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The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

  1. SINA M. ADL1,
  2. ALASTAIR G. B. SIMPSON1,
  3. MARK A. FARMER2,
  4. ROBERT A. ANDERSEN3,
  5. O. ROGER ANDERSON4,
  6. JOHN R. BARTA5,
  7. SAMUEL S. BOWSER6,
  8. GUY BRUGEROLLE7,
  9. ROBERT A. FENSOME8,
  10. SUZANNE FREDERICQ9,
  11. TIMOTHY Y. JAMES10,
  12. SERGEI KARPOV11,
  13. PAUL KUGRENS12,
  14. JOHN KRUG13,
  15. CHRISTOPHER E. LANE14,
  16. LOUISE A. LEWIS15,
  17. JEAN LODGE16,
  18. DENIS H. LYNN17,
  19. DAVID G. MANN18,
  20. RICHARD M. MCCOURT19,
  21. LEONEL MENDOZA20,
  22. ØJVIND MOESTRUP21,
  23. SHARON E. MOZLEY-STANDRIDGE22,
  24. THOMAS A. NERAD23,
  25. CAROL A. SHEARER24,
  26. ALEXEY V. SMIRNOV25,
  27. FREDERICK W. SPIEGEL26,
  28. MAX F. J. R. TAYLOR27

Article first published online: 19 OCT 2005

DOI: 10.1111/j.1550-7408.2005.00053.x

Issue

Journal of Eukaryotic Microbiology

Journal of Eukaryotic Microbiology

Volume 52, Issue 5, pages 399–451, October 2005

Additional Information

How to Cite

ADL, S. M., SIMPSON, A. G. B., FARMER, M. A., ANDERSEN, R. A., ANDERSON, O. R., BARTA, J. R., BOWSER, S. S., BRUGEROLLE, G., FENSOME, R. A., FREDERICQ, S., JAMES, T. Y., KARPOV, S., KUGRENS, P., KRUG, J., LANE, C. E., LEWIS, L. A., LODGE, J., LYNN, D. H., MANN, D. G., MCCOURT, R. M., MENDOZA, L., MOESTRUP, Ø., MOZLEY-STANDRIDGE, S. E., NERAD, T. A., SHEARER, C. A., SMIRNOV, A. V., SPIEGEL, F. W. and TAYLOR, M. F. J. R. (2005), The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists. Journal of Eukaryotic Microbiology, 52: 399–451. doi: 10.1111/j.1550-7408.2005.00053.x

Author Information

  1. 1

    Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada, and

  2. 2

    Center for Ultrastructural Research, Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, USA, and

  3. 3

    Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME 04575, USA, and

  4. 4

    Lamont-Dogherty Earth Observatory, Palisades, New York 10964, USA, and

  5. 5

    Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada, and

  6. 6

    Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA, and

  7. 7

    Biologie des Protistes, Université Blaise Pascal de Clermont-Ferrand, F63177 Aubiere cedex, France, and

  8. 8

    Natural Resources Canada, Geological Survey of Canada (Atlantic), Bedford Institute of Oceanography, PO Box 1006 Dartmouth, NS B2Y 4A2, Canada, and

  9. 9

    Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, USA, and

  10. 10

    Department of Biology, Duke University, Durham, North Carolina 27708-0338, USA, and

  11. 11

    Biological Faculty, Herzen State Pedagogical University of Russia, St. Petersburg 191186, Russia, and

  12. 12

    Department of Biology, Colorado State University, Fort Collins, Colorado 805232, USA, and

  13. 13

    Centre for Biodiversity and Conservation Biology, Mycology Section, Royal Ontario Museum, Toronto, ON M5S 2C6 and Department of Botany, University of Toronto, Toronto, ON M5S 3B2, Canada, and

  14. 14

    Department of Biochemistry, Dalhousie University, Halifax, NS B3H 4J1, Canada, and

  15. 15

    Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269, USA, and

  16. 16

    Center for Forest Mycology Research, USDA Forest Service, Forest Products Laboratory, Luquillo, Puerto Rico, and

  17. 17

    Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada, and

  18. 18

    Royal Botanic Garden, Edinburgh, EH3 5LR, United Kingdom, and

  19. 19

    The Academy of Natural Sciences, Philadelphia, Pennsylvania 19103, USA, and

  20. 20

    Medical Technology Program, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-1030, USA, and

  21. 21

    Department of Phycology, Kobenhavns Universitet, Copenhagen DK-1353, Denmark, and

  22. 22

    Department of Plant Biology, University of Georgia, Athens, Geogia 30606, USA, and

  23. 23

    George Mason University, PWII campus, Manassas, Virginia 20110, USA, and

  24. 24

    Department of Plant Biology, University of Illinois, Urbana, Illinois 61801, USA, and

  25. 25

    Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia, and

  26. 26

    Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA, and

  27. 27

    Department of Oceanography, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

*Corresponding Author: Denis H. Lynn, Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada—Telephone number: (519) 826 5724; Fax number: (519) 826 5725; e-mail: ddr@uoguelph.ca

Publication History

  1. Issue published online: 19 OCT 2005
  2. Article first published online: 19 OCT 2005
  3. Received: 05/20/05; accepted: 05/28/05

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Keywords:

  • Algae;
  • amoebae;
  • ciliates;
  • flagellates;
  • fungi;
  • microbiology;
  • microorganisms;
  • parasites;
  • plankton;
  • protozoa;
  • systematics;
  • taxonomy

Abstract

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)

Abstract. This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional “kingdoms.” The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.


