Csuros, and E. V. Koonin (2009)
Gen Biol Evol 2009, 99-113
   Abstract »    Full Text »    PDF »
Phylogenetically Close Group I Introns with Different Positions among Paramecium bursaria Photobionts Imply a Primitive Stage of Intron Diversification.
R. Hoshina and N. Imamura (2009)
Mol. Biol. Evol. 26, 1309-1319
   Abstract »    Full Text »    PDF »
Free Fatty Acids and Methyl Jasmonate Trigger Defense Reactions in Laminaria digitata.
F. C. Kupper, E. Gaquerel, A. Cosse, F. Adas, A. F. Peters, D. G. Muller, B. Kloareg, J.-P. Salaun, and P. Potin (2009)
Plant Cell Physiol. 50, 789-800
   Abstract »    Full Text »    PDF »
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups".
V. Hampl, L. Hug, J. W. Leigh, J. B. Dacks, B. F. Lang, A. G. B. Simpson, and A. J. Roger (2009)
PNAS 106, 3859-3864
   Abstract »    Full Text »    PDF »
Evolutionary position of breviate amoebae and the primary eukaryote divergence.
M. A. Minge, J. D Silberman, R. J.S Orr, T. Cavalier-Smith, K. Shalchian-Tabrizi, F. Burki, A. Skjaeveland, and K. S Jakobsen (2009)
Proc R Soc B 276, 597-604
   Abstract »    Full Text »    PDF »
PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae.
M. Oliva, G. Theiler, M. Zamocky, D. Koua, M. Margis-Pinheiro, F. Passardi, and C. Dunand (2009)
J. Exp. Bot. 60, 453-459
   Abstract »    Full Text »    PDF »
Evolutionary origins of human apoptosis and genome-stability gene networks.
M. A. A. Castro, R. J. S. Dalmolin, J. C. F. Moreira, J. C. M. Mombach, and R. M. C. de Almeida (2008)
Nucleic Acids Res. 36, 6269-6283
   Abstract »    Full Text »    PDF »
Cell Wall Chitosaccharides Are Essential Components and Exposed Patterns of the Phytopathogenic Oomycete Aphanomyces euteiches.
I. Badreddine, C. Lafitte, L. Heux, N. Skandalis, Z. Spanou, Y. Martinez, M.-T. Esquerre-Tugaye, V. Bulone, B. Dumas, and A. Bottin (2008)
Eukaryot. Cell 7, 1980-1993
   Abstract »    Full Text »    PDF »
From Drought Sensing to Developmental Control: Evolution of Cyclic AMP Signaling in Social Amoebas.
A. V. Ritchie, S. van Es, C. Fouquet, and P. Schaap (2008)
Mol. Biol. Evol. 25, 2109-2118
   Abstract »    Full Text »    PDF »
Rapamycin inhibits trypanosome cell growth by preventing TOR complex 2 formation.
A. Barquilla, J. L. Crespo, and M. Navarro (2008)
PNAS 105, 14579-14584
   Abstract »    Full Text »    PDF »
Spliceosomal snRNAs in the unicellular eukaryote Trichomonas vaginalis are structurally conserved but lack a 5'-cap structure.
A. Simoes-Barbosa, D. Meloni, J. A. Wohlschlegel, M. M. Konarska, and P. J. Johnson (2008)
RNA 14, 1617-1631
   Abstract »    Full Text »    PDF »
Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex.
H.-M. Bourbon (2008)
Nucleic Acids Res. 36, 3993-4008
   Abstract »    Full Text »    PDF »
Plasmodium falciparum possesses two GRASP proteins that are differentially targeted to the Golgi complex via a higher- and lower-eukaryote-like mechanism.
N. S. Struck, S. Herrmann, C. Langer, A. Krueger, B. J. Foth, K. Engelberg, A. L. Cabrera, S. Haase, M. Treeck, M. Marti, et al. (2008)
J. Cell Sci. 121, 2123-2129
   Abstract »    Full Text »    PDF »
DNA double-strand breaks, but not crossovers, are required for the reorganization of meiotic nuclei in Tetrahymena.
