Phylogeny and taxonomic revision of plastid-containing euglenophytes based on SSU rDNA sequence comparisons and synapomorphic signatures in the SSU rRNA secondary structure

Protist

Volumn 154, Issue 1, 2003, Pages 99-145

  Marin, Birger ^a   Palm, Anne ^a   Klingberg, Max ^a   Melkonian, Michael ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGAE; ASTASIA; COLACIUM; CRYPTOGLENA; DISTIGMA; EUGLENA; EUGLENA POLYMORPHA; EUGLENALES; EUGLENIDA; EUTREPTIA; EUTREPTIALES; EUTREPTIELLA; KHAWKINEA; LEPOCINCLIS; MONOMORPHINA; PHACUS; STROMBOMONAS; TETREUTREPTIA; TRACHELOMONAS;

EID: 0038805591     PISSN: 14344610     EISSN: None     Source Type: Journal    
DOI: 10.1078/143446103764928521     Document Type: Article

References (220)

1. Aimi T, Yamada T, Murooka Y (1994) A group-I selfsplicing intron in the nuclear small subunit rRNA-encoding gene of the green alga, Chlorella ellipsoidea C-87. Gene 139: 65-71
2. Amaral Zettler LA, Gómez F, Zettler E, Keenan BG, Amils, R, Sogin ML (2002) Eukaryotic diversity in Spain's river of fire. Nature 417: 137
3. Archer W, Barker J (1871) Remarks on Phacus and Euglena. Quart J Microscop Sci, Ser. 2, 11: 98-99
4. Barnes LSD, Walne PL, Dunlap JR (1986) Cytological and taxonomic studies of the Euglenales. I. Ultrastructure and envelope elemental composition in Trachelomonas. Br Phycol J 21: 387-397
5. Bhattacharya D (1998) The origin and evolution of protist group I introns. Protist 149: 113-122
6. Bhattacharya D, Friedl T, Damberger S (1996) Nuclear-encoded rDNA group I introns: origin and phylogenetic relationships of insertion site lineages in the green algae. Mol Biol Evol 13: 978-989
7. Bhattacharya D, Friedl T, Helms G (2002) Vertical evolution and intragenic spread of lichen-fungal group I introns. J Mol Evol 55: 74-84
8. Bhattacharyya R, Das K, Sen S, Roy S, Majumder HK (1996) Development of a genus specific primer set for detection of Leishmania parasites by polymerase chain reaction. FEMS Micobiol Lett 135: 195-200
9. Bourrelly P (1970) Les Algues d'eau douce. Initiation à la Systématique. Tome III: Les Algues bleues et rouges. Les Eugléniens, Peridiniens et Cryptomonadines. Éditions N. Boubée & Cie, Paris
10. Brinkmann H, Philippe H (1999) Archaea sister group of Bacteria? Indications from tree reconstruction artefacts in ancient phylogenies. Mol Biol Evol 16: 817-825
11. Brodersen DE, Clemons Jr WM, Carter AP, Wimberly BT, Ramakrishnan V (2002) Crystal structure of the 30S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16S RNA. J Mol Biol 316: 725-768
12. Brosnan S, Shin W, Kjer KM, Triemer RE (publ. online 8 Nov. 2002) Phylogeny of the photosynthetic euglenophytes inferred from the nuclear SSU and partial LSU rDNA. Int J Syst Evol Microbiol, papers in press, http://dx.doi.org/10.1099/ijs.0.02518-0
13. Buckley TR, Simon C, Shimodaira H, Chambers GK (2001) Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology. Mol Biol Evol 18: 223-234
14. Busse I, Preisfeld A (2002) Phylogenetic position of Rhynchopus sp. and Diplonema ambulator as indicated by analyses of euglenozoan small subunit ribosomal DNA. Gene 284: 83-91
15. Busse I, Preisfeld A (2003) Discovery of a group I intron in the SSU rDNA of Ploeotia costata (Euglenozoa). Protist 154: 57-69
16. Busse I, Preisfeld A (publ. online 16 Aug. 2002) Systematics of primary osmotrophic euglenids: a molecular approach to the phylogeny of Distigma and Astasia (Euglenozoa). Int J Syst Evol Microbiol, papers in press, http://dx.doi.org/10.1099/ijs.0.02295-0
