Evaluating support for the current classification of eukaryotic diversity

PLoS Genetics

Volumn 2, Issue 12, 2006, Pages 2062-2073

  Parfrey, Laura Wegener ^a   Barbero, Erika ^b   Lasser, Elyse ^b   Dunthorn, Micah ^a   Bhattacharya, Debashish ^c   Patterson, David J ^d   Katz, Laura A ^a,b  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

^b SMITH COLLEGE   (United States)

^c UNIVERSITY OF IOWA   (United States)

^d MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; EUKARYOTE; EVOLUTION; GENEALOGY; GENETIC ANALYSIS; GENETIC VARIABILITY; MOLECULAR DYNAMICS; MONOPHYLY; NONHUMAN; PHYLOGENY; TAXONOMY; ALGA; ANIMAL; CELL NUCLEUS; CHLOROPLAST; CLASSIFICATION; COMPARATIVE STUDY; EUKARYOTIC CELL; FUNGUS; GENETICS; HUMAN; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYSIOLOGY; PLANT;

ANIMALIA; EUKARYOTA; FUNGI; PROTISTA;

ALGAE; ANIMALS; CELL NUCLEUS; CHLOROPLASTS; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; FUNGI; HUMANS; MULTIGENE FAMILY; PHYLOGENY; PLANTS; VARIATION (GENETICS);

EID: 33845985995     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020220     Document Type: Article

References (145)