K. Mochizuki, M. Novatchkova, and J. Loidl (2008)
J. Cell Sci. 121, 2148-2158
   Abstract »    Full Text »    PDF »
Cell Cycle Synchrony in Giardia intestinalis Cultures Achieved by Using Nocodazole and Aphidicolin.
M. K. Poxleitner, S. C. Dawson, and W. Z. Cande (2008)
Eukaryot. Cell 7, 569-574
   Abstract »    Full Text »    PDF »
A conserved U-rich RNA region implicated in regulation of translation in Plasmodium female gametocytes.
J. A. M. Braks, G. R. Mair, B. Franke-Fayard, C. J. Janse, and A. P. Waters (2008)
Nucleic Acids Res. 36, 1176-1186
   Abstract »    Full Text »    PDF »
RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members.
R. H. Y. Jiang, S. Tripathy, F. Govers, and B. M. Tyler (2008)
PNAS 105, 4874-4879
   Abstract »    Full Text »    PDF »
Photosynthetic symbioses in animals.
A.A. Venn, J.E. Loram, and A.E. Douglas (2008)
J. Exp. Bot. 59, 1069-1080
   Abstract »    Full Text »    PDF »
Early evolution of histone mRNA 3' end processing.
M. Davila Lopez and T. Samuelsson (2008)
RNA 14, 1-10
   Abstract »    Full Text »    PDF »
Pathogen-Induced Defense and Innate Immunity in Macroalgae.
F. Weinberger (2007)
Biol. Bull. 213, 290-302
   Abstract »    Full Text »    PDF »
Architecture of the Sporulation-Specific Cdc14 Promoter from the Oomycete Phytophthora infestans.
A. M. V. Ah-Fong, Q. Xiang, and H. S. Judelson (2007)
Eukaryot. Cell 6, 2222-2230
   Abstract »    Full Text »    PDF »
Tousled-like kinase in a microbial eukaryote regulates spindle assembly and S-phase progression by interacting with Aurora kinase and chromatin assembly factors.
Z. Li, S. Gourguechon, and C. C. Wang (2007)
J. Cell Sci. 120, 3883-3894
   Abstract »    Full Text »    PDF »
Diversification of NRT2 and the Origin of Its Fungal Homolog.
J. C. Slot, K. N. Hallstrom, P. B. Matheny, and D. S. Hibbett (2007)
Mol. Biol. Evol. 24, 1731-1743
   Abstract »    Full Text »    PDF »
The secretory peptide gene EPF1 enforces the stomatal one-cell-spacing rule.
K. Hara, R. Kajita, K. U. Torii, D. C. Bergmann, and T. Kakimoto (2007)
Genes & Dev. 21, 1720-1725
   Abstract »    Full Text »    PDF »
BLASTO: a tool for searching orthologous groups.
Y. Zhou and L. F. Landweber (2007)
Nucleic Acids Res. 35, W678-W682
   Abstract »    Full Text »    PDF »
Three distinct modes of intron dynamics in the evolution of eukaryotes.
L. Carmel, Y. I. Wolf, I. B. Rogozin, and E. V. Koonin (2007)
Genome Res. 17, 1034-1044
   Abstract »    Full Text »    PDF »
PhyloGena a user-friendly system for automated phylogenetic annotation of unknown sequences.
K. Hanekamp, U. Bohnebeck, B. Beszteri, and K. Valentin (2007)
Bioinformatics 23, 793-801
   Abstract »    Full Text »    PDF »
A novel non-protein-coding infection-specific gene family is clustered throughout the genome of Phytophthora infestans.
A. O. Avrova, S. C. Whisson, L. Pritchard, E. Venter, S. De Luca, I. Hein, and P. R. J. Birch (2007)
Microbiology 153, 747-759
   Abstract »    Full Text »    PDF »
Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases.
