Родственные отношения различных групп солнечников с другими группами простейших на основе маркёров 18S рДНК и актинового гена тема диссертации и автореферата по ВАК РФ 03.00.03, кандидат биологических наук Николаев, Сергей Игоревич

  • Николаев, Сергей Игоревич
  • кандидат биологических науккандидат биологических наук
  • 2003, Москва
  • Специальность ВАК РФ03.00.03
  • Количество страниц 148
Николаев, Сергей Игоревич. Родственные отношения различных групп солнечников с другими группами простейших на основе маркёров 18S рДНК и актинового гена: дис. кандидат биологических наук: 03.00.03 - Молекулярная биология. Москва. 2003. 148 с.

Заключение диссертации по теме «Молекулярная биология», Николаев, Сергей Игоревич

Выводы

1. Гены 18S рРНК и актина являются высокоинформативными маркёрами для филогенетических исследований солнечников и амебоидных простейших в целом.

2. Топологии кладограмм, построенные на основании последовательностей генов 18S рРНК и актина, конгруэнтны и сходным образом отражают филогенетическую историю солнечников.

3. На основании филогенетических реконструкций с использованием генов 18S рРНК и актина установлена полифилия солнечников, а также выяснено положение ряда других организмов.

4. Определено филогенетическое положение основных групп «солнечников» на дереве жизни: актинофриид - в составе Stramenopiles, десмоторацид - в составе Cercozoa, центрохелид - как из одной из групп высокого ранга, возникшей при базальной радиации Bikonta.

Список литературы диссертационного исследования кандидат биологических наук Николаев, Сергей Игоревич, 2003 год

1. Антонов, A.C. 2000. Основы геносистематики высших растений.

2. Москва. МАИК. «Наука/интерпериодика», 135.

3. Микрюков, К. А. 1994. Морские и солоноватоводныецентрохелидные солненчики (Centroheliozoa, Sarcodina) Кандалакшкского залива Белого моря. Зоол. Журн. 73(6):5-17

4. Микрюков, К. А. 1998. К биологии солнечников: феноменобразования лучистых форм у бентосных саркодовых. Зоол. Журн. 76(4): 389-401.

5. Микрюков, К.А. 2000. Система и филогения солнечников (Heliozoa)должен ли существовать этот таксон в современных системах Protista? Москва, 79:883-897

6. Мыльников, А.П. 1988. Ультраструктура экструсом жгутиконосцев.

7. Цитология. Ленинград, 30: 1402-1408.

8. Мыльников, А.П., Мыльникова, З.М., Цветков, А.И., и Елизарова,

9. В.А. 1998. Ультраструктура хищного жгутиконосца Phyllomitus amylophagus, Биология внутренних вод. Москва. Наука. 2:21-27.

10. Остроумов, A.A. 1917. О новом виде солнечников в морскомпланктоне (.Acanthocystis Wiasemskii). Тр. Карадагск. Научн. Ст. им. Т.Н. Вяземского. 1:62-65

11. Петров, Н.Б., Алёшин, В.В. 2002. Условно-нейтральныефилогенетические признаки крупных таксонов новый аспект эволюции макромолекул. Генетика, Т. 38(8): 1043-1062.

12. Сопина, В.А. 1997. Акразиевые (Acrasea) грибы или простейшие?1. Зоол. Журн. 76:1266-1276.

13. Фролов, А.О., Мыльников, А.П и Малышева М.Н. 1997. Электронмикроскопические исследования нового свободноживущего жгутиконосца Dimastigella mimosa sp.n. Цитология. 39(6):442-448.

14. Шульман, С.С., Решетняк, В.В. 1980. Реально ли существование всистеме простейших надкласса Actinopoda? Принципы построения макросистемы одноклеточных животных. Труды ЗИН АН СССР. Т. 94:23-41.

15. Шульман, С.С., Решетняк, В.В. 1981. Явление конвергенции уфлотирующих саркодовых. Эволюция и филогения одноклеточных животных. Труды ЗИН АН СССР. 107:5-18.

16. Adachi, J., and Hasegawa, M. 1996. MOLPHY version 2.3: programs formolecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28:1-150.

17. Amaral Zettler, L.A., Nerad, T.A., O'Kelly, C. J., Peglar, M.T., Gillevet,

18. P.M., Silberman, J.D. and Sogin, M.L. 2000. A molecular reassessment of the leptomyxid amoebae. Protistologica 151:275-282.

19. Amaral Zettler, L.A., Nerad, T.A., O'Kelly, C. J., Sogin, M. L. 2001. Thenucleariid amoebae: more protists at the animal-fungal boundary. J. Eukaryot. Microbiol 48(3): 293-297.

20. Amaral Zettler, L.A., Sogin, M.L., Caron, D.A. 1997. Phylogeneticrelationship between the Acantharea and the Polycystinea: A molecular perspective on Haeckel's Radiolaria. Prot. Natl. Acad. Sci. USA 94:11411-11416.

21. Andersen, E., Beams, H.W. 1960. The fine structure of the heliozoan,

22. Actinosphaerium nucleofilum. J. Protozool. 7: 190-199

23. Andersen, R.A., Saunders, G.W., Paskind, M. P., Sexton, J. P. 1993.

24. Ultrastructure and 18S rRNA gene sequence for Pelagomonas calceolata gen. et sp. nov. and the description of a new algal class, the Pelagophyceae classis nov. J. Phycol. 29: 701-715

25. Anderson, C.L., Canning, E.U., Okamura, B. 1998. A triploblast origin for1. Myxozoa? Nature 392:346

26. Anderson, J.O., Sjogren, A.M., Davis, L.A.M., Embly T.M., Roger A.J.2003. Phylogenetic Analises of Diplomonas Genes Reveal Frequent1.teral Gene Transfers Affecting Eukaryotes. Current Biology, 13: 94100.