17. Butcher RW (1961) An introductory account of the smaller algae of British coastal waters. Part VIII: Euglenophyceae = Eugleninae. Ministry of Agriculture, Fisheries and Food. Fishery Investigations. Series IV: 1-17
18. Choe CP, Hancock JM, Hwang UW, Kim W (1999a) Analysis of the primary sequence and secondary structure of the unusually long SSU rRNA of the soil bug, Armadillidium vulgare. J Mol Evol 49: 798-805
19. Choe CP, Hwang UW, Kim W (1999b) Putative secondary structures of unusually long strepsipteran SSU rRNAs and its phylogenetic implications. Mol Cells 9: 191-199
20. Chu SP (1946) Contributions to our knowledge of the genus Euglena. Sinensia 17: 75-134
21. Christen HR (1962) Neue und wenig bekannte Eugleninen und Volvocalen. Revue Algologique 6: 162-202
22. Christensen T (1962) Botanik, Bind II: Systematisk botanik, Nr. 2, Alger. Copenhagen, Munksgaard
23. Christensen T (1980-1994) Algae. A taxonomic survey. AiO Print Ltd., Odense
24. Coleman AW (2000) The significance of a coincidence between evolutionary landmarks found in mating affinity and a DNA sequence. Protist 151: 1-9
25. Conforti V (1999) A taxonomic and ultrastructural study of Trachelomonas Ehr. from subtropical Argentina. Cryptogamie Algol 20: 167-207
26. Conrad W (1935) Étude systématique du genre Lepocinclis PERTY. Mém Musée Royal d'Hist Nat Belg 1: 1-85
27. Crease TJ, Colbourne JK (1998) The unusually long small-subunit ribosomal RNA of the crustacean, Daphnia pulex: sequence and predicted secondary structure. J Mol Evol 46: 307-313
28. Cronquist A (1960) The divisions and classes of plants. Bot Rev 26: 425-482
29. Da Cunha AM (1914) Contribuição para o conhecimento da fauna de Protozoarios do Brazil. II. Mem do Inst Oswaldo Cruz 6: 169-179
30. Dawson NS, Walne PL (1991a) Structural characterization of Eutreptia pertyi (Euglenophyta). I. General description. Phycologia 30: 287-309
31. Dawson NS, Walne PL (1991b) Structural characterization of Eutreptia (Euglenophyta). III. Flagellar structure and possible function of the paraxial rods. Phycologia 30: 415-437
32. Dawson NS, Walne PL (1994) Evolutionary trends in euglenoids. Arch Protistenkd 144: 221-225
33. Daugbjerg N, Moestrup Ø (1992) Ultrastructure of Pyramimonas cyrtoptera sp. nov. (Prasinophyceae), a species with 16 flagella from northern Foxe Basin, Arctic Canada, including observations on growth rates. Can J Bot 70: 1259-1273
34. Deflandre G (1926) Monographie du genre Trachelomonas EHR. Nemours, Imprimerie André Lesot, 175 pp. (also in Rev Gén Bot 38 [1926], 39 [1927])
35. Deflandre G (1927) Remarques sur la systématique du genre Trachelomonas EHR. Bull Soc Bot France 74: 285-287, 657-665
36. Deflandre G (1930) Strombomonas, nouveau genre d'Euglénacées (Trachelomonas EHR. pro parte). Arch Protistenkd 69: 551-614
37. Deflandre G, Dusi H (1935) Description d'une Euglène nouvelle, Euglena mesnili nov. spec. Arch Zool Exp Gén; Notes et Revues 77: 12-14
38. Dillard GE (2000) Freshwater algae of the southeastern United States. Part 7. Pigmented Euglenophyceae. Bibliotheca Phycologia, Band 106. Borntraeger Verlagsbuchhandlung, Berlin, Stuttgart
39. Dolezel D, Jirku M, Maslov DA, Lukes J (2000) Phylogeny of the bodonid flagellates (Kinetoplastida) based on small-subunit rRNA gene sequences. Int J Syst Evol Microbiol 50: 1943-1951
40. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15
41. Dragos N, Péterfi LS, Momeu L, Popescu C (1997) An introduction to the algae and the culture collection of algae at the institute of biological research Cluj-Napoca. Cluj University Press. 267 pp.