C. Zaros, J.-F. Briand, Y. Boulard, S. Labarre-Mariotte, M. C. Garcia-Lopez, P. Thuriaux, and F. Navarro (2007)
Nucleic Acids Res. 35, 634-647
   Abstract »    Full Text »    PDF »
Three-dimensional analysis of mitosis and cytokinesis in the binucleate parasite Giardia intestinalis.
M. S. Sagolla, S. C. Dawson, J. J. Mancuso, and W. Z. Cande (2006)
J. Cell Sci. 119, 4889-4900
   Abstract »    Full Text »    PDF »
Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha).
M. Blackwell, D. S. Hibbett, J. W. Taylor, and J. W. Spatafora (2006)
Mycologia 98, 829-837
   Abstract »    Full Text »    PDF »
Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column..
S.-O. Jeon, J. Bunge, T. Stoeck, K. J.-A. Barger, S.-H. Hong, and S. S. Epstein (2006)
Appl. Envir. Microbiol. 72, 6578-6583
   Abstract »    Full Text »    PDF »
From the Cover: Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features.
E. Derelle, C. Ferraz, S. Rombauts, P. Rouze, A. Z. Worden, S. Robbens, F. Partensky, S. Degroeve, S. Echeynie, R. Cooke, et al. (2006)
PNAS 103, 11647-11652
   Abstract »    Full Text »    PDF »
Comparative Genomic and Phylogenetic Analyses of Calcium ATPases and Calcium-Regulated Proteins in the Apicomplexa.
K. Nagamune and L. D. Sibley (2006)
Mol. Biol. Evol. 23, 1613-1627
   Abstract »    Full Text »    PDF »
Ancient origin, functional conservation and fast evolution of DNA-dependent RNA polymerase III.
G. M. Proshkina, E. K. Shematorova, S. A. Proshkin, C. Zaros, P. Thuriaux, and G. V. Shpakovski (2006)
Nucleic Acids Res. 34, 3615-3624
   Abstract »    Full Text »    PDF »
Early events in the perception of lipopolysaccharides in the brown alga Laminaria digitata include an oxidative burst and activation of fatty acid oxidation cascades.
F. C. Kupper, E. Gaquerel, E.-M. Boneberg, S. Morath, J.-P. Salaun, and P. Potin (2006)
J. Exp. Bot. 57, 1991-1999
   Abstract »    Full Text »    PDF »
Genomics and the irreducible nature of eukaryote cells..
C. G. Kurland, L. J. Collins, and D. Penny (2006)
Science 312, 1011-1014
   Abstract »    Full Text »    PDF »
Fungi and animals may share a common ancestor to nuclear receptors.
C. Phelps, V. Gburcik, E. Suslova, P. Dudek, F. Forafonov, N. Bot, M. MacLean, R. J. Fagan, and D. Picard (2006)
PNAS 103, 7077-7081
   Abstract »    Full Text »    PDF »
Diversity and distribution of marine microbial eukaryotes in the arctic ocean and adjacent seas..
C. Lovejoy, R. Massana, and C. Pedros-Alio (2006)
Appl. Envir. Microbiol. 72, 3085-3095
   Abstract »    Full Text »    PDF »
Cytoskeleton and Morphogenesis in Brown Algae.
C. KATSAROS, D. KARYOPHYLLIS, and B. GALATIS (2006)
Ann. Bot. 97, 679-693
   Abstract »    Full Text »    PDF »
An Aurora Kinase Homologue Is Involved in Regulating Both Mitosis and Cytokinesis in Trypanosoma brucei.
X. Tu, P. Kumar, Z. Li, and C. C. Wang (2006)
J. Biol. Chem. 281, 9677-9687
   Abstract »    Full Text »    PDF »
Single, Ancient Origin of a Plastid Metabolite Translocator Family in Plantae from an Endomembrane-Derived Ancestor.
A. P. M. Weber, M. Linka, and D. Bhattacharya (2006)
Eukaryot. Cell 5, 609-612
   Abstract »    Full Text »    PDF »
Species richness and ecological characterization of myxomycetes and myxomycete-like organisms in the canopy of a temperate deciduous forest..