1. Javaux EJ, Knoll AH, Walter MR (2001) Morphological and ecological complexity in early eukaryotic ecosystems. Nature 412: 66-69.
2. Whittaker RH (1969) New concepts of kingdoms of organisms. Science 163: 150-160.
3. Dobell CC (1911) The principles of protistology. Arch Protist 23: 269-310.
4. Copeland HF (1956) Classification of lower organisms. Palo Alto (California): Pacific Books. 302 p.
5. Margulis L, Schwartz K (1988) Five kingdoms: An illustrated guide to the phyla of life on earth. 2nd edition. New York: W. H. Freeman and Company. 520 p.
6. Cavalier-Smith T (1998) A revised six-kingdom system of life. Biol Rev Cambridge Philosophic Soc 73: 203-266.
7. Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, et al. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Euk Microbiol 52: 399-451.
8. Patterson DJ (1999) The diversity of eukaryotes. Am Nat 154: 96-124.
9. Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, et al. (2005) The tree of eukaryotes. Trends Ecol Evol 20: 670-676.
10. Baldauf SL (2003) The deep roots of eukaryotes. Science 300: 1703-1706.
11. Cavalier-Smith T (1996/97) Amoeboflagellates and mitochondrial cristae in eukaryote evolution: Megasystematics of the new protozoan subkingdoms Eozoa and Neozoa. Arch Protistenkd 147: 237-258.
12. Williams JG, Noegel AA, Eichinger L (2005) Manifestations of multicellularity: Dictyostelium reports in. Trends Genet 21: 392-398.
13. Stauffer W, Ravdin JI (2003) Entamoeba histolytica: An update. Curr Opin Infect Dis 16: 479-485.
14. Cavalier-Smith T (1999) Principles of protein and lipid targeting in secondary symbiogenesis: Euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J Euk Microbiol 46: 347-366.
15. Delwiche CF (1999) Tracing the tread of plastid diversity through the tapestry of life. Am Nat 154: 164-177.
16. Keeling PJ (2004) Diversity and evolutionary history of plastids and their hosts. Am J Bot 91: 1481-1493.
17. Cavalier-Smith T (1982) The origins of plastids. Biol J Linnean Soc 17: 289-306.
18. Prescott DM (1994) The DNA of ciliated protozoa. Microbiol Rev 58: 233-267.
19. May KJ, Ristaino JB (2004) Identity of the mtDNA haplotype(s) of Phytophthora infestans in historical specimens from the Irish Potato Famine. Mycol Res 108: 471-479.
20. Sherman IW (1998) Malaria. Washington (D. C.): ASM Press. 575 p.
21. Simpson AGB, Patterson DJ (1999) The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the "Excavate hypothesis." Eur J Protistol 35: 353-370.
22. Kreier J (1978) Parasitic Protozoa Volume II: Intestinal flagellates, histomonads, trichomonads, amoeba, opalinids, and ciliates. New York: Academic Press. 730 p.
23. Smith P (1996) Molecular biology of parasitic protozoa. Oxford: Oxford University Press. 233 p.
24. Wainright PO, Hinkle G, Sogin ML, Stickel SK (1993) Monophyletic origins of the Metazoa: An evolutionary link with fungi. Science 260: 340-342.
25. Cavalier-Smith T, Chao EE (1995) The opalozoan Apusomonas is related to the common ancestor of animals, fungi, and choanoflagellates. Proc Roy Soc Lond B-Biol Sci 261: 1-6.
26. Steenkamp ET, Wright J, Baldauf SL (2006) The protistan origins of animals and fungi. Mol Biol Evol 23: 93-106.
27. Baldauf SL, Palmer JD (1993) Animals and fungi are each other's closest relatives: Congruent evidence from multiple proteins. Proc Natl Acad Sci, U S A 90: 11558-11562.
28. Keeling PJ, Slamovits CH (2004) Simplicity and complexity of microsporidian genomes. Eukaryot Cell 3: 1363-1369.
29. King N (2004) The unicellular ancestry of animal development. Dev Cell 7: 313-325.
30. Cavalier-Smith T (1981) Eukaryote kingdoms - seven or nine. Biosystems 14: 461-481.
31. McFadden GI (2001) Primary and secondary endosymbiosis and the origin of plastids. J Phycol 37: 951-959.
32. Michod RE, Viossat Y, Solari CA, Hurand M, Nedelcu AM (2006) Life-history evolution and the origin of multicellularity. J Theor Bio 239: 257-272.
33. Cavalier-Smith T (2002) The phagotrophic origin of eukaryotes and phylogenetic classification of protozoa. Int J Syst Evol Microbiol 52: 297-354.
34. Cavalier-Smith T, Chao EE (1997) Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Arch Protistenkd 147: 227-236.