Literature Cited

Literature Cited

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Alexopoulos, C. J., Mims, C. W. & Blackwell, M. 1996. Introductory Mycology. 4th ed. John Wiley & Sons, New York.
  • Barr, D. J. S. 1990. Phylum Chytridiomycota. In: Margulis, L., Corliss, J. O., Melkonian, M. & Chapman, D. J. (ed.), Handbook of Protoctista. Jones & Bartlett, Boston. p. 454–466.
  • Barr, D. J. S. 2001. Chytridiomycota. In: McLaughlin, D. J., McLaughlin, E. G. & Lemke, P. A. (ed.), The Mycota. VIIA. Systematics and Evolution. Springer Verlag, Berlin. p. 93–112.
  • Bütschli, O. 1880–1889. Protozoa. Abt. I (1880–1882) Sarkodina und Sporozoa. Abt. II (1883–1887) Mastigophora. Abt. III (1887–1889) Infusoria und System der Radiolaria. In: Bronn, H. G. (ed.), Klassen und Ordnung des Thier-Reichs. Vol. 1, C. F. Winter, Leipzig. Pp. 1–616, 617–1097, 1098–2035.
  • Cavalier-Smith, T. 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol., 52: 297–354.
  • Cavalier-Smith, T. & Chao, E. E. 1997. Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Arch. Protistenkd., 147: 227–236.
  • Cavalier-Smith, T. & Chao, E. E. 2003. Molecular phylogeny of centrohelid Heliozoa, a novel lineage of bikont eukaryotes that arose by ciliary loss. J. Mol. Evol., 56: 387–396.
  • Delwiche, C. F. 1999. Tracing the thread of plastid diversity through the tapestry of life. Am. Nat., 154: S164–S177.
  • Delwiche, C. F., Andersen, R. A., Bhattacharya, D., Mishler, B. & McCourt, R. M. 2004. Algal evolution and the early radiation of green plants. In: Cracraft, J. & Donoghue, M. J. (ed.), Assembling the Tree of Life. Oxford University Press, New York. p. 121–137.
  • Ekelund, F., Daugbjerg, N. & Fredslund, L. 2004. Phylogeny of Heteromita, Cercomonas and Thaumatomonas based on SSU rDNA sequences, including the description of Neocercomonas jutlandica sp. nov., gen. nov. Eur. J. Protistol., 40: 119–135.
  • Emerson, R. & Whisler, H. C. 1968. Cultural studies of Oedogoniomyces and Harpochytrium and a proposal to place them in a new order of aquatic Phycomycetes. Arch. Mikrobiol., 61: 195–211.
  • Eriksson, O. E. & Winka, K. 1997. Supraordinal taxa of Ascomycota. Myconet, 1: 1–16. http://www.umu.se/myconet/Myconet.html.
  • Eriksson, O. E. & Winka, K. 1998. Families and higher taxa of Ascomycota. Myconet, 1: 17–24. http://www.ekbot.umu.se/pmg/18s/fam.rtf.html.
  • Eriksson, O. E., Baral, H. O., Currah, R. S., Hansen, K., Kurtzman, C. P., Læssøe, T. & Rambold, G. 2004. Outline of Ascomycota. Myconet, 10: 1–99. http://www.umu.se/myconet/Myconet.html.
  • Fast, N. M., Xue, L., Bingham, S. & Keeling, P. J. 2002. Re-examining alveolate evolution using multiple protein molecular phylogenies. J. Eukaryot. Microbiol., 49: 30–38.
  • Habura, A., Rosen, D. R. & Bowser, S. S. 2004. Predicted secondary structure of the foraminiferal SSU 3′ major domain reveals a molecular synapomorphy for granuloreticulosean protists. J. Eukaryot. Microbiol., 51: 464–471.
  • Haeckel, E. 1866. Generelle Morphologie der Organismen, Vol. 1, 574 p., Vol. 2, 462 p. Reimer, G., Berlin.
  • Harper, J. T. & Keeling, P. J. 2003. Nucleus-encoded, plastid-targeted glyceraldehydes-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolates plastids. Mol. Biol. Evol., 20: 1730–1735.
  • Harper, J. T., Waanders, E. & Keeling, P. J. 2005. On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int. J. Syst. Evol. Microbiol., 55: 487–496.
  • Hausmann, K., Hülsmann, N. & Radek, R. 2003. Protistology. 3rd ed. Schweizerbart'sche, Stuttgart. 379 p.
  • Hogg, J. 1860. On the distinctions of a plant and an animal, and on a fourth kingdom of nature. Edinburgh New Philos. J., 12 (N.S.): 216–225.
  • James, T. Y., Porter, D., Leander, C. A., Vilgalys, R. & Longcore, J. E. 2000. Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Can. J. Bot., 78: 336–350.
  • Karling, J. S. 1977. Chytridiomycetarum Iconographia. Lubrecht & Cramer, Monticello, New York.
  • Keeling, P. J. 2003. Congruent evidence from α-tubulin and β-tubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genet. Biol., 38: 298–309.
  • Kirk, P. M., Cannon, P. F., David, J. C. & Stalpers, J. A. 2001. Ainsworth & Bisby's Dictionary of the Fungi. 9th ed. CAB International, Wallingford, Oxon, UK.
  • Kooistra, W. H. C. F., De Stefano, M., Mann, D. G. & Medlin, L. K. 2003. The phylogeny of the diatoms. Progr. Mol. Subcell. Biol., 33: 59–97.
  • Kugrens, P., Lee, R. E. & Hill, D. R. A. 2002. Order Cryptomonadida. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Society of Protozoologists, Lawrence, KS. (Year 2000). p. 1111–1125.
  • Levine, N. D., Corliss, J. O., Cox, F. E. G., Deroux, G., Grain, J., Honigberg, B. M., Leedale, G. F., Loeblich, A. R., Lom, J., Lynn, D. H., Merinfeld, D., Page, F. C., Poljansky, G., Sprague, V., Vavra, J. & Wallace, F. G. 1980. A newly revised classification of the Protozoa. J. Protozool., 27: 37–58.
  • Liu, Y. J. & Hall, B. D. 2004. Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc. Natl. Acad. Sci. (USA), 101: 4507–4512.
  • Loeblich, A. R. & Tappan, H. 1988. Foraminiferal Genera and their Classification. Vols. 1–2. Van Nostrand Reinhold, New York.
  • Lutzoni, F., Kauff, F., Cox, C. J., McLaughlin, D., Celio, G., Dentinger, B., Padamsee, M., Hibbett, D., James, T. Y., Baloch, E., Grube, M., Reeb, V., Hofstetter, V., Schoch, C., Arnold, A. E., Miadlikowska, J., Spatafora, J., Johnson, D., Hambleton, S., Crockett, M., Shoemaker, R., Sung, G.-H., Lücking, R., Lumbsch, T., O'Donnell, K., Binder, M., Diederich, P., Ertz, D., Gueidan, C., Hansen, K., Harris, R. C., Hosaka, K., Lim, Y.-W., Matheny, B., Nishida, H., Pfister, D., Rogers, J., Rossman, A., Schmitt, I., Sipman, H., Stone, J., Sugiyama, J., Yahr, R. & Vilgalys, R. 2004. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am. J. Bot., 91: 1446–1480.
  • Medlin, L. K. & Kaczmarska, I. 2004. Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. Phycologia, 43: 245–270.
  • Patterson, D. J. 1989. Stramenopiles, chromophytes from a protistan perspective. In: Green, J. C., Leadbeater, B. S. C. & Diver, W. L. (ed.), The Chromophyte Algae, Problems and Perspectives. Clarendon Press, Oxford. p. 357–379.
  • Patterson, D. J. 2002. Changing views of protistan systematics: the taxonomy of protozoa—an overview. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Allen Press, Society of Protozoologists, Lawrence, KS. p. 2–9.
  • Pawlowski, J. 2000. Introduction to the molecular systematics of foraminifera. Micropaleontology, 46 (Suppl. 1): 1–12.
  • Pawlowski, J., Holzmann, M., Fahrni, J. & Richardson, S. L. 2003a. Small subunit ribosomal DNA suggests that the Xenophorean Syringammina corbicula is a foraminiferan. J. Eukaryot. Microbiol., 50: 483–487.
  • Pawlowski, J., Holzmann, M., Berney, C., Fahrni, J., Cedhagen, T., Habura, A. & Bowser, S. S. 2002. Phylogeny of allogromiid Foraminifera inferred from SSU rRNA gene sequences. J. Foram. Res., 32: 334–343.
  • Pawlowski, J., Holzmann, M., Berney, C., Fahrni, J., Gooday, A. J., Cedhagen, T., Habura, A. & Bowser, S. S. 2003b. The evolution of early Foraminifera. Proc. Natl. Acad. Sci. (USA), 100: 11494–11498.
  • Round, F. E., Crawford, R. M. & Mann, D. G. 1990. The Diatoms. Biology and Morphology of the Genera. Cambridge University Press, Cambridge.
  • Simpson, A. G. B. & Roger, A. J. 2002. Eukaryotic evolution: getting to the root of the problem. Curr. Biol., 12: R691–R693.
  • Simpson, A. G. B. & Roger, A. 2004. Excavata and the origin of the amitochondriate eukaryotes. In: Hirt, P. H. & Horner, D. S. (ed.), Organelles, Genomes and Eukaryotic Phylogeny. CRC Press, Boca Raton. p. 27–53.
  • Sparrow, F. K. 1960. The Aquatic Phycomycetes. University of Michigan Press, Ann Arbor, MI.
  • Walsh, D. A. & Doolittle, F. W. 2005. The real “domains” of life. Curr. Biol., 15: R237–R240.
  • Yoon, H. S., Hackett, J. D., Pinto, G. & Bhattacharya, D. 2002. The single ancient origin of chromist plastids. Proc. Natl. Acad. Sci., 99: 15507–15512.

APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Cavalier-Smith, T. & Chao, E. E. 2004. Protalveolate phylogeny and systematics and the origins of Sporozoa and dinoflagellates. Eur. J. Protistol., 40: 185–212.
  • Fast, N.M, Xue, L., Bingham, S. & Keeling, P. J. 2002. Re-examining alveolate evolution using multiple protein molecular phylogenies. J. Eukaryot. Microbiol., 49: 30–38.
  • Fensome, R. A., Taylor, F. J. R., Norris, G., Sarjeant, W. A. S., Wharton, D. I. & Williams, G. L. 1993. A classification of fossil and living dinoflagellates. Micropaleontology, Special Paper No. 7, 351 p.
  • Fensome, R. A., Saldarriaga, J. F. & Taylor, F. J. R. 1999. Dinoflagellate phylogeny revisited: reconciling morphological and molecular-based phylogenies. Grana, 38: 66–80.
  • Lynn, D. H. 2004. Morphology or molecules: how do we identify the major lineages of ciliates (Phylum Ciliophora)? Eur. J. Protistol., 39 (Year 2003): 356–364.
  • Lynn, D. H. & Corliss, J. O. 1991. Ciliophora. In: Harrison, F. W. & Corliss, J. O. (ed.), Microscopic Anatomy of Invertebrates. Alan R. Liss, New York. Ch. 5, p. 333–467.
  • Lynn, D. H. & Small, E. B. 2002. Phylum Ciliophora. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Society of Protozoologists, Lawrence, KS. p. 371–656.
  • Puytorac, P. de, Batisse, A., Deroux, G., Fleury, A., Grain, J., Laval-Peuto, M. & Tuffrau, M. 1993. Proposition d'une nouvelle classification du phylum des protozoaires Ciliophora Doflein, 1901. C. R. Acad. Sci., Paris, 316: 716–720.

AMOEBOZOA

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Amaral Zettler, L. A., Nerad, T. A., O'Kelly, C. J., Peglar, M. T., Gillevet, P. M., Silberman, J. D. & Sogin, M. L. 2000. A molecular reassessment of the leptomyxid amoebae. Protist, 151: 275–282.
  • Bolivar, I., Fahrni, J. F., Smirnov, A. & Pawlowski, J. 2001. SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): the origin of Gymnamoebae revisited. Mol. Biol. Evol., 18: 2306–2314.
  • Cavalier-Smith, T. 1998. A revised six-kingdom system of life. Biol. Rev., 73: 203–266.
  • Cavalier-Smith, T. & Chao, E. E. 2003. Molecular phylogeny of centrohelid Heliozoa, a novel lineage of bikont eukaryotes that arose by ciliary loss. J. Mol. Evol., 56: 387–396.
  • Edgcomb, V. P., Simpson, A. G., Zettler, L. A., Nerad, T. A., Patterson, D. J., Holder, M. E. & Sogin, M. L. 2002. Pelobionts are degenerate protists: insights from molecules and morphology. Mol. Biol. Evol., 19: 978–982.
  • Fahrni, J. F., Bolivar, I., Berney, C., Nassonova, E., Smirnov, A. & Pawlowski, J. 2003. Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes. Mol. Biol. Evol., 20: 1881–1886.
  • Meisterfeld, R. 2002. Order Arcellinida Kent 1880. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Society of Protozoologists, Lawrence, KS. (Year 2000). p. 827–860.
  • Milyutina, I. A., Aleshin, V. V., Mikrjukov, K. A., Kedrova, O. S. & Petrov, N. B. 2001. The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris: its rRNA predicted secondary structure and phylogenetic implication. Gene, 272: 131–139.
  • Olive, L. S. 1970. The Mycetozoa: a revised classification. Bot. Rev., 36: 59–87.
  • Olive, L. S. 1975. The Mycetozoans. Academic Press, New York.
  • Page, F. C. 1987. The classification of “naked” amoebae (Phlyum Rhizopoda). Arch. Protistenkd., 133: 199–217.
  • Page, F. C. 1991. Nackte Rhizopoda. In: Page, F. C. & Siemensma, F. J. (ed.), Nackte Rhizopoda und Heliozoa. Gustav Fischer Verlag, Stuttgart, New York.
  • Peglar, M. T., Amaral Zettler, L. A., Anderson, O. R., Nerad, T. A., Gillevet, P. M., Mullen, T. E., Frasca Jr., S., Silberman, J. D., O'Kelly, C. J. & Sogin, M. L. 2003. Two new small-subunit ribosomal RNA gene lineages within the subclass Gymnamoebia. J. Eukaryot Microbiol., 50: 224–332.
  • Smirnov, A. V. 1999. An illustrated survey of gymnamoebae—Euamoebida and Leptomyxida (Rhizopoda, Lobosea), isolated from an anaerobic sediments of the Nivaa Bay (Baltic Sea, The Sound). Ophelia, 50: 113–148.
  • Smirnov, A. V. & Goodkov, A. V. 1993. Paradermamoeba valamo gen. n., sp., n. (Gymnamoebia, Thecamoebidae)—a freshwater amoeba from bottom sediments. Zool. Zh., 72: 5–11.
  • Smirnov, A. V., Nassonova, E. S., Berney, C., Fahrni, J., Bolivar, I. & Pawlowski, J. 2005. Molecular phylogeny and classification of the lobose amoebae. Protist, 156: 129–142.
  • Spiegel, F. W. 1990. Phylum plasmodial slime molds, Class Protostelida. In: Margulis, L., Corliss, J. O., Melkonian, M. & Chapman, D. (ed.), Handbook of Protoctista. Jones & Bartlett, Boston. p. 484–497.