M. Schnittler, M. Unterseher, and J. Tesmer (2006)
Mycologia 98, 223-232
   Abstract »    Full Text »    PDF »
Comprehensive Multigene Phylogenies of Excavate Protists Reveal the Evolutionary Positions of "Primitive" Eukaryotes.
A. G. B. Simpson, Y. Inagaki, and A. J. Roger (2006)
Mol. Biol. Evol. 23, 615-625
   Abstract »    Full Text »    PDF »
Ancient Origin of Elicitin Gene Clusters in Phytophthora Genomes.
R. H. Y. Jiang, B. M. Tyler, S. C. Whisson, A. R. Hardham, and F. Govers (2006)
Mol. Biol. Evol. 23, 338-351
   Abstract »    Full Text »    PDF »
Niche metabolism in parasitic protozoa.
M. L Ginger (2006)
Phil Trans R Soc B 361, 101-118
   Abstract »    Full Text »    PDF »
Comparative Genomics and Evolution of Proteins Associated with RNA Polymerase II C-Terminal Domain.
Z. Guo and J. W. Stiller (2005)
Mol. Biol. Evol. 22, 2166-2178
   Abstract »    Full Text »    PDF »
The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes.
J. Slapeta, D. Moreira, and P. Lopez-Garcia (2005)
Proc R Soc B 272, 2073-2081
   Abstract »    Full Text »    PDF »
Diversity of the Microeukaryotic Community in Sulfide-Rich Zodletone Spring (Oklahoma).
Q. Luo, L. R. Krumholz, F. Z. Najar, A. D. Peacock, B. A. Roe, D. C. White, and M. S. Elshahed (2005)
Appl. Envir. Microbiol. 71, 6175-6184
   Abstract »    Full Text »    PDF »
A NIMA-related Protein Kinase Is Essential for Completion of the Sexual Cycle of Malaria Parasites.
L. Reininger, O. Billker, R. Tewari, A. Mukhopadhyay, C. Fennell, D. Dorin-Semblat, C. Doerig, D. Goldring, L. Harmse, L. Ranford-Cartwright, et al. (2005)
J. Biol. Chem. 280, 31957-31964
   Abstract »    Full Text »    PDF »
Chlorophyll c-Containing Plastid Relationships Based on Analyses of a Multigene Data Set with All Four Chromalveolate Lineages.
T. R. Bachvaroff, M. V. Sanchez Puerta, and C. F. Delwiche (2005)
Mol. Biol. Evol. 22, 1772-1782
   Abstract »    Full Text »    PDF »
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell.
K. S. Makarova, Y. I. Wolf, S. L. Mekhedov, B. G. Mirkin, and E. V. Koonin (2005)
Nucleic Acids Res. 33, 4626-4638
   Abstract »    Full Text »    PDF »
Reciprocal Fusions of Two Genes in the Formaldehyde Detoxification Pathway in Ciliates and Diatoms.
N. A. Stover, A. R. O. Cavalcanti, A. J. Li, B. C. Richardson, and L. F. Landweber (2005)
Mol. Biol. Evol. 22, 1539-1542
   Abstract »    Full Text »    PDF »
Origin and Evolution of Kinesin-Like Calmodulin-Binding Protein.
S. E. Abdel-Ghany, I. S. Day, M. P. Simmons, P. Kugrens, and A. S.N. Reddy (2005)
Plant Physiology 138, 1711-1722
   Abstract »    Full Text »    PDF »
Evolution of gap junction proteins - the pannexin alternative.
Y. V. Panchin (2005)
J. Exp. Biol. 208, 1415-1419
   Abstract »    Full Text »    PDF »
Towards Building the Tree of Life: A Simulation Study for All Angiosperm Genera.