27. Archibald, J. M., Teh, E. M. and Keeling, P. J. 2003. Novel ubiquitinfusion proteins: ribosomal protein PI and actin. J. Mol. Biol., 328: 771778.

28. Archibald, J. M. and Keeling, P. J. 2002. Recycled plastids: a "greenmovement" in eukaryotic evolution. Trends Genet., 18: 577-584.

29. Arisue, N., Hashimot, T., Lee, J. A., Moore, D.V., Gordon, P., Sensen,

30. C.W., Gaasterland, T., Hasegawa, M. and Muller, M. 2002. The phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1 alpha and EF-2. J. Eukaryot. Microbiol. 49:1-10.

31. Atkins, M.S., McArthur, A.G., Teske, A.P. 2000. Ancyromonadida: Anew phylogenetic lineage among the protozoa closely related to the common ancestor of metazoans, fungi, and choanoflagellates. J. Mol. Evol. 51:278-285

32. Baldauf, S.L. 2003. The Deep Roots of Eukaryotes. Science. 300:17031706.

33. Baldauf, S.L. and Palmer, L.D. 1993. Animals and fungi are each other'sclosest relatives: congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA 90:11558- 11562.

34. Baldauf, S.L., Doolittle, W.F. 1997. Origin and Evolution of the Slime

35. Molds (Mycetozoa). Prot. Natl. Acad. Sci. USA 94: 12007-12012.

36. Baldauf, S.L., Palmer, L.D., Doolitttle W.F. 1996. The root of theuniversal tree and the origin of Eukaryotes based on elongation factor phylogeny. Prot. Natl. Acad. Sci. USA 93:7749-7754

37. Baldauf, S.L., Roger, A. J., Wenk-Siefert, L. and Doolittle, W.F. 2000. Akingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977.

38. Bapteste, E., Brinkmann, H., Lee, J.A., Moore, D.V., Sensen, C.W.,

39. Bardele, C. F. 1972. Cell cycle, morphogenesis, and ultrastructure in thepseudoheliozoan Clathrulina elegans. Zeitschrift fur Zellforschung 130:219-242.

40. Bernard, C.A., Simpson, G. B. and Patterson, D. J. 1997. Anultrastructural study of a free-living retortamonad, Chilomastix cuspidata (Larsen and Patterson, 1990) n. comb. (Retortamonadida, Protista). European Journal of Protistology 33:254-265.

41. Berney, C., Pawlowski, J. 2003. Revised small subunit rRNA analysisprovides further evidence that Foraminifera are related to Cercozoa. J. Mol. Evol. (in press)

42. Bhattacharya, D., Oliveira, M.C. 2000. The SSU rDNA coding region of afllose amoeba contains a group I intron lacking the universally conserved G at the 3'-terminus. J. Eukaryot. Microbiol. 47: 585- 589

43. Bock, W., Hay, W., Lee, J.J. 1985. Order Foraminiferida D'Orbigny,1826. In: An Illustrated Guide to the Protozoa (Eds. J. J. Lee, S. H. Hutner, E. C. Bovee). Society of Protozoologists, Lawrence, Kansas, 252-273.

44. Bolivar, I., Fahrni, J., Smirnov, A. and Pawlowski, J. 2001. SSU rRNAbased Phylogenetic Position of the Genera Amoeba and Chaos (Lobosea, Gymnamoebia): The Origin of Gymnamoebae Revisited Mol. Biol. Evol. 18(12):2306-2314.

45. Bovee, E.C. 1985 a. Class Filosea Leidy, 1879. In: An Illustrated Guide tothe Protozoa (Eds. J. J. Lee, S. H. Hutner, E. C. Bovee). Society of Protozoologists, Lawrence, Kansas, 228-245

46. Bovee, E.C. 1985 b. Class Granuloreticulosea De Saedeleer, 1934. In: An1.lustrated Guide to the Protozoa (Eds. J. J. Lee, S. H. Hutner and E. C. Bovee). Society of Protozoologists, Lawrence, Kansas, 246-252

47. Briderre, C., Pages, M., Metenier, G., Canning, E.U. and Vivares C.P.1995. Evidence for the smallest nuclear genome (2.9Mb) in the microsporidium Encephalitozoon cunicili Mol. Biochem. Parasitol. 74: 229-231.

48. Brugerolle, G., Mignot, J.-P. 1984. The cell characters of twohelioflagellates related to the centroheliozoan lineage: Dimorpha and Tetradimorpha. Origins of life. 13:305-314.

49. Brugerolle, G. 1985a. Ultrastructure d'Hedriocystis pellucida (Heliozoa

50. Desmothoracida) et de sa forme megratiree flagellee Protistologica 21(2): 259-265.

51. Brugerolle, G. 1985b. Des trichocystes chez les bodonidés, un caractèrephylogénétique supplémentaire entre Kinetoplastida et Euglenida. Protistologica 21(3):339-348.

52. Bulman, S.R., Kühn, S.F., Marshall, J.W., Schnepf E. 2001. Aphylogenetic analysis of the SSU rRNA from members of the Plasmodiophorida and Phagomyxida. Protist 152: 43-51

53. Burki, F., Berney, C., Pawlowski, J. 2002. Phylogenetic position of

54. Gromia oviformis Dujardin inferred from nuclear-encoded small subunit ribosomal DNA. Protist 153: 251-260

55. Burzell, L.A. 1975. Fine structure of Bodo curvifilus Griessmann

56. Kinetoplastida: Bodonidae). J.Protozool. 22(l):35-39.

57. Cachon, J. and Cachon, M. 1978. Sticholonche zanclea Hertwig: areinterpretation of its phylogenetic position based upon new observations on its ultrastructure. Archiv fur Protistenkunde 120:148-168.