APUSOMONADIDAE

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Cavalier-Smith, T. & Chao, E. E. 1995. The opalozoan Apusomonas is related to the common ancestor of animals, fungi and choanoflagellates. Proc. Roy. Soc. Lond. B, 261: 1–6.
  • Cavalier-Smith, T. & Chao, E. E. 2003. Phylogeny of Choanozoa, Apusozoa, and other Protozoa and early eukaryote megaevolution. J. Mol. Evol., 56: 540–563.
  • Karpov, S. A. & Myl'nikov, A. P. 1989. Biology and ultrastructure of colourless flagellates Apusomonadida ord. n. Zool. Zhurn., 68: 5–17. (in Russian)
  • Patterson, D. J., Vørs, N., Simpson, A. G. B. & O'Kelly, C. 2002. Residual heterotrophic flagellates. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Society of Protozoologists, Lawrence, KS. (Year 2000). p. 1302–1327.

ARCHAEPLASTIDA

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Bremer, K. 1985. Summary of green plant phylogeny and classification. Cladistics, 1: 369–385.
  • Lewis, L. A. & McCourt, R. M. 2004. Green algae and the origin of land plants. Am. J. Bot., 91: 1535–1556.
  • McCourt, R. M., Delwiche, C. F. & Karol, K. G. 2004. Charophyte algae and land plant origins. Tr. Ecol. Evol., 19: 661–666.
  • Saunders, G. W. & Hommersand, M. H. 2004. Assessing red algal supra-ordinal diversity and taxonomy in the context of contemporary systematic data. Am. J. Bot., 91: 1494–1507.

CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Cho, G. Y., Lee, S. H. & Boo, S. M. 2004. A new brown algal order, Ishigeales (Phaeophyceae), established on the basis of plastid protein-coding rbcL, psaA, and psbA region comparisons. J. Phycol., 40: 921–936.
  • Delwiche, C. F. 1999. Tracing the thread of plastid diversity through the tapestry of life. Am. Nat., 154: S164–S177.
  • Draisma, S. G. A., Peters, A. F. & Fletcher, R. L. 2003. Evolution and taxonomy in the Phaeophyceae: effects of the molecular age on brown algal systematics. In: Norton, T. A. (ed.), Out of the Past. Collected Reviews to Celebrate the Jubilee of the British Phycological Society. The British Phycological Society, Belfast. p. 87–102.
  • Draisma, S. G. A., Prud'homme van Reine, W. F., Stam, W. T. & Olsen, J. L. 2001. A reassessment of phylogenetic relationships in the Phaeophyceae based on RUBISCO large subunit and ribosomal DNA sequences. J. Phycol., 37: 586–603.
  • Fresnel, J. & Probert, I. 2005. The ultrastructure and life cycle of the coastal coccolithophorid Ochrosphaera neapolitana (Prymnesiophyceae). Eur. J. Phycol., 40: 105–122.
  • Harper, J. T. & Keeling, P. J. 2003. Nucleus-encoded, plastid-targeted glyceraldehydes-3-phosphate dehycrogenase (GAPDH) indicates a single origin for chromalveolates plastids. Mol. Biol. Evol., 20: 1730–1735.
  • Hoef-Emden, K. & Melkonian, M. 2003. Revision of the genus Cryptomonas (Cryptophyceae): a combination of molecular phylogeny and morphology provides insights into a long-hidden dimorphism. Protist, 154: 371–409.
  • Keeling, P. J. 2003. Congruent evidence from α-tubulin and β-tubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genet. Biol., 38: 298–309.
  • Kooistra, W. H. C. F., De Stefano, M., Mann, D. G. & Medlin, L. K. 2003. The phylogeny of the diatoms. Progr. Mol. Subcell. Biol., 33: 59–97.
  • Kugrens, P. & Lee, R. E. 1987. An ultrastructural survey of cryptomonad periplasts using quick-freezing freeze-fracture techniques. J. Phycol., 23: 365–376.
  • Kugrens, P., Clay, B. L. & Lee, R. E. 1999. Ultrastructure and systematics of two new freshwater red cryptomonads, Storeatula rhinosa, sp. nov. and Pyrenomonas ovalis, sp. nov. J. Phycol., 35: 1079–1089.
  • Kugrens, P., Lee, R. E. & Hill, D. R. A. 2002. Order Cryptomonadida. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Society of Protozoologists, Lawrence, KS. (Year 2000). p. 1111–1125.
  • Medlin, L. K. & Kaczmarska, I. 2004. Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. Phycologia, 43: 245–270.
  • Novarino, G. 2003. A companion to the identification of cryptomonad flagellates (Cryptophyceae=Cryptomonadea). Hydrobiologia, 502: 225–270.
  • Patterson, D. J. 1989. Stramenopiles, chromophytes from a protistan perspective. In: Green, J. C., Leadbeater, B. S. C. & Diver, W. L. (ed.), The Chromophyte Algae, Problems and Perspectives. Clarendon Press, Oxford. p 357–379.
  • Peters, A. F. & Ramírez, M. E. 2001. Molecular phylogeny of small brown algae, with special reference to the systematic position of Caepidium antarcticum (Adenocystaceae, Ectocarpales). Cryptogamie, Algol., 22: 187–200.
  • Peters, A. F. & Clayton, M. N. 1998. Molecular and morphological investigation of three brown algal genera with stellate plastids: evidence for Scytothamnales ord. nov. (Phaeophyceae). Phycologia, 37: 106–113.
  • Round, F. E., Crawford, R. M. & Mann, D. G. 1990. The Diatoms. Biology and Morphology of the Genera. Cambridge University Press, Cambridge.
  • Rousseau, F. & De Reviers, B. 1999a. Phylogenetic relationships within the Fucales (Phaeophyceae) based on combined partial SSU+LSU rDNA sequence data. Eur. J. Phycol., 34: 53–64.
  • Rousseau, F. & De Reviers, B. 1999b. Circumscription of the order Ectocarpales (Phaeophyceae): bibliographical synthesis and molecular evidence. Cryptogamie, Algol., 20: 5–18.
  • Rousseau, F., Burrowes, R., Peters, A. F., Kuhlenkamp, R. & De Reviers, B. 2001. A comprehensive phylogeny of the Phaeophyceae based on nrDNA sequences resolves the earliest divergences. C. R. Acad. Sci. Paris III, 324: 305–319.
  • Silva, P. C. & De Reviers, B. 2000. Ordinal names in the Phaeophyceae. Cryptogamie, Algol., 21: 49–58.
  • Sym, S. & Kawachi, M. 2000. Ultrastructure of Calyptrosphaera radiata, sp. nov. (Pyrmnesiophyceae, Haptophyta). Eur. J. Phycol., 35: 283–293.
  • Yoon, H. S., Hackett, J. D., Pinto, G. & Bhattacharya, D. 2002. The single ancient origin of chromist plastids. Proc. Natl. Acad. Sci. (USA), 99: 15507–15512.