35. Bhattacharya D, Helmchen T, Melkonian M (1995) Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify an independent rhizopod lineage containing the euglyphina and the chlorarachniophyta. J Euk Microbiol 42: 65-69.
36. Archibald JM, Longet D, Pawlowski J, Keeling PJ (2003) A novel polyubiquitin structure in Cercozoa and Foraminifera: Evidence for a new eukaryotic supergroup. Mol Biol Evol 20: 62-66.
37. Yoon HS, Reyes-Prieto A, Melkonian M, Bhattacharya D (2006) Minimal plastid genome evolution in the Paulinella endosymbiont. Curr Biol 16: R670-R672.
38. Marin B, Nowack ECM, Melkonian M (2005) A plastid in the making: Primary endosymbiosis. Protist 156: 425-432.
39. Loeblich AR Jr, Tappan H (1987) Foraminiferal genera and their classification. New York: Van Nostrand Reinhold Company. 970 p.
40. Simpson AGB (2003) Cytoskeletal organization, phylogenetic affinities, and systematics in the contentious taxon Excavata (Eukaryota). Int J Syst Evol Micr 53: 1759-1777.
41. Doyle JJ (1992) Gene trees and species trees: Molecular systematics as onecharacter taxonomy. Syst Bot 17: 144-163.
42. Maddison WP (1997) Gene trees in species trees. Syst Biol 46: 523-536.
43. Hennig W (1966) Phylogenetic systematics. Urbana: University of Illinois Press. 263 p.
44. Lühe M (1913) Erstes Urreich der Tiere. In: Lang A, editor. Handbuch der morphologie der wirbellosen Tiere. Jena: G. Fischer. 416 p.
45. Cavalier-Smith T, Chao EEY, Oates B (2004) Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium. Eur J Protistol 40: 21-48.
46. Kudryavtsev A, Bernhard D, Schlegel M, Chao EEY, Cavalier-Smith T (2005) 18S ribosomal RNA gene sequences of Cochliopodium (Himatismenida) and the phylogeny of Amoebozoa. Protist 156: 215-224.
47. Smirnov A, Nassonova E, Berney C, Fahrni J, Bolivar I, et al. (2005) Molecular phylogeny and classification of the lobose amoebae. Protist 156: 129-142.
48. Fahrni JF, Bolivar I, Berney U, Nassonova E, Smirnov A, et al. (2003) Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes. Mol Biol Evol 20: 1881-1886.
49. Cavalier-Smith T (2004) Only six kingdoms of life. Proc Biol Sci 271: 1251-1262.
50. Cavalier-Smith T, Chao EEY (2003) Phylogeny and classification of phylum Cercozoa (Protozoa). Protist 154: 341-358.
51. Philippe H, Adoutte A (1998) The molecular phylogeny of Eukaryota: Solid facts and uncertainties. In: Coombs GH, Vickerman K, Sleigh MA, Warren A, editors. Evolutionary relationships among protozoa. Dodrecht: Kluwer Academic Publishers. pp. 25-56.
52. Haeckel EHPA (1866) Generelle morphologie der organismen. Allgemeine grundzüge der organischen Formen-Wissenschaft, mechanisch begründet durch die von Charles Darwin reformirte Descendenztheorie. Berlin: G. Reimer.
53. Moreira D, Le Guyader H, Philippe H (2000) The origin of red algae and the evolution of chloroplasts. Nature 405: 69-72.
54. Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, et al. (2005) Monophyly of primary photosynthetic eukaryotes: Green plants, red algae, and glaucophytes. Curr Biol 15: 1325-1330.
55. Nishi A, Ishida K, Endoh H (2005) Reevaluation of the evolutionary position of opalinids based on 18S rDNA, and alpha- and beta-tubulin gene phylogenies. J Mol Evol 60: 695-705.
56. Harper JT, Waanders E, Keeling PJ (2005) On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int J Syst Evol Micr 55: 487-496.
57. Longet D, Burki F, Flakowski J, Berney C, Polet S, et al. (2004) Multigene evidence for close evolutionary relations between Gromia and Foraminifera. Acta Protozool 43: 303-311.
58. Keeling PJ, Deane JA, McFadden GI (1998) The phylogenetic position of alpha- and beta-tubulins from the Chlorarachnion host and Cercomonas (Cercozoa). J Eukaryot Microbiol 45: 561-570.
59. Reece KS, Siddall ME, Stokes NA, Burreson EM (2004) Molecular phylogeny of the Haplosporidia based on two independent gene sequences. J Parasitol 90: 1111-1122.
60. Cavalier-Smith T (2003) The excavate protozoan phyla Metamonada Grasse emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): Their evolutionary affinities and new higher taxa. Int J Syst Evol Micr 53: 1741-1758.