42. Dunlap JR, Walne PL (1987) Variations in envelope morphology and mineralization in Trachelomonas lefevrei (Euglenophyceae). J Phycol 23: 556-564
43. Dunlap JR, Walne PL, Bentley J (1983) Microarchitecture and elemental spatial segregation of envelopes of Trachelomonas lefevrei (Euglenophyceae)
44. Dunlap JR, Walne PL, Kivic PA (1986) Cytological and taxonomic studies of the Euglenales. II. Comparative microarchitecture and cytochemistry of envelopes of Strombomonas and Trachelomonas. Br Phycol J 21: 399-405
45. Dujardin F (1841) Histoire naturelle des Zoophytes. Infusoires. Paris 1841
46. Ehrenberg CG (1830) Neue Beobachtungen über blutartige Erscheinungen in Ägypten, Arabien und Sibirien, nebst einer Übersicht und Kritik der früher bekannten. Pogg Ann Physik Chem 94: 477-514
47. Ehrenberg CG (1832a) Beiträge zur Kenntniss der Organisation der Infusorien und ihrer geographischen Verbreitung, besonders in Sibirien. Physik Abh Königl Akad Wiss Berlin 1830 (1832): 1-88
48. Ehrenberg CG (1832b) Über die Entwicklung und Lebensdauer der Infusionsthiere; nebst ferneren Beiträgen zu einer Vergleichung ihrer organischen Systeme. Physik Abh Königl Akad Wiss Berlin 1831 (1832): 1-154
49. Ehrenberg CG (1835) Dritter Beitrag zur Erkenntniss grosser Organisation in der Richtung des kleinsten Raumes. Physik Abh Königl Akad Wiss Berlin 1833 (1835): 145-336
50. Ehrenberg CG (1838) Die Infusionsthierchen als vollkommene Organismen. Ein Blick in das tiefere organische Leben der Natur. Nebst einem Atlas von vierundsechszig colorirten Kupfertafeln, gezeichnet vom Verfasser. Leipzig 1838
51. Ehrenberg CG (1840) Charakteristik von 274 neuen Arten von Infusorien [short title given in the "Namen-Register"; publication without title]. Ber Bekanntm Verhandl Königl Preuss Akad Wiss Berlin 1840: 197-219
52. Elenkin AA (1924) De Euglenarum sine flagello sectione nova. Not Syst Inst Cryptog Horti Bot Rei publ Rossicae (Leningrad) 3: 129-169
53. Erwin D (2000) Life's downs and ups. Nature 404: 129-130
54. Ettl H (1980) Grundriß der allgemeinen Algologie. Gustav Fischer Verlag, Stuttgart
55. Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27: 401-410
56. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791
57. Fenchel T, Bernhard C, Esteban G, Finlay BJ, Hansen PJ, Iversen N (1995) Microbial diversity and activity in a Danish fjord with anoxic deep water. Ophelia 43: 45-100
58. Friedl T, Besendahl A, Pfeiffer P, Bhattacharya D (2000) The distribution of group I introns in lichen algae suggests that lichenization facilitates intron lateral transfer. Mol Phylogenet Evol 14: 342-352
59. Fritsch FE (1944) Present-day classification of algae. Bot Rev 10: 233-277
60. Fott B (1971) Algenkunde. Gustav Fischer Verlag, Stuttgart
61. Fott B (1974) The phylogeny of eukaryotic algae. Taxon 23: 446-461
62. Gibbs S (1978) The chloroplasts of Euglena may have evolved from symbiotic green algae. Can J Bot 56: 2883-2889
63. Gockel G, Hachtel W (2000) Complete gene map of the plastid genome of the nonphotosynthetic euglenoid flagellate Astasia longa. Protist 151: 347-351
64. Gojdics M (1953) The genus Euglena. Madison, University of Wisconsin Press
65. Goldman N, Anderson JP, Rodrigo AG (2001) Likelihood-based tests of topologies in phylogenetics. Syst Biol 49: 1-19
66. Gourse RL, Gerbi SA (1980) Fine structure of ribosomal RNA. IV. Extraordinary evolutionary conservation in sequences that flank introns in rDNA. Nucleic Acids Res 8: 3623-3637
67. Graybeal A (1998) Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol 47: 9-17
68. Gunderson JH, Sogin ML (1986) Length variation in eukaryotic rRNA's: small subunit rRNA's from the protists Acanthamoeba castellanii and Euglena gracilis. Gene 44: 63-70
69. Gutell RR (1996) Comparative sequence analysis and the structure of 16S and 23S rRNA. In Zimmermann RA, Dahlberg AE (eds) Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis. CRC Press, Boca Raton, Florida, pp 111-128
70. Gutell RR, Larsen N, Woese CR (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58: 10-26
71. Hall RP Jahn TL (1929) On the comparative cytology of certain euglenoid flagellates and the systematic position of the families Euglenidae Stein and Astasiidae Bütschli. Trans Amer Micr Soc 48: 388-405
72. Hartskeerl RA, Schuitema AR, De Wachter R (1993) Secondary structure of the small subunit ribosomal RNA sequence of the microsporidium Encephalitozoon cuniculi. Nucleic Acids Res 21: 1489-1489