EXCAVATA

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Busse, I. & Preisfeld, A. 2002. Systematics of primary osmotrophic euglenids: a molecular approach to the phylogeny of Distigma and Astasia (Euglenozoa). Int. J. Syst. Evol. Microbiol., 53: 617–624.
  • O'Kelly, C. J., Silberman, J. D., Amaral Zettler, L. A., Nerad, T. A. & Sogin, M. L. 2003. Monopylocystis visvesvarai. n. gen., n. sp. and Sawyeria marylandensis n. gen., n. sp: two new amitochondrial heterolobosean amoebae from anoxic environments. Protist, 154: 281–290.
  • Moreira, D., Lopez-Garcia, P. & Vickerman, K. 2004. An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea. Int. J. Syst. Evol. Microbiol., 54: 1861–1865.
  • Simpson, A. G. B. 1997. The identity and composition of the Euglenozoa. Archiv. Protist., 148: 318–328.
  • Simpson, A. G. B. 2003. Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). Int. J. Syst. Evol. Microbiol., 53: 1759–1779.
  • Simpson, A. G. B. & Roger, A. J. 2004. Excavata and the origin of the amitochondriate eukaryotes. In: Hirt, P. H. & Horner, D. S. (ed.), Organelles, genomes and eukaryotic phylogeny. CRC Press, Boca Raton, FL. p. 27–53.
  • Simpson, A. G. B., Gill, E. E., Callahan, H. A., Litaker, R. W. & Roger, A. J. 2004. Early evolution within kinetoplastids (Euglenozoa) and the late emergence of trypanosomatids. Protist, 155: 407–422.

FORAMINIFERA

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Archibald, J. M., Longet, D., Pawlowski, J. & Keeling, P. J. 2003. A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol., 20: 62–66.
  • Bowser, S. S. & Travis, J. L. 2002. Reticulopodia: structural and behavioral basis for the suprageneric placement of Granuloreticulosan protists. J. Foram. Res., 32: 440–447.
  • Habura, A., Rosen, D. R. & Bowser, S. S. 2004. Predicted secondary structure of the foraminiferal SSU 3′ major domain reveals a molecular synapomorphy for granuloreticulosean protists. J. Eukaryot. Microbiol., 51: 464–471.
  • Keeling, P. J. 2001. Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Mol. Biol. Evol., 18: 1551–1557.
  • Lee, J. J., Pawlowski, J., Debenay, J.-P., Whittaker, J., Banner, F., Gooday, A. J., Tendal, O., Haynes, J. & Faber, W. W. 2002. Phylum Granuloreticulosa. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Society of Protozoologists, Lawrence, KS. (Year 2000). p. 872–951.
  • Loeblich, A. R. & Tappan, H. 1988. Foraminiferal Genera and their Classification. Vols. 1–2. Van Nostrand Reinhold, New York.
  • Longet, D., Archibald, J. M., Keeling, P. J. & Pawlowski, J. 2003. Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies. Int. J. Syst. Evol. Microbiol., 53: 1735–1739.
  • Pawlowski, J. 2000. Introduction to the molecular systematics of foraminifera. Micropaleontology, 46 (Suppl. 1): 1–12.
  • Pawlowski, J., Holzmann, M., Fahrni, J. & Richardson, S. L. 2003a. Small subunit ribosomal DNA suggests that the Xenophorean Syringammina corbicula is a foraminiferan. J. Eukaryot. Microbiol., 50: 483–487.
  • Pawlowski, J., Holzmann, M., Berney, C., Fahrni, J., Cedhagen, T., Habura, A. & Bowser, S. S. 2002. Phylogeny of allogromiid Foraminifera inferred from SSU rRNA gene sequences. J. Foram. Res., 32: 334–343.
  • Pawlowski, J., Holzmann, M., Berney, C., Fahrni, J., Gooday, A. J., Cedhagen, T., Habura, A. & Bowser, S. S. 2003b. The evolution of early Foraminifera. Proc. Natl. Acad. Sci. (USA), 100: 11494–11498.
  • Sen Gupta, B. K. 1999. Modern Foraminifera. Kluwer Academic Publishers, Dordrecht, The Netherlands.
  • Travis, J. L. & Bowser, S. S. 1991. The Motility of Foraminifera. In: Lee, J. J. & Anderson, O. R. (ed.), Biology of Foraminifera. Academic Press, London. p. 91–155.