58. Cachon, J. and Cachon, M. 1985a. Class Phaeodarea Haeckel emend

59. Haeckel, Reschetnyak. Pages 295-302 in: J. J. Lee, S. H. Hutner, and E. C. Bovee, eds. An illustrated guide to the Protozoa. Society of Protozoologists, Lawrence, Kans.

60. Cachon, J. and Cachon, M. 1985&. Class Polycystinea Ehrenberg 1838,emend Riedel 1967. Pages 283-295 in J. J. Lee, S. H. Hutner, and E. C. Bovee. eds. An illustrated guide to the Protozoa. Society of Protozoologists, Lawrence, Kansas.

61. Cachon, J., Cachon, M. 1982. Actinopoda. In: Synopsis and Classificationof Living Organisms. (Ed. S. P. Parker) McGraw-Hill, New York, 553568

62. Cachon, J., Cachon, M. and Estep, K.W. 1990. Phylum Actinopoda

63. Classes Polycystina (=Radiolaria) and Phaeodaria. Pages 334-346 in L. Margulis, J. O. Corliss, M. Melkonian, and D. J. Chapman. Handbook of Protoctista. Jones and Bartlett, Boston.

64. Callahan, H.A., Litaker, R.W. and Noga, E.J. 2002. Molecular Taxonomyof the Suborder Bodonina (Order Kinetoplastida), Including the Important Fish Parasite, Ichthyobodo necator. Journal of Eukaryotic Microbiology 49: 119-128.

65. Cavalier-Smith, T. 1981. Eukaryotic kingdoms: seven or nine?1. Biosystems 14:461-481.

66. Cavalier-Smith, T. 1983. A six-kingdom classification and a unifiedphylogeny. Endocytobiology 2:1027-1034.

67. Cavalier-Smith, T. 1987. Eukaryotes with no mitochondria. Nature1.ndon) 326:332-333

68. Cavalier-Smith, T. 1989. Archaebacteria and Archezoa. Nature (London)339:100-101.

69. Cavalier-Smith, T. 1991. Cell diversification in heterotrophic flagellates.1.: Patterson, D.J., Larsen, J., (eds). The biology of free living heterotrophic flagellates. Oxford University Press, New York pp. 113131.

70. Cavalier-Smith, T. 1993a. Kingdom Protozoa and its 18 Phyla.

71. Microbiological Reviews 57:953-994.

72. Cavalier-Smith, T. 1993b. Percolozoa and the symbiotic origin of themetakaryote cell. Pp.399-406 in H. Ishikawa, M. Ishida, and S. Sato, eds. Endocytobyology V. Tübingen University Press, Tübingen.

73. Cavalier-Smith, T. 1998. A revised six-kingdom system of life. Biol. Rev.

74. Camb. Philos. Soc. 73:203-266

75. Cavalier-Smith, T. 1999. Principles of protein and lipid targeting insecondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J. Eukaryot. Microbiol. 46:347-366.

76. Cavalier-Smith, T. 2000. Flagellate megaevolution: the basis foreukaryote diversification. In: The Flagellates: Unity, Diversity and Evolution (Eds. B. S. C. Leadbeater, J. C. Green). Taylor and Francis Limited, London, 361-390

77. Cavalier-Smith, T. 2002. The phagotrophic origin of eukaryotes andphylogenetic classification of Protozoa. Int. J. Syst and Evol. Microb. 52:297-354.

78. Cavalier-Smith, T. and Chao, E.E. 1995. The opalozoan Apusomonas isrelated to the common ancestor of animals, fungi and choanoflagellates. Proceedings of the Royal Society of London B, Biological Sciences 261:1-6.

79. Cavalier-Smith, T. and Chao, E.E. 2003. Phylogeny of Coanozoa,

80. Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution. J. Mol. Evol. 36:540-563.

81. Cavalier-Smith, T., Chao, E. E. 1997. Sarcomonad ribosomal RNAsequences, rhizopod phylogeny and the origin of euglyphid amoebae. Arch. Protistenkd. 147: 227-236

82. Cavalier-Smith, T., Chao, E.E. 2003. Molecular phylogeny of centrohelidheliozoa, a novel a novel lineage of bikont eukaryotes that arose by ciliary loss. J.Mol.Evol. 56:387-396.

83. Cienkowski, L. 1881. An account on the White Sea excursion on 1880.

84. Proc. St.-Petersb. Imp. Soc. Nat. 12:130-171

85. Clark, C.G., Roger, A.J. 1995. Direct evidence for secondary loss ofmitochondria in Entamoeba histolitica Prot. Natl. Acad. Sci. USA 92:6518-6521.

86. Cleveland, L.R. 1956. Brief account of the sexual cycles of the flagellatesof Cryptocercus. J. Protozool. 3:161-180. DACKS, J., and A. J. ROGER. 1999. The first sexual lineage and the relevance of facultative sex. J. Mol. Evol. 48:779-783.

87. Corliss, J. O. 1984. The Kingdom Protista and its 45 phyla. Biosystems17:87-126.

88. Corliss, J.O. 1975. The ciliated protozoacharacterization, classificationand guide to the literature. 2. ed. Pergamon Press, Oxford.

89. Dacks, J.B., Jeffrey, D., Silberman, J.D., Simpson, A.G.B., Shigeharu, M.,

90. Kudo, T., Ohkuma, M. and Redfield, R.J. 2001.0xymonads Are Closely Related to the Excavate Taxon Trimastix. Mol. Biol. Evol. 18(6): 1034— 1044.

91. De Rijk, P. & De Wächter, R. 1997. RnaViz, a program for thevisualisation of RNA secondary structure. Nucleic Acids Res. 25:46794684.