73. Hillis DM (1996) Inferring complex phylogenies. Nature 383: 130-131
74. Huber-Pestalozzi G (1955) Das Phytoplankton des Süßwassers. Systematik und Biologie. 4. Teil. Euglenophyceen. Die Binnengewässer, Band XVI. Schweizerbart'sche Verlagsbuchhandlung Stuttgart
75. Huchon D, Madsen O, Sibbald MJJB, Ament K, Stanhope MJ, Catzeflis F, De Jong WW, Douzery EJP (2002) Rodent phylogeny and a timescale for the evolution of glires: evidence from an extensive taxon sampling using three nuclear genes. Mol Biol Evol 19: 1053-1065
76. Katinka MD, Duprat S, Cornillot E, Méténier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El Alaoui H, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivarès CP (2001) Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414: 450-453
77. Kim J (1996) General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Syst Biol 45: 363-374
78. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120
79. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of the Hominoidea. J Mol Evol 29: 170-179
80. Kivic P, Walne PL (1984) An evaluation of a possible phylogenetic relationship between the Euglenophyta and Kinetoplastida. Origins of Life 13: 269-288
81. Klebs G (1883) Über die Organisation einiger Flagellatengruppen und ihre Beziehungen zu Algen und Infusorien. Unters Bot Inst Tübingen 1: 233-261
82. Kohara Y, Noda H, Okano K, Kambara H (2002) DNA probes on beads arrayed in a capillary, 'Bead-array', exhibited high hybridization performance. Nucleic Acids Res 30: e87
83. Kreimer G (1994) Cell biology of phototaxis in flagellated algae. Int Rev Cyto1148: 229-310
84. Kusber W-H (1998) A study on Phacus smulkowskianus (Euglenophyceae) - a rarely reported taxon found in waters of the Botanic Garden Berlin-Dahlem. Willdenowia 28: 239-247
85. Kusel-Fetzmann E (2002) Die Euglenophytenflora des Neusiedler Sees (Burgenland, Österreich). Abhandlungen der Zoologisch-Botanischen Gesellschaft Österreich 32: 1-115
86. Kusel-Fetzmann E, Schagerl M (1992) Verzeichnis der Sammlung von Algen-Kulturen an der Abteilung für Hydrobotanik am Institut für Pflanzenphysiologie der Universität Wien. Phyton 32: 209-234
87. Lange M, Medlin LK (2002) Design and testing of ITS probes for distinguishing Phaeocystis species. Protist 153: 275-282
88. Larsen NH, Moestrup Ø, Pedersen PM (1994) Scandinavian Culture Centre for Algae & Protozoa. Catalogue 1994. Department of Phycology, Botanical Institute, University of Copenhagen
89. Leander BS, Farmer MA (2000a) Comparative morphology of the euglenid pellicle. I. Patterns of strips and pores. J Eukaryot Microbiol 47: 469-479
90. Leander BS, Farmer MA (2000b) Epibiotic bacteria and a novel pattern of strip reduction on the pellicle of Euglena helicoideus (Bernard) Lemmermann. Europ J Protistol 36: 405-413
91. Leander BS, Farmer MA (2001a) Comparative morphology of the euglenid pellicle. II. Diversity of strip substructure. J Eukaryot Microbiol 48: 202-217
92. Leander BS, Farmer MA (2001b) Evolution of Phacus (Euglenophyceae) as inferred from pellicle morphology and SSU rDNA. J Phycol 37: 143-159
93. Leander BS, Witek RP, Farmer MA (2001) Trends in the evolution of the euglenid pellicle. Evolution 55: 2215-2235
94. Lee RE (1999) Phycology. Third Edition. Cambridge University Press
95. Leedale GF (1967) Euglenoid flagellates. Prentice-Hall, Englewood Cliffs, N. J.
96. Leedale GF (1975) Envelope formation and structure in the euglenoid genus Trachelomonas. Br Phycol J 10: 17-41
97. Leedale GF (1978) Phylogenetic criteria in euglenoid flagellates. BioSystems 10: 183-187
98. Lemmermann E (1901) Beiträge zur Kenntniss der Planktonalgen, XII: Notizen über einige Schwebealgen. Ber Deutsch Bot Ges 19: 85-95
99. LeQuesne WJ (1969) A method of selection of characters in numerical taxonomy. Syst Zool 18: 201-205
100. Linton EW, Hittner D, Lewandowski C, Auld T, Triemer RE (1999) A molecular study of euglenoid phylogeny using small subunit rDNA. J Euk Microbiol 46: 217-223
101. Linton EW, Nudelman MA, Conforti V, Triemer RE (2000) A molecular analysis of the euglenophytes using SSU rDNA. J Phycol 36: 740-746
102. Lockhart PJ, Steel MA, Hendy MD, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11: 605-612