FUNGI

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Alexopoulos, C. J., Mims, C. W. & Blackwell, M. 1996. Introductory Mycology. 4th ed. John Wiley & Sons, New York.
  • Barr, D. J. S. 1990. Phylum Chytridiomycota. In: Margulis, L., Corliss, J. O., Melkonian, M. & Chapman, D. J. (ed.), Handbook of Protoctista. Jones & Bartlett, Boston. p. 454–466.
  • Barr, D. J. S. 2001. Chytridiomycota. In: McLaughlin, D. J., McLaughlin, E. G. & Lemke, P. A. (ed.), The Mycota. VIIA. Systematics and Evolution. Springer Verlag, Berlin. p. 93–112.
  • Bauer, R., Oberwinkler, F. & Vinky, K. 1997. Ultrastructure markers and systematics in smut fungi and allied taxa. Can. J. Bot., 73: 1273–1275.
  • Bauer, R., Begerow, D., Oberwinkler, F., Piepenbring, M. & Berbee, M. L. 2001. Ustilaginomycetes. In: McLaughlin, D. J., McLaughlin, E. G. & Lemke, P. A. (ed.), The Mycota VII: Part B. Systematics and Evolution. Springer Verlag, Berlin. p. 57–83.
  • Begerow, D., Baur, R. & Oberwinkler, F. 1997. Phylogenetic studies on nuclear large subunit ribosomal DNA sequences of smut fungi and related taxa. Can. J. Bot., 75: 2045–2056.
  • Benny, G. L. 2001. Zygomycota: Trichomycetes. In: McLaughlin, D. J., McLaughlin, E. G. & Lemke, P. A. (ed.), The Mycota VII. Systematics and Evolution. Part A. Springer-Verlag, New York. p. 147–160.
  • Benny, G. L., Humber, R. A. & Morton, J. B. 2001. Zygomycota: Zygomycetes. In: McLaughlin, D. J., McLaughlin, E. G. & Lemke, P. A. (ed.), The Mycota VII. Systematics and Evolution. Part A. Springer-Verlag, New York. p. 113–146.
  • Cavalier-Smith, T. 2001. What are fungi? In: McLaughlin, D. J., McLaughlin, E. G. & Lemke, P. A. (ed.), The Mycota VII, Part A, Systematics. Springer-Verlag, New York. p. 3–37.
  • Dick, M. W. 2001. Straminipilous Fungi: Systematics of the Peronosporomycetes including Accounts of the Marine Straminipilous Protists, the Pasmodiophorids and Similar Organisms. Kluwer Academic Publishers, Dordrecht.
  • Eriksson, O. E. & Winka, K. 1997. Supraordinal taxa of Ascomycota. Myconet, 1: 1–16. http://www.umu.se/myconet/Myconet.html
  • Eriksson, O. E. & Winka, K. 1998. Families and higher taxa of Ascomycota. Myconet, 1: 17–24. http://www.ekbot.umu.se/pmg/18s/fam.rtf.html
  • Eriksson, O. E., Baral, H. O., Currah, R. S., Hansen, K., Kurtzman, C. P., Læssøe, T. & Rambold, G. 2004. Outline of Ascomycota. Myconet, 10: 1–99. http://www.umu.se/myconet/Myconet.html
  • Emerson, R. & Whisler, H. C. 1968. Cultural studies of Oedogoniomyces and Harpochytrium and a proposal to place them in a new order of aquatic Phycomycetes. Arch. Mikrobiol., 61: 195–211.
  • Fast, N. M., Logsdon, J. M. Jr. & Doolittle, W. F. 1999. Phylogenetic analysis of the TATA box binding protein (TBP) gene from Nosema locustae: evidence for a Microsporidia-Fungi relationship and spliceosomal intron loss. Mol. Biol. Evol., 16: 1415–1419.
  • Gargas, A., DePriest, P. T., Grube, M. & Tehler, A. 1995. Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. Science, 268: 1492–1495.
  • Hirt, R. P., Logsdon, J. M. Jr., Healy, B., Dorey, M. W., Doolittle, W. F. & Embley, T. M. 1999. Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc. Natl. Acad. Sci. (USA), 96: 580–585.
  • James, T. Y., Porter, D., Leander, C. A., Vilgalys, R. & Longcore, J. E. 2000. Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Can. J. Bot., 78: 336–350.
  • Karling, J. S. 1977. Chytridiomycetarum Iconographia. Lubrecht & Cramer, Monticello, New York.
  • Keeling, P. J. 2003. Congruent evidence from α tubulin and β tubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genet. Biol., 38: 298–309.
  • Kirk, P. M., Cannon, P. F., David, J. C. & Stalpers, J. A. 2001. Ainsworth & Bisby's Dictionary of the Fungi. 9th ed. CAB International, Wallingford, Oxon, UK.
  • Liu, Y. J. & Hall, B. D. 2004. Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc. Natl. Acad. Sci. (USA), 101: 4507–4512.
  • Lumbsch, H. T., Schmitt, I., Lindemuth, R., Miller, A., Mangold, A., Fernandez, F. & Huhndorf, S. 2000. Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta). Mol. Phylogenet. Evol., 34: 512–524.
  • Lutzoni, F., Kauff, F., Cox, C. J., McLaughlin, D., Celio, G., Dentinger, B., Padamsee, M., Hibbett, D., James, T. Y., Baloch, E., Grube, M., Reeb, V., Hofstetter, V., Schoch, C., Arnold, A. E., Miadlikowska, J., Spatafora, J., Johnson, D., Hambleton, S., Crockett, M., Shoemaker, R., Sung, G.-H., Lücking, R., Lumbsch, T., O'Donnell, K., Binder, M., Diederich, P., Ertz, D., Gueidan, C., Hansen, K., Harris, R. C., Hosaka, K., Lim, Y.-W., Matheny, B., Nishida, H., Pfister, D., Rogers, J., Rossman, A., Schmitt, I., Sipman, H., Stone, J., Sugiyama, J., Yahr, R. & Vilgalys, R. 2004. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am. J. Bot., 91: 1446–1480.
  • Moncalvo, J.-M. 2005. Molecular systematics—major fungal phylogenetic groups and fungal species concepts. In: Xu., J.-P. (ed.), Evolutionary Genetics of Fungi. Horizon Scientific Press, Wymondham, Norfolk, UK. (in press)
  • Nishida, H. & Sugiyama, J. 1994. Archiascomycetes: detection of a major new linage within the Ascomycota. Mycoscience, 35: 361–366.
  • Schüßler, A., Schwarzott, D. & Walker, C. 2001. A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol. Res., 105: 1413–1421.
  • Shaffer, R. L. 1975. The major groups of Basidiomycetes. Mycologia, 75: 1011–1018.
  • Sparrow, F. K. 1960. The Aquatic Phycomycetes. University of Michigan Press, Ann Arbor, MI.
  • Swann, E. C. & Taylor, J. W. 1995. Phylogenetic perspectives on Basidiomycete systematics: evidence from the 18S rRNA gene. Can. J. Bot., 73 (Suppl. 1): S862–S868.
  • Swann, E. C., Frieders, E. M. & McLaughlin, D. J. 2001. Urediniomycetes. In: McLaughlin, D. J., McLaughlin, E. G. & Lemke, P. A. (ed.), The Mycota VII Part B. Systematics and Evolution. Springer Verlag, Berlin. p. 37–83.
  • Tanabe, Y., O'Donnell, K., Saikawa, M. & Sugiyama, J. 2000. Molecular phylogeny of parasitic Zygomycota (Dimargaritales, Zoopagales) based on nuclear small subunit ribosomal DNA sequences. Mol. Phylogenet. Evol., 16: 253–262.
  • Tanabe, Y., Saikawa, M., Watanabe, M. M. & Sugiyama, J. 2004. Molecular phylogeny of Zygomycota based on EF-1 and RPB1 sequences: limitations and utility of alternative markers to rDNA. Mol. Phylogenet. Evol., 30: 438–449.