92. De Saedeleer, H. 1934. Beitrag zur Kenntnis der Rhizopoden:morphologische und systematische Untersuchungen und eine Klassifikationsversuch. Mem. du Mus. Roy. d'Hist. Nat. de Belgique 60: 1-112

93. Dolezel, D., Jirku, M., Maslov, D.A. and Lukes, J. 2000. Phylogeny of thebodonid flagellates (Kinetoplastida) based on small-subunit rRNA gene sequences. International Journal of Systematic and Evolutionary Microbiology 50:1943-1951.

94. Edgcomb, V.P., Simpson, A.G., Zettler L.A., Nerad, T.A., Patterson, DJ.,

95. Holder, M.E., Sogin, M.L. 2002. Pelobionts are degenerate protests: Insights from molecules and morphology. Mol. Biol. Evol. 19:978-982.

96. Elbrächter, M., Schnepf, E., and Balzer, I. 1996. Hemistasiaphaeocysticola (Scherffel) comb.nov., redescription of a free-living, marine, phagotrophic kinetoplastid flagellate. Arch.Protistenkd. 147(2): 125-136.

97. Eyden, B.P. 1977. Morphology and ultrastructure of Bodo designis

98. Skuja,1948. Protistologica 13(2): 169-179.

99. Fast, N. M. and Keeling, P. J. 2001. A common origin for alveolate andheterokont plastids. (translated to Japanese by K. Ishida) Jpn. J. Phycol. 49:137-140.

100. Fast, N. M., Kissinger, J. C., Roos, D. S. and Keeling, P. J. 2001. Nuclearencoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol. Biol. Evol., 18:418-426.

101. Fast, N. M., Xue, L., Bingham, S. and Keeling, P. J. 2002. Re-examining

102. Alveolate Phylogeny Using Multiple Protein Molecular Phylogenies . J. Eukaryot. Microbiol. 49:30-37.

103. Febvre, J. 1990. Phylum Actinopoda, Class Acantharia. Pages 363-379 in

104. Margulis, J. O. Corliss, M. Melkonian, and D. J. Chapman, eds. Handbook of Protoctista. Jones and Bartlett, Boston.

105. Febvre-Chevalier, C. 1982. Revision of the taxonomy of the Heliozoawith attention to electron microscopical criteria. Ann. Inst. Oceanogr., Paris 58(Suppl.): 173-178

106. Febvre-Chevalier, C. 1985. Class Heliozoea Haeckel 1866. In: An1.lustrated Guide to the Protozoa. (Eds. J.J. Lee, S.H. Hutner and E.C. Bovee) Society of Protozoologists, Kansas, 302-317

107. Febvre-Chevalier, C. 1990. Phylum Actinopoda, class Heliozoa. In.

108. Handbook of Protoctista (Eds. L. Margulis, J.O. Corliss, M. Melhonian and D. J. Chapman) Jones and Bartlett, Boston, 347- 362

109. Febvre-Chevalier, C., Febvre, J. 1984. Axonemal microtubule pattern of

110. Cienkowskya mereschkowskyi and a revision of heliozoan taxonomy. Origins of Life 13: 315-338

111. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach usingthe bootstrap. Evolution 39:783-791.

112. Felsenstein, J. 2002. PHYLIP (phylogeny inference package) version3.6a3. Distributed by the author. Department of Genetics, University of Washington, Seattle.

113. Fenchel, T. and Patterson, D. J. 1986. Percolomonas cosmopolitus

114. Ruinen) n. gen., a new type of filter feeding flagellate from marine plankton. J. Mar. Biol. Ass. U.K. 66:465-482.

115. Finlay, M., Fenchel, T. 1989. Hydrogenosomes in some anaerobicprotozoa resemble mitochondria. FEMS. Microbiol. Lett. 65:311-314.

116. Flegel, T.W., and Pasharawipas, T. 1995. A proposal for typicaleukaryotic meiosis in Microsporidias. Can. J. microbial.41:l 1-14

117. Foissner, W, Blatterer, H, Foissner, I. 1988. The Hemimastigophora

118. Hemimastix amphikineta nov. gen., nov. spec), a new protistan phylum from Gondwanian soils. Eur J Protistol 23:361- 383

119. Frolov, A.O., Karpov S.A.and Mylnikov A.P. 2001. The ultrastructure of

120. Procryptobia sorokini (Zhukov) comb.nov. and rootlet homology in kinetoplastids. Protistology. 2(2): 85-95.

121. Funes, S., Davidson, E., Reyes-Prieto, A., Mallagon, S., Herion, P., King,

122. M.P., Gonzalez-Halphen, D. 2002. A green Algal Apicoplast Ancestor. Science. 289:2155

123. Gibbs, S.P. 1978. The chloroplasts of Euglena may have evolved fromsymbiotic green algae. Can. J. Bot. 56(22): 2883-2889.

124. Goodey, T. 1914. A preliminary communication on three newproteomyxian rhizopods from soil. Arch. Protistenk. 35:80- 102.

125. Grell, K. G. 1989. The life-cycle of the marine protist Reticulosphaerasocial is Grell. Arch.Protistenkd. 137:177-197.

126. Grell, K. G. 1990. Reticulosphaera japonensis n.sp. (Heterokontophyta)from Tide pools of the Japanese coast. Arch.Protistenkd. 138:257-269.

127. Grell, K. G. 1991. Leucodictyon marinum n.gen.,n.sp., a plasmodialprotist with zoospore formation from the Japanese coast. Arch.Protistenkd. 140:1-21.

128. Grell, K. G. 1994a. Reticulamoeba gemmipara n.gen., n.sp., an "amoeboflagellate" with reticulopodia and zoosporogenesis. Arch.Protistenkd. 144:55-61.