61. Nikolaev SI, Berney C, Fahrni JF, Bolivar I, Polet S, et al. (2004) The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc Natl Acad Sci U S A 101: 8066-8071.
62. Penny D, McComish BJ, Charleston MA, Hendy MD (2001) Mathematical elegance with biochemical realism: The covarion model of molecular evolution. J Mol Evol 53: 711-723.
63. Philippe H, Lopez P, Brinkmann H, Budin K, Germot A, et al. (2000) Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proc Biol Sci 267: 1213-1221.
64. Felsenstein J (1988) Phylogenies from molecular sequences: Inference and reliability. Annu Rev Genet 22: 521-565.
65. Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27: 401-410.
66. Sogin ML (1991) Early evolution and the origin of eukaryotes. Curr Opin Genet Dev 1: 457-463.
67. Cavalier-Smith T (1983) A 6-kingdom classification and a unified phylogeny. In: Schenk HEA, Schwemmler W, editors. Endocytobiology II: Intracellular space as oligogenetic ecosystem. Berlin: Walter de Gruyter. pp. 1027-1034.
68. Van de Peer Y, Ben Ali A, Meyer A (2000) Microsporidia: Accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi. Gene 246: 1-8.
69. Keeling PJ, Luker MA, Palmer JD (2000) Evidence from Beta-tubulin phylogeny that Microsporidia evolved within the fungi. Mol Biol Evol 17: 23-31.
70. Embley TM, van der Giezen M, Horner DS, Dyal PL, Bell S, et al. (2003) Hydrogenosomes, mitochondria, and early eukaryotic evolution. IUBMB Life 55: 387-395.
71. Susko E, Inagaki Y, Field C, Holder ME, Roger AJ (2002) Testing for differences in rates-across-sites distributions in phylogenetic subtrees. Mol Biol Evol 19: 1514-1523.
72. Gribaldo S, Philippe H (2002) Ancient phylogenetic relationships. Theor Popul Biol 61: 391-408.
73. Philippe H, Germot A (2000) Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution. Mol Biol Evol 17: 830-834.
74. Roger AJ (1999) Reconstructing early events in eukaryotic evolution. Am Nat 154: 146-163.
75. Philippe H, Forterre P (1999) The rooting of the universal tree of life is not reliable. J Mol Evol 49: 509-523.
76. Inagaki Y, Susko E, Fast NM, Roger AJ (2004) Covarion shifts cause a longbranch attraction artifact that unites Microsporidia and Archaebacteria in EF-1 alpha phylogenies. Mol Biol Evol 21: 1340-1349.
77. Yang ZH (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Bio 13: 555-556.
78. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Evolution - Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314.
79. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
80. Katz LA (2002) Lateral gene transfers and the evolution of eukaryotes: Theories and data. Int J Syst Evol Micr 52: 1893-1900.
81. Katz LA (1999) The tangled web: Gene genealogies and the origin of eukaryotes. Am Nat 154: 137-145.
82. Andersson JO (2005) Lateral gene transfer in eukaryotes. Cell Mol Life Sci 62: 1182-1197.
83. Huang JL, Mullapudi N, Sicheritz-Ponten T, Kissinger JC (2004) A first glimpse into the pattern and scale of gene transfer in the Apicomplexa. Int J Parasitol 34: 265-274.
84. Bolivar I, Fahrni JF, 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.
85. Walker G, Dacks JB, Embley TM (2006) Ultrastructural description of Breviata anathema, n. Gen., n. Sp., the organism previously studied as "Mastigamoeba invertens." J Euk Microbiol 53: 65-78.
86. Patterson DJ (1985) The fine structure of Opalina ranarum (family Opalinidae): Opalinid phylogeny and classification. Protistologica 4: 413-428.
87. Karpov S, Sogin ML, Silberman JD (2001) Rootlet homology, taxonomy, and phylogeny of bicosoecids based on 18S rRNA gene sequences. Protistology 2: 34-47.
88. Guillou L, Chretinnot-Dinet MJ, Boulben S, Moon-Van der Staay SY, Vaulot D (1999) Symbiomonas scintillans gen. et sp. nov. Picophagus flagellatus gen. et sp. nov. (Heterokonta): Two new heterotrophic flagellates of picoplanctonic size. Protist 150: 383-398.
89. Kostka M, Hampl V, Cepicka I, Flegr J (2004) Phylogenetic position of Protoopalina intestinalis based on SSU rRNA gene sequence. Mol Phy Evol 33: 220-224.