HELIOZOA

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Cavalier-Smith, T. & Chao, E. E. 2003. Molecular phylogeny of centrohelid Heliozoa, a novel lineage of bikont eukaryotes that arose by ciliary loss. J. Mol. Evol., 56: 387–396.
  • Mikrjukov, K. A. 2000. System and phylogeny of Heliozoa: should this taxon exist in modern systems of protists? Zool. Zhur., 79: 883–897.
  • Nikolaev, S. I., Berny, C., Fahrni, J., Bolivar, I., Polet, S., Myl'nikov, A. P., Aleshin, V. V., Petrov, N. B. & Pawlowski, J. 2004. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc. Natl. Acad. Sci. (USA), 101: 8066–8071.
  • Nikolaev, S. I., Berny, C., Fahrni, J., Myl'nikov, A. P., Petrov, N. B. & Pawlowski, J. 2003. Genetic relationships between desmothoracid Heliozoa and Gymnophryid amoebas as evidenced by comparison of the nucleotide sequences of 18S rRNA genes. Doklady Biol. Sci., 393: 553–556.

OPISTHOKONTA (SEE ALSO FUNGI)

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Adoutte, A., Balavoine, G., Lartillot, N., Lespinet, O., Prud'homme, B. & De Rosa, R. 2000. The new animal phyogeny: reliability and implications. Proc. Natl. Acad. Sci. (USA), 97: 4453–4456.
  • Borchiellini, C., Chombard, C., Manuel, M., Alivon, E., Vacelet, J. & Boury-Esnault, N. 2004. Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution. Mol. Phylogenet. Evol., 32: 823–837.
  • Borchiellini, C., Manuel, M., Alivon, E., Le Parco, Y., Vacelet, J. & Boury-Esnault, N. 2003. Phylogeny and evolution of calcareous sponges: monophyly of Calcinea and Calcaronea, high level of morphological homoplasy, and the primitive nature of axial symmetry. Syst. Biol., 52: 311–333.
  • Cavalier-Smith, T. & Chao, E. E. 1995. The opalozoan Apusomonas is related to the common ancestor of animals, fungi and choanoflagellates. Proc. Roy. Soc. Lond. B, 261: 1–6.
  • Cavalier-Smith, T. & Chao, E. E. 1997. Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Arch. Protistenkd., 147: 227–236.
  • Cavalier-Smith, T. & Chao, E. E. 2003. Phylogeny of Choanozoa, Apusozoa, and other Protozoa and early eukaryote megaevolution. J. Mol. Evol., 56: 540–563.
  • Eriksson, O. E., Baral, H.-O., Currah, R. S., Hansen, K., Kurtzman, C. P., Rambold, G. & Laessøe, T. 2004. Outline of Ascomycota. Myconet, 10: 1–99.
  • Gromov, B. V. 2000. Algal parasites of the genera Aphelidium, Amoeboaphelidium, and Pseudoaphelidium from the Cienkovski's “Monadinea” group as representatives of a new class. Zool. Zhurn., 79: 517–525.
  • Hertel, L. A., Bayne, C. J. & Loker, E. S. 2002. The symbiont Capsaspora owczarzaki, nov. gen. nov. sp., isolated from three strains of the pulmonate snail Biomphalaria glabrata is related to members of the Mesomycetozoea. Int. J. Parasitol., 32: 1183–1191.
  • Karpov, S. A. & Leadbeater, B. S. C. 1997. Cell and nuclear division in freshwater choanoflagellate Monosiga ovata. Eur. J. Protistol., 33: 323–334.
  • Karpov, S. A. & Leadbeater, B. S. C. 1998. The cytoskeleton structure and composition in choanoflagellates. J. Eukaryot. Microbiol., 45: 361–367.
  • Leadbeater, B. S. C. & Thomson, H. 2002. Choanoflagellata. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Society of Protozoologists, Lawrence, KS. (Year 2000). p. 14–38.
  • Medina, M., Collins, A. G., Silberman, J. D. & Sogin, M. L. 2001. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc. Natl. Acad. Sci. (USA), 98: 9707–9712.
  • Mendoza, L., Taylor, J. W. & Ajello, L. 2002. The class Mesomycetozoa: a heterogeneous group of microorganisms at the animal-fungal boundary. Ann. Rev. Microbiol., 56: 315–344.
  • Mollicone, M. R. & Longcore, J. E. 1999. Zoospore ultrastructure of Gonapodya polymorpha. Mycologia, 91: 727–734.
  • Raghu-Kumar, S. 1987. Occurrence of the thraustochytrid, Corallochytrium limacisperum gen. et sp. nov. in the coral reef lagoons of the Lakshadweep Islands in the Arabian Sea. Bot. Mar., 30: 83–89.
  • Ruiz-Trillo, I., Inagaki, Y., Davis, L. A., Landfald, B. & Roger, A. J. 2004. Capsaspora owczazaki is an independent opisthokont lineage. Curr. Biol., 14: R946–R947.
  • Tong, S. M. 1997. Heterotrophic flagellates and other protists from Southampton waters, UK. Ophelia, 47: 71–131.
  • Wallberg, A., Thollesson, M., Farris, J. S. & Jondelius, U. 2004. The phylogenetic position of the comb-jellies (Ctenophora) and the importance of taxonomic sampling. Cladistics, 20: 558–578.
  • Zhukov, B. F. & Karpov, S. A. 1985. Freshwater choanoflagellates. L. Nauka (in Russian with English contents)
  • Zrvavy, J., Mihulka, S., Kepka, P. & Bezdek, A. 1998. Phylogeny of the Metazoa based on morphological and 18S ribosomal DNA evidence. Cladistics, 14: 249–285.