129. Grell, K. G. 1994b. The feeding community of Synamoeba arenarian.gen., n.sp. Arch.Protistenkd. 144:143-146.

130. Grell, K. G. 1995. Reticulamoeba minor n.sp.and its reticulopodia.

131. Arch.Protistenkd. 145(2):3-9.

132. Grell, K. G., Heini,A., Sshüller,S. 1990. The ultrastructure of

133. Reticulosphaera social is Grell (Heterokontophyta). Europ.J.Protistol. 26(l):37-54.

134. Grell, K. G., Schüller, S. 1991. The ultrastructure of the plasmodial protist1.ucodictyon marinum Grell. Europ.J.Protistol. 27:168-177.

135. Groome, R.L. 1986. Observations of the heliozoan genera Acanthocystisand Raphidiocystis from Australia. Arch. Protistenkd. 131:189-199.

136. Haeckel, E. 1866. Generelle Morphologie der Organismen. B., Reimer,2:462.

137. Hartmann, M. 1913. Rhizopoda. In: Handwörterbuch der

138. Naturwissenschaften, Jena 8: 422-446

139. Hertwig R. 1899. Über Kerntheilung, Richtungskörperbildung und

140. Befruchtung von Actinosphaerium eichhornii. Abhandl. math.-phys. Königl. Bayer. Akad. Wiss. München 19: 631-734

141. Hasegawa, M., Kishino, H. 1994. Accuracies of the simple methods forestimating the bootstrap probability of a maximum likelihood tree. Mol. Biol. Evol. 11:142-145.

142. Hasegawa, M., Kishino, H., Yano, T. 1985. Dating of the human-apesplitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174

143. Hausmann, K., Hulsmann, N. 1996. Protozoology, 2nd edn. Stuttgart:1. Thieme.

144. Huelsenbeck, J.P. and Ronquist, F. 2001. MRBAYES: Bayesian inferenceof phylogenetic trees. Bioinformatics 17:754-755

145. Hughes, A.L. and Piontkivska H. 2003. Phylogeny of Trypanosomatidaeand Bodonidae (Kinetoplastida) Based on 18S rRNA: Evidence for Paraphyly of Trypanosoma and Six Other Genera. Molecular Biology and Evolution. 20(4):644-52.

146. Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. The rapid generationof mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.

147. Kamaishi, T., Hashimoto, T., Nakamura, Y., Murata, S., Okada, N.,

148. Okamoto, K.-I., Shimuzu, M. and Hasegava, M. 1996. Protein phylogeny of translation elongation factor EF1-A suggests Microsporidias are extremely ancient eukaryotes. J. Mol. Evol. 42:257263.

149. Karpov, S. A. 2000. Flagellate phylogeny: an ultrastructural approach. In:

150. The Flagellates: Unity, Diversity and Evolution (Eds. B. S. C. Leadbeater, J. C. Green). Taylor and Francis Limited, London, 336-360

151. Keeling, P. J. 2001. Foraminifera and Cercozoa are related in actinphylogeny: two orphans find a home? Mol. Biol. Evol. 18: 1551- 1557

152. Keeling, P. J., Deane, J. A., McFadden, G. J. 1998. The phylogeneticposition of alpha- and beta- tubulins from the Chlorarachnion host and Cercomonas (Cercozoa). J. Eukaryot. Microbiol. 45: 561-570

153. Keeling, P.J. 1998. A Kingdom's progress: Archezoa and the origin ofeukaryotes. BioEssays 20:87-95.

154. Keeling, P.J. 2003. Congruent evidence from alpha-tubulin and betatubulin gene phylogenies for a zygomycete origin of microsporidia. Fung. Genet. Biol., 38:298-309.

155. Keeling, P.J. and Palmer, J.D. 2000. Parabasalian flagellates are ancienteukaryotes. Nature 405:635-63.

156. Keeling, P.J. and Palmer, J.D. 2001. Lateral transfer at the gene andsubgenic levels in the evolution of eukaryotic enolase. Proc. Natl. Acad. Sci. USA 98:10745-10750.

157. Keeling, P.J., and Doolittle, W.F. 1997. Widespread and ancientdistribution of a noncanonical genetic code in diplomonads. Mol. Biol. Evol. 14:895-901.

158. Keeling, P.J., and Fast, N.M. 2002. Microsporidia: Biology and evolutionof highly reduced intracellular parasites. Ann. Rev. Microbiol. 56:93116.

159. Keeling, P. J., and McFadden, G.I. 1998. Origins of microsporidia. Trends1. Microbiol. 6:19-23.

160. Keeling, P.J., Deane, J.A., Hink-Schauer, C., Douglas, S., Maier, U.-G.and McFadden, G.I. 1999. The secondary symbiont of the cryptomonad Guillardia theta contains alpha, beta, and gamma-tubulins. Mol. Biol. Evol. 16:1308-1313.

161. Keeling, P.J., Luker, M.A. and Palmer, J.D. 2000. Evidence from betatubulin that microsporidia evolved from fungi. Mol. Biol. Evol. 17:1-9.

162. Kishino, H. and Hasegawa, M. 1989. Evaluation of the maximumlikelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29:170-179.

163. Kishino, H., Miyata T. and Hasegawa, M. 1990. Maximum likelihoodinference of protein phylogeny, and the origin of chloroplasts. J. Mol. Evol. 31:151-160.

164. Kuhn, S., Lange, M., Medlin, L.K. 2000. Phylogenetic position of

165. Cryothecomonas inferred from nuclear-encoded small subunit ribosomal RNA. Protist 151:337-345

166. Kumar, R. 1980. Morphology and taxonomy of the protist

167. Gymnophrydium marinum Dangeard from the North Sea. Botanica Marina. 23:353-360.

168. Lanave, C., Preparata, G., Saccone, C., Serio, G. 1984. A new method forcalculating evolutionary substitution rates. J. Mol. Evol. 20: 86-93

169. Lang, B.F., Burger, G., O'Kelly, C. J., Cedergren, R., Golding, G.B.,1.mieux, C., Sankoff, D., Turmel, M. and Gray, M.W. 1997. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387: 493-497.