103. Luis L, Ramírez AH, Ramírez R, Vélez ID, Mendoza-León (2001) Nuclear DNA sequence specific to Leishmania (Viannia) subgenus: a molecular marker for species identification. Parasitology 122: 405-414
104. Lwoff A (1938) Remarques sur la physiologie comparée des Protistes eucaryotes. Les Leucophytes et l'oxytrophie. Arch Protistenkd 90: 194-209
105. Lwoff A (1950) La synthèse de l'amydon chez les leucophytes et la valeur du réseau de Volkonsky. New Phytol 49: 72-80
106. Lwoff A, Dusi H (1935) La suppression expérimentale des chloroplastes chez Euglena mesnili. C R Soc Biol Paris 119: 1092-1095
107. Mai JC, Coleman AW (1997) The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. J Mol Evol 44: 258-271
108. Mainx F (1927) Beiträge zur Morphologie und Physiologie der Eugleninen. I. Teil. Morphologische Beobachtungen, Methoden und Erfolge der Reinkultur. II. Teil. Untersuchungen über die Ernährungs- und Reizphysiologie. Arch Protistenkd 60: 305-414
109. Marin B, Klingberg M, Melkonian M (1998) Phylogenetic relationships among the Cryptophyta: analyses of nuclear-encoded SSU rRNA sequences support the monophyly of extant plastid-containing lineages. Protist 149: 265-276
110. Mathews DH, Andre TC, Kim J, Turner DH, M. Zuker M (1998) An updated recursive algorithm for RNA secondary structure prediction with improved free energy parameters. American Chemical Society Symposium 682: 246-257
111. McFadden GI, Melkonian M (1986) Use of Hepes buffer for microalgal culture media and fixation for electron microscopy. Phycologia 25: 551-557
112. McLachlan JL, Seguel MR, Fritz L (1994) Tetreutreptia pomquetensis gen. et sp. nov. (Euglenophyceae): a quadriflagellate, phototrophic marine euglenoid. J Phycol 30: 583-544
113. Mears JA, Cannone JJ, Stagg SM, Gutell RR, Agrawal RK, Harvey SC (2002) Modeling a minimal ribosome based on comparative sequence analysis. J Mol Biol 321: 215-234
114. Medlin L, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA coding regions. Gene 71: 491-499
115. Melkonian M, Preisig HR (1984) Ultrastructure of the flagellar apparatus in the green flagellate Spermatozopsis similis. Plant Syst Evol 146: 145-162
116. Melkonian M, McFadden GI, Reize IB, Preisig HR (1987) A light and electron microscopic study of the quadriflagellate green alga Spermatozopsis exsultans. Plant Syst Evol 158: 47-61
117. Mereschkowsky KS (1877) Etjudy nad prostejsimi zivotnymi severa Rossii. Trudy S-Peterburgsk Obsc Estestvoisp 8.2.
118. Merzlyak E, Yurchenko V, Kolesnikov AA, Alexandrov K, Podlipaev SA, Maslov DA (2001) Diversity and phylogeny of insect trypanosomatids based on small subunit rRNA genes: polyphyly of Leptomonas and Blastocrithidia. J Eukaryot Microbiol 48: 161-169
119. Mignot JP (1966) Structure et ultrastructure de quelques euglénomonadines. Protistologia 2: 51-140
120. Milanowski R, Zakrys B, Kwiatowski J (2001) Phylogenetic analysis of chloroplast small-subunit rRNA genes of the genus Euglena Ehrenberg. Int J Syst Evol Microbiol 51: 773-781
121. Milyutina IA, Aleshin VV, Mikrjukov KA, Kedrova OS, Petrov NB (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
122. Minkevich P (1899) Nekotorie nabludenija nad prosteishimi na Bologovskoi Stancii. Trudy S-Peterburgsk Obsc Estestvoisp, Vyp 1, Protok Zased 29 (November 1898): 239-246
123. Montegut-Felkner A, Triemer RE (1997) Phylogenetic relationships of selected euglenoid genera based on morphological and molecular data. J Phycol 33: 512-519
124. Moore PB, Steitz TA (2002) The involvement of RNA in ribosome function. Nature 418: 229-235
125. Moreira D, Le Guyader H, Philippe H (1999) Unusually high evolutionary rate of the elongation factor 1 alpha genes from the Ciliophora and its impact on the phylogeny of eukaryotes. Mol Biol Evol 16: 234-245
126. Moreira D, López-García P, Rodríguez-Valera F (2001) New insights into the phylogenetic position of diplonemids: G+C content bias, differences of evolutionary rate and a new environmental sequence. Int J Syst Evol Microbiol 51: 2211-2219
127. Morosoli R, Lafontaine JG (1977) Characterization of ribonucleoprotein particles from the protozoa Astasia longa. Biochim Biophys Acta 476: 57-64
128. Müller KM, Cannone JJ, Gutell RR, Sheath RG (2001) A structural and phylogenetic analysis of the group IC1 introns in the order Bangiales (Rhodophyta). Mol Biol Evol 18: 1654-1667