N. Salamin, T. R. Hodkinson, and V. Savolainen (2005)
Syst Biol 54, 183-196
   Abstract »    Full Text »    PDF »
Root of the Eukaryota Tree as Inferred from Combined Maximum Likelihood Analyses of Multiple Molecular Sequence Data.
N. Arisue, M. Hasegawa, and T. Hashimoto (2005)
Mol. Biol. Evol. 22, 409-420
   Abstract »    Full Text »    PDF »
Beringian Paleoecology Inferred from Permafrost-Preserved Fungal DNA.
M. C. Lydolph, J. Jacobsen, P. Arctander, M. T. P. Gilbert, D. A. Gilichinsky, A. J. Hansen, E. Willerslev, and L. Lange (2005)
Appl. Envir. Microbiol. 71, 1012-1017
   Abstract »    Full Text »    PDF »
The diversity of dolichol-linked precursors to Asn-linked glycans likely results from secondary loss of sets of glycosyltransferases.
J. Samuelson, S. Banerjee, P. Magnelli, J. Cui, D. J. Kelleher, R. Gilmore, and P. W. Robbins (2005)
PNAS 102, 1548-1553
   Abstract »    Full Text »    PDF »
Comparative Genomics of the Pennate Diatom Phaeodactylum tricornutum.
A. Montsant, K. Jabbari, U. Maheswari, and C. Bowler (2005)
Plant Physiology 137, 500-513
   Abstract »    Full Text »    PDF »
Gene Transfers from Nanoarchaeota to an Ancestor of Diplomonads and Parabasalids.
J. O. Andersson, S. W. Sarchfield, and A. J. Roger (2005)
Mol. Biol. Evol. 22, 85-90
   Abstract »    Full Text »    PDF »
New keys to the Past: Current and future DNA studies in Coccolithophores.
C. de Vargas and I. Probert (2004)
Micropaleontology 50, 45-54
   Abstract »    Full Text »    PDF »
The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?.
E. J. P. Douzery, E. A. Snell, E. Bapteste, F. Delsuc, and H. Philippe (2004)
PNAS 101, 15386-15391
   Abstract »    Full Text »    PDF »
The Evolution of Modern Eukaryotic Phytoplankton.
P. G. Falkowski, M. E. Katz, A. H. Knoll, A. Quigg, J. A. Raven, O. Schofield, and F. J. R. Taylor (2004)
Science 305, 354-360
   Abstract »    Full Text »    PDF »
Phylogenetic and Ecological Analysis of Novel Marine Stramenopiles.
R. Massana, J. Castresana, V. Balague, L. Guillou, K. Romari, A. Groisillier, K. Valentin, and C. Pedros-Alio (2004)
Appl. Envir. Microbiol. 70, 3528-3534
   Abstract »    Full Text »    PDF »
From the Cover: The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes.
S. I. Nikolaev, C. Berney, J. F. Fahrni, I. Bolivar, S. Polet, A. P. Mylnikov, V. V. Aleshin, N. B. Petrov, and J. Pawlowski (2004)
PNAS 101, 8066-8071
   Abstract »    Full Text »    PDF »
Evolutionary Genomics of Chromoviruses in Eukaryotes.
B. Gorinsek, F. Gubensek, and D. Kordis (2004)
Mol. Biol. Evol. 21, 781-798
   Abstract »    Full Text »    PDF »
A Molecular Timeline for the Origin of Photosynthetic Eukaryotes.
H. S. Yoon, J. D. Hackett, C. Ciniglia, G. Pinto, and D. Bhattacharya (2004)
Mol. Biol. Evol. 21, 809-818
   Abstract »    Full Text »    PDF »
Novel Eukaryotes from the Permanently Anoxic Cariaco Basin (Caribbean Sea).
T. Stoeck, G. T. Taylor, and S. S. Epstein (2003)
Appl. Envir. Microbiol. 69, 5656-5663
   Abstract »    Full Text »    PDF »
Biomineralization and Evolutionary History.
A. H. Knoll and A. H. Knoll (2003)
Reviews in Mineralogy and Geochemistry 54, 329-356
   Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)