170. Levine, N.D., Corliss, J.O., Cox F.E.G., Deroux, G., Grain, J., Honigberg,

171. B.M., Leedale, G.F., Loeblich, A.R., Lom, J., Lynn, D., Merinfeld, E.J., Page, F.C., Poljansky, G., Sprague, V., Vávra, J., Wallace, F.G., Weiser, J.A. 1980. A new revised classification of the Protozoa. J. Protozool. 27: 37-58

172. Lipscomb, D., Corliss, J. O. 1982. Stephanopogon, a phylogeneticalyimportant "ciliate", shown by ultrastructural studies to be a flagellate. Science, 215:303-304.

173. Lopes-Garcia, P., Rodrigues-Valera, F., Moreira, D. 2002. Toward themonophyly of Haeckel's Radiolaria: 18S rRNA environmental DNA support the sisterhood of polycystinea and acantharea. Mol. Biol. Evol. 19:118-121.

174. Lukes, J., Guilbride, D.L., Votypka, J., Zikova, A., Benne, R. and

175. Englund, P.T. 2002. The kinetoplast DNA network: Evolution of an improbable structure. Eukaryotic Cell, 1:495-502.

176. Martin, W., Stoebe, B., Goremykin, V., Hansmann, S., Hasegava, M.,

177. Kovallik, K. 1998. Gene transfer to the nucleus and the evolution of the evolution of chloroplasts. Nature. 393:162-165.

178. Maslov, D.A, Podlipaev, S.A. and Lukes, J. 2001. Phylogeny of the

179. Kinetoplastida: Taxonomic Problems and Insights into the Evolution of Parasitism. Mem Inst Oswaldo Cruz, Rio de Janeiro. 96(3):397-402.

180. Medina, M, Collins, A.G., Silberman, J.D., Sogin, M.L. 2001. Evaluatinghypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc Natl Acad Sci USA. 98(17):9707-12.

181. Medlin, L., Elwood, H. J., Stickel, S., and Sogin, M. L. 1988 Thecharacterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71:491-499

182. Meisterfeld, R. 2000. Testate amoebae with filopodia. In: The Illustrated

183. Guide to the Protozoa (Eds. J. J. Lee, G. F. Leedale, P. Bradbury). 2 ed. Allen Press, Lawrence, KS, 2: 1054-1084

184. Mikrjukov, K.A. 1996a. Revision of genera and species composition inlower Centroheliozoa. I. Family Heterophryidae Poche. Arch. Protistenkd. 147: 107-113

185. Mikrjukov, K.A. 1996b. Revision of genera and species composition inlower Centroheliozoa. II. Family Raphidiophryidae n. fam. Arch. Protistenkd. 147: 205-212

186. Mikrjukov, K.A. 1999. Taxonomic revision of scale-bearing heliozoonlike amoebae (Pompholyxophryidae, Rotosphaerida). Acta Protozool. 38: 119-131

187. Mikrjukov, K.A. 2000a. Taxonomy of heliozoa. I. The order

188. Desmothoracida Hertwig et Lesser, 1874. Acta Protozool. 39: 81-97

189. Mikrjukov, K.A. 2000b. Taxonomy of heliozoa II. Dimorphidhelioflagellates (Dimorphida, Cercomonadea classis n.): biodiversity and relatedness with cercomonads. Acta Protozool. 39: 99-115

190. Mikrjukov, K.A., and Mylnikov, A.P. 1998a. The fine structure of acarnivorous multiflagellar protist, Mulicilia marina Cienkowski, 1881 (Flagellata Incertae sedis). European Journal of Protistology 34:391401.

191. Mikrjukov, K.A., Mylnikov, A.P. 2001. A study of the fine structure andthe mitosis of a lamellicristate amoeba, Micronuclearia podoventralisgen. et sp. n. (Nucleariidae, Rotosphaerida). Europ. J. Protistol. (submitted).

192. Milyutina, I.A., Aleshin, V.V., Mikrjukov, K.A., Kedrova, O.S., Petrov,

193. N.B. The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris: its rRNA predicted secondary structure and phylogenetic implication. Gene. 2001 Jul 11 ;272(l-2): 131-9.

194. Moreira, D., Guyader, L. E., and Philippe, H. 2000. The origin of redalgae and the evolution of chloroplasts. Nature 405:69-72.

195. Mylnikov, A.P. 1986. Ultrastructure of a colourless flagellate Phyllomitusapiulatus Skuja, 1948 (Kinetoplastida). Arch.Protistenkd. 132:1-10.

196. Nichols, K.H. 1983. Little-known an ew heliozoan: the Centrohelidiangenus Acanthocystis, including description of nine new taxa. Can. J.Z00I. 61(6):1369-1386

197. Olsen, G. J., Matsuda, H., Hagstrom, R. & Overbeek, R. 1994.fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10:41-48.

198. Ostenfeld, C.D. 1904. On the new marine Heliozoa occurring in theplankton of the Noth Sea and Scager Rak. Medd. Komm. Havunters ogelzer. Ser. Plankton. 1:3-5.

199. Page, F.C., and Blanton, R.L. 1985. The Heterolobosea (Sarcodina:rhizopoda), a new class uniting the Schizopyrenida and the Acrasidae. Protistologica. 21:121-132.

200. Patterson, D.J. 1988. The evolution of Protozoa. Mem. Inst. Oswaldo

201. Cruz. Rio de Janeiro. Supl 1.83: 588-600.

202. Patterson, D.J. 1989. Stramenopiles: chromophytes from a protistanperspective. Pages 357-379In: The Chromophytes Algae: Problems and Perspectives (eds) Green, G.C., Leadeater, B.S.C., Diver, W.L. Clarendon. Oxford.