129. Müllner AN, Angeler DG, Samuel R, Linton EW, Triemer RE (2001) Phylogenetic analysis of phagotrophic, phototrophic and osmotrophic euglenoids by using the nuclear 18S rDNA sequence. Int J Syst Evol Microbiol 51: 783-791
130. Nakatsu C, Hutchinson TC (1988) Extreme metal and acid tolerance of Euglena mutabilis and an associated yeast from Smoking Hills, Northwest Territories and their apparent mutualism. Microbiol Ecol 16: 213-231
131. Nikoh N, Fukatsu T (2001) Evolutionary dynamics of multiple group I introns in nuclear ribosomal RNA genes of endoparasitic Fungi of the genus Cordyceps. Mol Biol Evol 18: 1631-1642
132. Nudelman MA, Rossi MS, Conforti V, Triemer RE (2003) Phylogeny of Euglenophyceae based on small subunit rDNA sequences: taxonomic implications. J Phycol 39: 226-235
133. Olsen G (1987) Earliest phylogenetic branching: comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harb Symp 52: 825-837
134. Olsen G (1990) Sequence editor and analysis program. University of Illinois, Urbana
135. Owens KJ, Farmer MA, Triemer RE (1988) The flagellar apparatus and reservoir/canal cytoskeleton of Cryptoglena pigra (Euglenophyceae). J Phycol 24: 520-528
136. Page RDM (1996) TreeView: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358
137. Pandolfi JM, Lovelock CE, Budd AF (2002) Character release following extinction in a carribean reef coral species complex. Evolution 56: 479-501
138. Pankow H (1990) Ostsee-Algenflora. Gustav Fischer Verlag Jena
139. Pascher A (1931) Systematische Übersicht über die mit Flagellaten in Zusammenhang stehenden Algenreihen und Versuch einer Einreihung dieser Algenstämme in die Stämme des Pflanzenreiches. Beih Bot Centralbl 48: 317-332
140. Patterson DJ (1999) The diversity of eukaryotes. Am Nat 154 (Oct. Suppl.): 96-124
141. Perty M (1849) Über verticale Verbreitung mikroskopischer Lebensformen. Mitth Naturf Gesellsch Bern 144-166 (ausgegeben 15 Feb 1849): 17-45
142. Perty M (1852) Zur Kenntniss kleinster Lebensformen nach Bau, Funktionen, Systematik, mit Specialverzeichniss der in der Schweiz beobachteten. Jent & Reinert. Bern, 1852
143. Peyretaillade E, Biderre C, Peyret P, Duffieux F, Metenier G, Gouy M, Michot B, Vivares CP (1998) Microsporidian Encephalitozoon cuniculi, a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core. Nucleic Acids Res 26: 3513-3520
144. Philippe H (2000) Opinion: Long Branch Attraction and Protist Phylogeny. Protist 151: 307-316
145. Philippe H, Laurent J (1998) How good are deep phylogenetic trees? Curr Opin Genet Dev 8: 616-623
146. Pochmann A (1942) Synopsis der Gattung Phacus. Arch Protistenkd 95: 81-252
147. Poe S (1998) The effect of taxonomic sampling on accuracy of phylogenetic estimation: test case of a known phylogeny. Mol Biol Evol 15: 1086-1090
148. Poe S, Swofford DL (1999) Taxon sampling revisited. Nature 398: 299-300
149. Popova TG (1947) Sistematiceskije zametki po evglenovym. Izv Zap Sib Fil AN SSSR Ser biol (Novosibirsk) 2: 47-71
150. Popova TG (1951) Evglenovyje (Eugleninae) evropejskogo severa SSSR. Tr Bot Akad Nauka SSSR Ser 2, 7: 165-414
151. Popova TG (1966) Evglenovyje vodorosli vyp. 1. Flora Sporovych Rastenij SSSR. 8. Izddatel'stvo Nauka, Moskva-Leningrad
152. Popova TG, Safonova TA (1976) Evglenovyje vodorosli 2. Flora Sporovych Rastenij SSSR. 9 Izddatel'stvo Nauka, Moskva-Leningrad
153. Posada D, Crandal KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818
154. Preisfeld A, Berger S, Busse I, Liller S, Ruppel HG (2000) Phylogenetic analyses of various euglenoid taxa (Euglenozoa) based on 18S rDNA sequence data. J Phycol 36: 220-226
155. Preisfeld A, Busse I, Klingberg M, Talke S, Ruppel HG (2001) Phylogenetic position and inter-relationships of the osmotrophic euglenids based on SSU rDNA data, with emphasis on the Rhabdomonadales (Euglenozoa). Int J Syst Evol Microbiol 51: 751-758
156. Pringsheim EG (1936) Zur Kenntnis saprotropher Algen und Flagellaten. 1. Mitteilung. Über Anhäufungskulturen polysaprober Flagellaten. Arch Protistenkd 87: 43-96
157. Pringsheim EG (1942) Contributions to our knowledge of saprophytic algae and flagellata. III. Astasia, Distigma, Menoidium and Rhabdomonas. New Phytol 41: 171-205
158. Pringsheim EG (1948) Taxonomic problems in the Eugleninae. Biol Rev Cambridge Phil Soc 23: 46-61
159. Pringsheim EG (1953a) Salzwasser-Eugleninen. Arch Mikrobiol 18: 149-164