90. Lipscomb DL (1984) Methods of systematic analysis: The relative superiority of phylogenetic systematics. Orig Life 13: 235-240.
91. Simpson AGB (1997) The identity and composition of the Euglenozoa. Archiv Fur Protistenkunde 148: 318-328.
92. Hendy MD, Penny D (1989) A framework for the quantitative study of evolutionary trees. Syst Zool 38: 297-309.
93. Amaral-Zettler LA, Nerad TA, O'Kelly CJ, Sogin ML (2001) The nucleariid amoebae: More protists at the animal-fungal boundary. J Euk Microbiol 48: 293-297.
94. 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.
95. Cummings MP, Meyer A (2005) Magic bullets and golden rules: Data sampling in molecular phylogenetics. Zoology 108: 329-336.
96. Cummings MP, Otto SP, Wakeley J (1995) Sampling properties of DNA-sequence data in phylogenetic analysis. Mol Biol Evol 12: 814-822.
97. Bapteste E, Brinkmann H, Lee JA, Moore DV, Sensen CW, et al. (2002) The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci U S A 99: 1414-1419.
98. Rokas A, Carroll SB (2005) More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol 22: 1337-1344.
99. DeBry RW (2005) The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony. Syst Biol 54: 432-440.
100. Hillis DM (1998) Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst Biol 47: 3-8.
101. Hillis DM, Pollock DD, McGuire JA, Zwickl DJ (2003) Is sparse taxon sampling a problem for phylogenetic inference? Syst Biol 52: 124-126.
102. Taylor FJR (1999) Ultrastructure as a control for protistan molecular phylogeny. Am Nat 154: 125-136.
103. Nosenko T, Lidie KL, Van Dolah FM (2006) Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis. Mol Biol Evol 23: 2026-2038.
104. Bhattacharya D, Yoon HS, Hackett JD (2004) Photosynthetic eukaryotes unite: Endosymbiosis connects the dots. Bioessays 26: 50-60.
105. McFadden GI, van Dooren GG (2004) Evolution: Red algal genome affirms a common origin of all plastids. Curr Biol 14: R514-R516.
106. Weber A, Linka M, Bhattacharya D (2006) Single, ancient origin of a plastid metabolite translocator family in Plantae from an endomembranes-derived ancestor. Eukaryot Cell 5: 609-612.
107. Yoon HS, Hackett JD, Van Dolah FM, Nosenko T, Lidie L, et al. (2005) Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. Mol Biol Evol 22: 1299-1308.
108. Sanchez-Puerta MV, Bachvaroff TR, Delwiche CF (2005) The complete plastid genome sequence of the haptophyte Emiliania huxleyi: A comparison to other plastid genomes. DNA Res 12: 151-156.
109. APG II (2003) An update of the Angiosperm Phylogeny group classification for the orders and families of flowering plants. Bot J Linnean Soc: 399-436.
110. APG I (1998) An ordinal classification for the families of flowering plants. Ann Missouri Bot Gard: 531-553.
111. Felsenstein J (2004) Inferring phylogenies. Sunderland, Massachusetts: Sinaur Associates. 580 p.
112. Efron B, Halloran E, Holmes S (1996) Bootstrap confidence levels for phylogenetic trees. Proc Natl Acad Sci, U S A 93: 13429-13434.
113. Lewis PO, Holder MT, Holsinger KE (2005) Polytomies and Bayesian phylogenetic inference. Syst Biol 54: 241-253.
114. Cavalier-Smith T (1997) Amoeboflagellates and mitochondrial cristae in eukaryote evolution: Megasystematics of the new protozoan subkingdoms Eozoa and Neozoa. Arch Protistenkd 147: 237-258.
115. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290: 972-977.
116. Zhang Z, Green BR, Cavalier-Smith T (1999) Single-gene circles in dinoflagellate chloroplast genomes. Nature 400: 155-160.
117. Yoon HS, Hackett JD, Pinto G, Bhattacharya D (2002) The single, ancient origin of chromist plastids. Proc Natl Acad Sci U S A 99: 15507-15512.
118. Harper JT, Keeling PJ (2003) Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol 20: 1730-1735.
119. Inagaki Y, Simpson AGB, Dacks JB, Roger AJ (2004) Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: Dinoflagellate plastid origins as a case study. Syst Biol 53: 582-593.
120. Patron NJ, Rogers MB, Keeling PJ (2004) Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates. Eukaryot Cell 3: 1169-1175.
121. Bachvaroff TR, Puerta MVS, Delwiche CF (2005) Chlorophyll c-containing plastid relationships based on analyses of a multigene dataset with all four chromalveolate lineages. Mol Biol Evol 22: 1772-1782.