203. Patterson, D.J. 1994. Protozoa: evolution and systematics. In:Progress in

204. Protozoology. Proc. IXth Int. Congr. Protozool., Berlin 1993. (Eds. K. Hausmann and N. Hülsmann) Gustav Fischer Verlag, Stuttgart-Jena-New York 1-14

205. Patterson, D.J. 1999. The diversity of eukaryotes. Am. Nat. 154: 96-124

206. Patterson, D.J. and Brugerolle, G. 1988. The ultrastructural identity of

207. Stephanopogon apogon and its relatedness to other kinds of protists. European Journal of Protistology 23:279-290.

208. Patterson, D.J., Sogin, M. 1992. Eukaryote origin and protistan diversity.

209. Eds. Hartman H., Matsuno K. The origin and evolution of the cell. Proc. Conf. On the Origin and Evolution of Prokariotic and Eukaryoticcells. Shimoda, Japan. P. 13-46.

210. Pawlowski, J., Bolivar, I., Fahrni, J. F., De Vargas, C. 1999. Molecularevidence that Reticulomyxa filosa is a freshwater naked foraminifer. J. Eukaryot. Microbiol. 46: 612-617

211. Philippe, H. 2000. Opinion: Long Branch Attraction and Protist

212. Phylogeny. Protist. 151(4):307-16

213. Philippe, H., and Germot, A. 2000. Phylogeny of eukaryotes based onribosomal RNA: long-branch attraction and models of sequence evolution. Mol. Biol. Evol. 17:830-834.

214. Philippe, H., Germot, A. and Moreira, D. 2000. The new phylogeny ofeukaryotes. Curr. Opin. Genet. Dev. 10:596- 601.

215. Posada, D., Crandall, K. A. 1998. Modeltest: testing the model of DNAsubstitution. Bio informatics 14: 817-818

216. Pussard, M, Pons R. 1976. Etude des Leptomyxa et Gephyramoeba

217. Protozoa, Sarcodina) lll-Gephyramoeba delicatula Goodey, 1915. Protistologica, 7(2):351-383.

218. Rainer, H. 1968. Urtiere, Protozoa; Wurzelfüßler, Rhizopoda;

219. Sonnentierchen, Heliozoa. Die Tierwelt Deutschlands (Ed. F. Dahl) Jena: Gustav Fischer Verlag. Bd. 56: 176.

220. Rodriguez, R., Olivier, J. L., Marin, A., Medina, J. R. 1990. The generalstochastic model of nucleotide substitution. J. Theor. Biol. 142: 485-501

221. Roger, A.J., Smith, M.W., Doolittle, R.F., Doolittle W.F. 1996. Evidencefor the Heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3-phosphate dehydrogenase. J. Eukaryotic Microbiol. 43:475-485.

222. Rokas, A., and Holland, P. W. Rare genomic changes as a tool forphylogenetics Trends Ecol Evol. 15:454-459

223. Ruinen, J. 1938. Notizen über Sazflagellaten. II. Uber die Vertebreiungder Sazflagellaten. Archiv fur Protistenkunde, 90: 210-258.

224. Saitou, N., Nei, M. 1987. The neighbor-joining method: a new method forreconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425

225. Saldarriaga, J., Taylor, F.J.R., Keeling, P.J. and Cavalier-Smith T. 2001.

226. Dinoflagellate nuclear SSU rDNA phylogeny suggests multiple plastid losses and replacements. J. Mol. Evol. 53: 204-213.

227. Sekiguchi, H., Moriya, M., Nakayama, T., Inoye, I. 2002. Vestigalchloroplasts in heterotrophic Stramenopiles Pteridomonas dantica and Ciliophrys infusionum (Dictiohophyceeae). Protist 153: 157-167.

228. Shaudinn, F. 1896. Uber das Centra;korn der Heliozoen. Ein Beitrag zur

229. Centrosom enfrage. Verhande Deutsh. Zool. Ges. Bonn, 6:113-130.

230. Siddal, M.E., Martin, D.S., Bridge, D., Desser, S.S. and Cone, D.K. 1995.

231. The demise of a phylum of protists: phylogeny of Myxozoa and other parasitic cnidarians. J. Parasitol. 81:961-967.

232. Silberman, J.D., Clark, C.G., Diamond, L.S. and Sogin, M.L. 1999.

233. Phylogeny of the genera Entamoeba and Endolimax as deduced from small-subunit ribosomal RNA sequences. Mol. Biol. Evol. 16:1740— 1751.

234. Simpson, A.G., Patterson, D.J. 1999. The ultrastructure of Carpediemonasmembranifera (Eukaryota) with reference to the Excavate hypothesis. Europ. J. Protistol. 35: 357-370.

235. Simpson, A.G., Patterson, D.J. 2001. On core jakobiids and excavate taxa:the ultrastructure of Jacoba incarcerata J.Eukaryot. Microbiol. 48: 480492.

236. Simpson, A.G., Roger, A.J., Silberman, J.D., Leipe, D.D., Edgcomb, V.P.,

237. Jermiin, L.S., Patterson, D.J., and Sogin, M.L. 2002. Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia. Mol. Biol. Evol. 19:17821791.

238. Simpson, A.G.B. 1997. The identity and composition of the Euglenozoa.

239. Arch. Protistenkd. 148:318-328.

240. Simpson, A.G.B., Hoff, J., Van den, Bernard C., Burton H.R. and

241. Patterson D. J. 1997. The ultrastructure and systematic position of the euglenozoon Postgaardi managerens is, Fenchel et al. Arch.Protistenkd. 147(3-4): 213-225.

242. Simpson, A.G.B., Lukes, J. and Roger, A.J. 2002. Evolutionary history ofkinetoplastids, and their kinetoplasts. Molecular Biology and Evolution 19:2071-2083.