160. Pringsheim EG (1953b) Observations on some species of Trachelomonas as grown in culture. New Phytol 52: 93-113, 238-266
161. Pringsheim EG (1953c) Notiz über Colacium (Euglenaceae). Österr Bot Z 100: 270-275
162. Pringsheim EG (1956) Contributions towards a monograph of the genus Euglena. Nova Acta Leopoldina 18: 1-168
163. Pringsheim EG (1957) Two species of Trachelomonas (Eugleninae) without chlorophyll. Nature 180: 1296-1297
164. Pringsheim EG (1963) Farblose Algen. Ein Beitrag zur Evolutionsforschung. Gustav Fischer Verlag, Stuttgart
165. Pringsheim EG (1968) Zur Kenntnis einiger Arten von Euglena. Österr Bot Z 115: 201-223
166. Pringsheim EG, Hovasse R (1950) Les relations de parentéentre Astasiacées et Euglénacées. Arch Zool Exp 86: 499-549
167. Pröschold T, Marin B, Schlösser UG, Melkonian M (2001) Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov. Protist 152: 265-300
168. Rawson JR, Stutz E (1968) Characterization of Euglena cytoplasmic ribosomes and ribosomal RNA by zone velocity sedimentation in sucrose gradients. J Mol Biol 33: 309-314
169. Reize IB, Melkonian M (1989) A new way to investigate living flagellated/ciliated cells in the light microscope: immobilization of cells in agarose. Bot Acta 102: 145-151
170. Robinson M, Gouy M, Gautier C, Mouchiroud D (1998) Sensitivity of the relative - rate test to taxonomic sampling. Mol Biol Evol 15: 1091-1098
171. Rosenberg MS, Kumar S (2001) Incomplete taxon sampling is not a problem for phylogenetic inference. Proc Natl Acad Sci USA 98: 10751-10756
172. Rosowski JR, Kugrens P (1973) Observations on the euglenoid Colacium with special reference to the formation and morphology of attachment material. J Phycol 9: 370-383
173. Rosowski JR, Lee KW (1978) Cryptoglena pigra: a euglenoid with one chloroplast. J Phycol 14: 160-166
174. Rosowski JR, Willey RL (1977) Development of mucilaginous surfaces in euglenoids. I. Stalk morphology of Colacium mucronatum. J Phycol 13: 16-21
175. Rosowski JR, Vadas RL, Kugrens P (1975) Surface configuration of the Iorica of the euglenoid Trachelomonas as revealed with scanning electron microscopy. Am J Bot 62: 48-57
176. Salazar O, Gonzalez I, Genilloud O (2002) New genus-specific primers for the PCR identification of novel isolates of the genera Nocardiopsis and Saccharothrix. Int J Syst Evol Microbiol 52: 1411-1421
177. Sakharkar MK, Tan TW, De Souza SJ (2001) Generation of a database containing discordant intron positions in eukaryotic genes (MIDB). Bioinformatics 17: 671-675
178. Schlösser UG (1994) Sammlung von Algenkulturen at the University of Göttingen - catalogue of strains 1994. Bot Acta 107: 113-186
179. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16: 1114-1116
180. Shin W, Boo SM (2001) Ultrastructure of Phacus trypanon (Euglenophyceae) with an emphasis on striated fiber and microtubule arrangement. J Phycol 37: 95-105
181. Shin W, Boo SM, Triemer RE (2001) Ultrastructure of the basal body complex and putative vestigial feeding apparatus in Phacus pleuronectes (Euglenophyceae). J Phycol 37: 913-921
182. Shin W, Brosnan S, Triemer RE (2002) Are cytoplasmic pockets (MTR/pocket) present in all photosynthetic euglenoid genera? J Phycol 38: 790-799
183. Simpson AGB (1997) The identity and composition of the Euglenozoa. Arch Protistenkd 148: 318-328
184. Simpson AGB, van den Hoff J, Bernhard C, Burton HR, Patterson DJ (1997) The ultrastructure and systematic position of the euglenozoon Postgaardi mariagerensis, FENCHEL et al. Arch Protistenkd 147: 213-225
185. Skuja H (1926) Vorarbeiten zu einer Algenflora von Lettland. I. Acta Horti Bot Univ Latviensis 1: 33-54
186. Skuja H (1948) Taxonomie des Phytoplanktons einiger Seen in Uppland, Schweden. Symbolae Bot Upsaliensis 9: 1-399
187. Solomon JA, Walne PL, Dawson NS, Willey RL (1991) Structural characterization of Eutreptia (Euglenophyta). II. The flagellar root system and putative vestigial cytopharynx. Phycologia 30: 402-414
188. Sommer JR, Blum JJ (1965) Cell division in Astasia longa. Exp Cell Res 39: 504-527
189. Starmach K (1983) Euglenophyta - Eugleniny. In: Starmach K, Sieminska J (ed.) Flora Slodkowodna Polski 3. Warszawa, Krakow
190. Starr RC, Zeikus JA (1993) UTEX: the culture collection of algae at the University of Texas at Austin. J Phycol 29 (Suppl.): 1-106
191. Stein F (1878) Der Organismus der Infusionsthiere, Abt. 3: Der Organismus der Flagellaten, 1. Hälfte. Leipzig 1878