122. Stechmann A, Cavalier-Smith T (2003) Phylogenetic analysis of eukaryotes using heat-shock protein Hsp90. J Mol Evol 57: 408-419.
123. Dacks JB, Silberman JD, Simpson AGB, Moriya S, Kudo T, et al. (2001) Oxymonads are closely related to the excavate taxon Trimastix. Mol Biol Evol 18: 1034-1044.
124. Silberman JD, Simpson AGB, Kulda J, Cepicka I, Hampl V, et al. (2002) Retortamonad flagellates are closely related to diplomonads - Implications for the history of mitochondrial function in eukaryote evolution. Mol Biol Evol 19: 777-786.
125. Simpson AGB, Roger AJ, Silberman JD, Leipe DD, Edgcomb VP, et al. (2002) Evolutionary history of "early-diverging" eukaryotes: The excavate taxon Carpediemonas is a close relative of Giardia. Mol Biol Evol 19: 1782-1791.
126. Moriya S, Dacks JB, Takagi A, Noda S, Ohkuma M, et al. (2003) Molecular phylogeny of three oxymonad genera: Pyrsonympha, Dinenympha, and Oxymonas. J Eukaryot Microbiol 50: 190-197.
127. Simpson AGB, Inagaki Y, Roger AJ (2006) Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes. Mol Biol Evol 23: 615-625.
128. Hampl V, Horner DS, Dyal P, Kulda J, Flegr J, et al. (2005) Inference of the phylogenetic position of oxymonads based on nine genes: Support for Metamonada and Excavata. Mol Biol Evol 22: 2508-2518.
129. Cavalier-Smith T, Allsopp M (1996) Corallochytrium, an enigmatic non-flagellate protozoan related to choanoflagellates. Eur J Protistol 32: 306-310.
130. Ragan MA, Goggin CL, Cawthorn RJ, Cerenius L, Jamieson AVC, et al. (1996) A novel clade of protistan parasites near the animal-fungal divergence. Proc Natl Acad Sci U S A 93: 11907-11912.
131. Cavalier-Smith T, Chao EEY (2003) Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution. J Mol Evol 56: 540-563.
132. Ragan MA, Murphy CA, Rand TG (2003) Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor 1 alpha of Ichthyophonus irregularis. Mol Phylogenet Evol 29: 550-562.
133. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, et al. (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A 99: 12246-12251.
134. Hagopian JC, Reis M, Kitajima JP, Bhattacharya D, de Oliveira MC (2004) Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts and their relationship to other plastids. J Mol Evol 59: 464-477.
135. Chu KH, Qi J, Yu ZG, Anh V (2004) Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Mol Biol Evol 21: 200-206.
136. Bhattacharya D, Helmchen T, Bibeau C, Melkonian M (1995) Comparisons of nuclear-encoded small-subunit ribosomal-RNAs reveal the evolutionary position of the Glaucocystophyta. Mol Biol Evol 12: 415-420.
137. Bhattacharya D, Weber K (1997) The actin gene of the glaucocystophyte Cyanophora paradoxa: Analysis of the coding region and introns, and an actin phylogeny of eukaryotes. Curr Genet 31: 439-446.
138. Stiller JW, Riley J, Hall BD (2001) Are red algae plants? A critical evaluation of three key molecular datasets. J Mol Evol 52: 527-539.
139. Nozaki H (2005) A new scenario of plastid evolution: Plastid primary endosymbiosis before the divergence of the "Plantae," emended. J Plant Res 118: 247-255.
140. Cavalier-Smith T, Chao EE (1997) Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Archiv Fur Protistenkd 147: 227-236.
141. Keeling PJ (2001) Foraminifera and Cercozoa are related in actin phylogeny: Two orphans find a home? Mol Biol Evol 18: 1551-1557.
142. Berney C, Pawlowski J (2003) Revised small subunit rRNA analysis provides further evidence that foraminifera are related to Cercozoa. J Mol Evol 57: S120-S127.
143. Nikolaev SI, Berney C, Fahrni J, Mylnikov AP, Aleshin VV, et al. (2003) Gymnophrys cometa and Lecythium sp are core Cercozoa: Evolutionary implications. Acta Protozool 42: 183-190.
144. Longet D, Archibald JM, Keeling PJ, Pawlowski J (2003) Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies. Int J Syst Evol Micr 53: 1735-1739.
145. Archibald JM, Keeling PJ (2004) Actin and ubiquitin protein sequences support a cercozoan/foraminiferan ancestry for the plasmodiophorid plant pathogens. J Eukaryot Microbiol 51: 113-118.