243. Smith, R., Patterson D.J. 1986. Analysis of heliozoan interrelationships:an example of the potential and limitations of ultrastructural approaches to the study of protisten phylogeny. Proc. Roy Soc. London B 277: 325366

244. Smothers, J.F., Von Dohlen, C.C., Smith, L.H. and Spall, R.D. 1994.

245. Molecular evidence that the myxozoan protists are Metazoans. Science 265:1719-1721

246. Sogin, M.L. 1989. Evolution of Eukaryotic microorganisms and theirsmall subunit ribosomal RNAs. Am. Zool. V.29. P. 487-489. organelle origins; energy-producing symbionts in early eukaryotes? Curr. Biol. 7: 315-317.

247. Sogin, M.L., Gunderson, J.H., Elwood, H.J., Alonso, R.A., Peattie, D.A.1989. Phylogenetic meaning o the Kingdom concept: An unusual ribosomal RNA from Giardia lamblia. Science. 243:75 77.

248. Stechmann, A., Cavalier-Smith, T. 2002. Rooting the eukaryote tree byusing a derived gene fusion. Science 297: 89-91

249. Strimmer, K., and von Haeseler, A. 1996. Quartet puzzling: a quartetmaximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.

250. Swofford, D.L. 1998. PAUP*: phylogenetic analyses using parsimonyand other methods). Sinauer Associates, Sunderland, Mass.

251. Tamura, K. and Nei, M. 1993. Estimation of the number of nucleotidesubstitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526.

252. Taylor, F.J.R. 1976. Flagellate phylogeny: a study in conflicts. J.1. Protozool. 23: 28-40

253. Taylor, F.J.R. 1999. Ultrastructure as a control for protistan molecularphylogeny. Am. Nat. 154 (Suppl. 4): S125-S136.

254. Thomsen, H. A., Buck, K. R., Bolt, P. A., Garrison D. L. 1991. Finestructure and biology of Cryothecomonas gen. nov. (Protista incertae sedis) from the ice biota. Can. J. Zool. 69: 1048-1070

255. Thorley, J.L., Page, R.D.M. 2000. RadCon: phylogenetic tree comparisonand consensus. BIOINF: Bioinformatics.

256. Trégouboff, G. 1953. Classe de Heliozoaires. In: Traité de Zoologie (Ed.

257. P.-P. Grassé) Paris: Masson et Cie. 1: 437-489

258. Van de Peer, Y., De Rijk, P., Wuyts, J., Winkelmans, T. and De Wachter,

259. R. 2000. The European Small Subunit Ribosomal RNA database. Nucleic Acids Res. 28:175-176.

260. Van de Peer, Y., Rensing, S.A., Maier, U.G. and De Wachter, R. 1996.

261. Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae. Proc Natl Acad Sci USA. 93(15):7732-6

262. Vickerman, K. 1991. Organisation of the bodonid flagellates. The Biologyof Free-living Heterotrophic Flagellates. Eds. Patterson, J. David, Larsen, Jacob. Oxford. Clarendon Press. 159-176.

263. Visvesvara, G., Martinez, A., Schuster, F., Leitch, G., Wallace, S.,

264. Sawyer, T. and Anderson, M. 1990. Leptomyxid amoeba, a new agent of amoebic meningoencephalitis in humans and animals. J. Clin. Microbiol. 28:2750-2756.

265. Visvesvara, G., Schuster, F. and Martinez, A. 1993. Balamuthiamadrillaris, n. g., n. sp., agent of amebic meningoencephalitis in humans and other animals. J. Eukaryot. Microbiol. 40:504-514.

266. Vivares, C., Biderre, C., Duffieux, F., Peyret, P., Metenier, G. and Pages,

267. M. 1996. Chromosomal localization of five genes in Encephalitozoon cunicili (Microsporidia). J.Eukaryot. Microbiol. 43:97.

268. Voigt, K, Wostemeyer, J. 2000. Reliable amplification of actin genesfacilitates deep-level phylogeny. Microbiol. Res. 155:179-195.

269. Von Benwitz, G., and K. G. Grell. 1971a. Ultrastruktur mariner Amo"ben.1.. Stereomyxa ramosa. Arch. Protistenk. 113: 51-67.

270. Von Benwitz, G., and K. G. Grell. 19716. Ultrastruktur mariner Amo"ben.

271. I. Stereomyxa angulosa. Arch. Protistenk. 113:68-79.

272. Vossbrinck, C.R., Maddox., J.V., Friedman, S., Debrunner-Vossbrinck,

273. B.A. and Woesse, C.R. 1987. Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes. Nature 326:411-414.

274. Weekers, P.H.H., Kleyn, J. and Vogels, G.D. 1997. Phylogenetic positionof Psalteriomonas lanterna deduced from the SSU rDNA sequence. J. Euk. Microbiol. 44:467-470.

275. Wu, G., Henze, K., Muller, M. 2001. Evolutionary relationships of theglucokinaze from the amitochondriate protist Trichomonas vaginalis. Gene. 264-265.

276. Wuyts, J., De Rijk, P., Van de Peer, Y., Pison G., Rousseeuw, P., De

277. Wachter, R. 2000. Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res. 28: 4698-4708.

278. Wuyts, J., Van de Peer, Y. and De Wachter, R. 2001. Distribution ofsubstitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res. 29:5017-5028.

279. Wylezich, C., Meisterfeld, R., Meisterfeld, S., Schlegel, M. 2002.

280. Phylogenetic analyses of small subunit ribosomal RNA coding regions reveal a monophyletic lineage of euglyphid testate amoebae (order Euglyphida). J. Eukaryot. Microbiol. 49: 108-118

281. Yoon, H.S., Hackett, J.D., Bhattacharya, D. 2002. A single origin of theperidinin- and fucoxanthin- containing plastids in dinoflagellates through tertiary endosymbiosis. Prot. Natl. Acad. Sci. USA 99:11724-11729.