RADIOLARIA

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Amaral Zettler, L., Sogin, M. L. & Caron, D. A. 1997. Phylogenetic relationships between the Acantharea and the Polycystinea: a molecular perspective on Haeckel's Radiolaria. Proc. Natl. Acad. Sci. (USA), 94: 1141–1416.
  • Anderson, O. R. 1983. Radiolaria. Springer-Verlag, New York.
  • Anderson, O. R., Nigrini, C., Boltovskoy, D., Takahashi, K. & Swanberg, N. R. 2002. Class Polycystinea. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Society of Protozoologists, Lawrence, KS. (Year 2000). p. 994–1022.
  • Polet, S., Berney, C., Fahrni, J. & Pawlowski, J. 2004. Small-subunit ribosomal RNA gene sequences of Phaeodarea challenge the monophyly of Haeckel's Radiolaria. Protist, 155: 53–63.
  • Riedel, W. R. 1971. Systematic classification of polycystine Radiolaria. In: Riedel, W. R. & Funnell, B. M. (ed.), The Micropaleontology of Oceans. Cambridge University Press, Cambridge. p. 649–660.
  • Takahashi, K. & Anderson, O. R. 2002. Class Phaeodaria. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Society of Protozoologists, Lawrence, KS. (Year 2000). p. 981–994.

RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)

  1. Top of page
  2. Abstract
  3. Acknowledgments
  4. Literature Cited
  5. APPENDIX 1. SELECTED REFERENCES TO PROTIST GROUPS ALVEOLATA
  6. AMOEBOZOA
  7. APUSOMONADIDAE
  8. ARCHAEPLASTIDA
  9. CHROMALVEOLATA/STRAMENOPILES/CRYPTOPHYCEAE/HAPTOPHYTA
  10. EXCAVATA
  11. FORAMINIFERA
  12. FUNGI
  13. HELIOZOA
  14. OPISTHOKONTA (SEE ALSO FUNGI)
  15. RADIOLARIA
  16. RHIZARIA (SEE ALSO FORAMINIFERA AND RADIOLARIA)
  • Cavalier-Smith, T. & Chao, E. E. 1997. Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Arch. Protistenkd., 147: 227–236.
  • Cavalier-Smith, T. & Chao, E. E. 2003. Phylogeny and classification of phylum Cercozoa (Protozoa). Protist, 154: 341–358.
  • Ekelund, F., Daugbjerg, N. & Fredslund, L. 2004. Phylogeny of Heteromita, Cercomonas and Thaumatomonas based on SSU rDNA sequences, including the description of Neocercomonas jutlandica sp. nov., gen. nov. Eur. J. Protistol., 40: 119–135.
  • Flavin, M., O'Kelly, C. J., Nerad, T. A. & Wilkinson, G. 2000. Cholamonas cyrtodiopsidis gen.n., sp., (Cercomonadida), an endocommensal, mycophagous heterotrophic flagellate with a doubled kinetid. Acta Protozool., 39: 51–60.
  • Hibberd, D. J. 1983. Ultrastructure of the colonial colourless zooflagellates Phalansterium digitatum Stein (Phalansteriida ord. nov.) and Spongomonas uvella Stein (Spongomonadida ord. nov.). Protistologica. 19: 523–535.
  • Hibberd, D. J. 1985. Observations on the ultrastructure of the species of Pseudodendromonas Bourrelli (P. operculifera and P. insignis) and Cyathobodo Petersen et Hansen (C. peltatus and C. gemmatus), Pseudodendromonadida ord.nov. Arch. Protistenk., 129: 3–11.
  • Karpov, S. A. 1990. Analysis of the orders Phalansteriida, Spongomonadida and Thaumatomonadida. Zool. Zhurn., 69: 5–12. (in Russian)
  • Karpov, S. A. 2000. Ultrastructure of the aloricate bicosoecid Pseudobodo tremulans, with revision of the order Bicosoecida. Protistology, 1: 100–108.
  • Karpov, S. A. & Zhukov, B. F. 1987. Cytological peculiarities of colourless flagellate Thaumatomonas lauterborni. Tsitologia, 29: 1168–1171. (in Russian)
  • Karpov, S. A., Ekelund, F. & Moestrup, Ø. 2003. Katabia gromovi nov. gen. nov sp.—a new soil flagellate with affinities to Heteromita (Cercomonadida). Protistology, 3: 30–41.
  • Karpov, S. A., Kersanach, R. & Williams, D. M. 1998. Ultrastructure and 18S rRNA gene sequence of a small heterotrophic flagellate Siluania monomastiga gen. et sp. nov. (Bicosoecida). Eur. J. Protistol., 34: 415–425.
  • Mikrjukov, K. A. 2000. System and phylogeny of Heliozoa: should this taxon exist in modern systems of protists? Zool. Zhur., 79: 883–897.
  • Moreira, D., Lopez-Garcia, P. & Vickerman, K. 2004. An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea. Int. J. Syst. Evol. Microbiol., 54: 1861–1875.
  • Mylnikov, A. P. 1990. Characteristic features of the ultrastructure of the colourless flagellate Heteromita sp. Tsitologiya, 32: 567–571.
  • Mylnikov, A. P. & Karpov, S. A. 2004. Review of the diversity and taxonomy of cercomonads. Protistology, 3: 201–217.
  • Nikolaev, S. I., Berny, C., Fahrni, J., Bolivar, I., Polet, S., Myl'nikov, A. P., Aleshin, V. V., Petrov, N. B. & Pawlowski, J. 2004. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc. Natl. Acad. Sci. (USA), 101: 8066–8071.
  • Nikolaev, S. I., Berny, C., Fahrni, J., Myl'nikov, A. P., Petrov, N. B. & Pawlowski, J. 2003. Genetic relationships between desmothoracid Heliozoa and Gymnophryid amoebas as evidenced by comparison of the nucleotide sequences of 18S rRNA genes. Doklady Biol. Sci., 393: 553–556.
  • Nikolaev, S. I., Berny, C., Fahrni, J., Myl'nikov, A. P., Aleshin, V. V., Petrov, N. B. & Pawlowski, J. 2003. Gymnophrys cometa and Lecythium sp. are core Cercozoa: evolutionary implications. Acta Protozoologica, 42: 183–190.
  • Patterson, D. J., Vørs, N., Simpson, A. G. B. & O'Kelly, C. 2002. Residual heterotrophic flagellates. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), An Illustrated Guide to the Protozoa. 2nd ed. Society of Protozoologists, Lawrence, KS. (Year 2000). p. 1302–1327.
  • Riedel, W. R. 1967. Some new families of Radiolaria. Proc. Geol. Soc. Lond., 1640: 148–149.
  • Shirkina, N. I. 1987. On the biology of Thaumatomonas lauterborni de Saedeleer, 1931 (Zoomastigophorea Calkins; Protozoa). Information Bulletin Biology of Inland Waters. Nauka (Leningrad), 49: 25–29. (in Russian)
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