192. Stevens J, Rambaut A (2001) Evolutionary rate differences in trypanosomes. Infection, Genetics and Evolution 1: 143-150
193. Stuessy TF (1990) Plant taxonomy. The systematic evaluation of comparative data. Columbia University Press, New York
194. Sullivan J, Swofford DL, Naylor GJP (1999) The effect of taxon sampling on estimating rate heterogeneity parameters of maximum-likelihood models. Mol Biol Evol 16: 1347-1356
195. Surek B, Melkonian M (1986) A cryptic cytostome is present in Euglena. Protoplasma 133: 39-49
196. Surek B, Beemelmanns U, Melkonian M, Bhattacharya D (1994) Ribosomal RNA sequence comparisons demonstrate an evolutionary relationship between Zygnematales and charophytes. Plant Syst Evol 191: 171-181
197. Suzaki T, Williamson RE (1986) Pellicular ultrastructure and euglenoid movement in Euglena ehrenbergii Klebs and Euglena oxyuris Schmarda. J Protozool 33: 165-171
198. Swofford DL (1998) PAUP* Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts
199. Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP (2002) DNA points the way ahead in taxonomy. Nature 418: 479
200. Thompson MD, Copertino DW, Thompson E, Favreau MR, Hallick RB (1995) Evidence for the late origin of introns in chloroplast genes from an evolutionary analysis of the genus Euglena. Nucleic Acids Res 23: 4745-4752
201. Throndsen J (1969) Flagellates of Norwegian coastal waters. Nytt Mag Bot 16: 161-216
202. Throndsen J (1973) Fine structure of Eutreptiella gymnastica (Euglenophyceae). Norw J Bot 20: 271-280
203. Triemer RE, Farmer MA (1991) An ultrastructural comparison of the mitotic apparatus, feeding apparatus, flagellar apparatus and cytoskeleton in euglenoids and kinetoplastids. Protoplasma 164: 91-104
204. Triemer RE, Lewandowski CL (1994) Ultrastructure of the basal apparatus and putative vestigial feeding apparatus in a quadriflagellate euglenoid (Euglenophyta). J Phycol 30: 28-38
205. Van de Peer Y, Baldauf SL, Doolittle WF, Meyer A (2000) An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances. J Mol Evol 51: 565-576
206. Walne PL, Arnott HJ (1967) The comparative ultrastructure and possible function of eyespots: Euglena granulata and Chlamydomonas eugametos. Planta 77: 325-353
207. Walne PL, Kivic PA (1990) Phylum Euglenida. In Margulis L, Corliss JO, Melkonian M Chapman D (eds) Handbook of Protoctista. Jones and Bartlett Publishers, Boston, pp 270-287
208. Walne PL, Moestrup Ø, Norris RE, Ettl H (1986) Light and electron microscopical studies of Eutreptiella eupharyngea sp. nov. (Euglenophyceae) from Danish and American waters. Phycologia 25: 109-126
209. Wehrle E (1939) Zur Kenntnis der Algen im Naturschutzgebiet Weingartener Moor bei Karlsruhe a. Rh. Beitr naturkundl Forsch Südwestdeutschl Band IV (Heft 1): 1-84
210. West LK, Walne PL (1980) Trachelomonas hispida var. coronata (Euglenophyceae). II. Envelope substructure. J Phycol 16: 498-506
211. Willey RL, Wibel RG (1985a) The reservoir cytoskeleton and a possible cytostomal homologue in Colacium (Euglenophyceae). J Phycol 21: 570-577
212. Willey RL, Wibel RG (1985b) A cytostomeicytopharynx in green euglenoid flagellates (Euglenales) and its phylogenetic implications. BioSystems 18: 369-376
213. Willey RL, Wibel RG (1987) Flagellar roots and the reservoir cytoskeleton of Colacium libellae (Euglenophyceae). J Phycol 23: 283-288
214. Wuyts J, De Rijk P, Van de Peer Y, Pison G, Rousseeuw P, De 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
215. Wuyts J, Van de Peer Y, De Wachter R (2001) Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res 29: 5017-5028
216. Wuyts J, Van de Peer Y, Winkelmans T, De Wachter R (2002) The European database on small subunit ribosomal RNA. Nucleic Acids Res 30: 183-185
217. Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JHD, Noller HF (2001) Crystal structure of the ribosome at 5.5 Å resolution. Science 292: 883-896
218. Zakrys B (1986) Contribution to the monograph of Polish members of the genus Euglena Ehrenberg 1830. Nova Hedwigia 42: 491-540
219. Zakrys B, Cambra-Sanchez, Walne PL (2001) Chloroplast ultrastructure of Euglena cuneata Pringsheim, E. deses Ehrenberg and E. mutabilis (Euglenophyceae): taxonomic significance. Acta Protozool 40: 161-167
220. Zwickl DJ, Hillis DM (2002) Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 51: 588-598