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References

 

 

 

Amaral Zettler LA, Nerad TA, O'Kelly CJ, Peglar MT, Gillevet PM, Silberman JD, Sogin ML (2000) A molecular reassessment of the leptomyxid amoebae. Protist 151:275-282.

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.

Archibald JM, Longet D, Pawlowski J, Jeeling PJ (2003) A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol. 20:62-66. Download PDF

Arisue N, Hashimoto T, Lee JA, Moore DV, Gordon P, Sensen CW, Gaasterland T, Hasegawa M, Müller M (2002) The phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1alpha and EF-2. J. Eukaryot. Microbiol. 49:1-10.

Atkins MS, Teske AP, Anderson OR (2000) A survey of flagellate diversity at four deep-sea hydrothermal vents in the Eastern Pacific Ocean using structural and molecular approaches. J. Eukaryot. Microbiol. 47:400-411.

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Baldauf SL, Doolittle WF (1997) Origin and evolution of slime molds (Mycetozoa). Proc. Natl. Acad. Sci. USA 94:12007-12012.

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.

Bapteste E, Brinkmann H, Lee JA, Moore DV, Sensen CW, Gordon P, Durufle L, Gaasterland T, Lopez P, Müller M, Philippe H (2002) The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. USA 99:1414-1419.

Bark AW (1973) A study of the genus Cochliopodium Hertwig and Lesser 1874. Protistologica 9:119-138.

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. Download PDF

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 Clorarachniophyta. J. Eukaryot. Microbiol. 42:65-69.

Bhattacharya D, Oliveira MC (2000) The SSU rDNA coding region of a filose amoeba contains a group I intron lacking the universally conserved G at the 3’-terminus. J. Eukaryot. Microbiol. 47:585-589. 

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. Download PDF

Booton GC, Rogerson A, Bonilla TD, Seal DV, Kelly DJ, Beattie TK, Tomlinson A, Lares-Villa F, Fuerst PA, Byers TJ (2004) Molecular and physiological evaluation of subtropical environmental isolates of Acanthamoeba spp., causal agent of Acanthamoeba keratitis. J. Eukaryot. Microbiol. 51:192-200.

Bovee EC (1985) Class Lobosea Carpenter, 1861. In Lee JJ, Hutner SH, Bovee EC (eds) An Illustrated Guide to the Protozoa. Allen Univ. Press, Lawrence, pp 158-211.

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Burki F, Berney C, Pawlowski J (2002) Phylogenetic position of Gromia oviformis Dujardin inferred from nuclear-encoded small subunit ribosomal DNA. Protist 153:251-260. Download PDF

Cavalier-Smith T (1998) A revised six-kingdom system of life. Biol. Rev. Camb. Philos. Soc. 73:203-266.

Cavalier-Smith T (2002) The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. 52:297-354.

Cavalier-Smith T, Chao EE (1997) Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Arch. Protistenkd. 147:227-236.

Cavalier-Smith T, Chao EE (2003a) Phylogeny of Choanozoa, Apusozoa, and other Protozoa and early eukaryote megaevolution. J.Mol. Evol. 56:540-563.

Cavalier-Smith T, Chao EE (2003b) Phylogeny and classification of phylum Cercozoa (Protozoa). Protist 154:341-358.

Cavalier-Smith T, Chao EE, Oates B (2004) Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium. Eur. J. Protistol. 40:21-48.

Deol I, Robledo L, Meza A, Visvesvara GS, Andrews RJ (2000) Encephalitis due to a free-living amoeba (Balamuthia mandrillaris): case report with literature review. Surg. Neurol. 53:611-616.

Dykstra MJ, Keller HW (2001) Class Mycetozoa. In Lee JJ, Leedale GF, Bradbury P (eds) An Illustrated Guide to the Protozoa, 2nd edition. Society of Protozoologists, Lawrence, Kansas, Vol. II, pp 952–981.

Fahrni JF, Bolivar I, Berney C, Nassonova E, Smirnov A, Pawlowski J (2003) Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes. Mol. Biol. Evol. 20:1881-1886. Download PDF

Forget L, Ustinova J, Wang Z, Huss VAR, Lang BF (2002) Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi. Mol. Biol. Evol. 19:310-319.

Gillevet PM, O’Kelly C (2003) Progress in Paramoeba research. Proc. Third Long Island Sound Lobster health Symposium, pp 50-52.

Grebecki A, Grebecka L (1978) Morphodynamic types of Amoeba proteus: a terminological proposal. Protistologica 14:349-358.

Haberey M, Huelsmann N (1973) Vergleichende mikrokinematographische Untersuchungen an 4 Amoebenspecies. Protistologica 9:247-254.

Hollande A (1945) Biologie et reproduction des Rhizopodes des genres Pelomyxa et Amoeba et cycle evolutif de l’Amoephylus destructor nov. gen. sp. (Chytridinae?) parasite de Pelomyxa palustris. Greef. Bull. Biol. Fr. Belg. 79:31-66.

Keeling PJ (2001) Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Mol. Biol. Evol. 18:1551-1557.

Kudryavtsev AA (1999) Description of Cochliopodium larifeili n. sp., an amoeba with peculiar scale structure, and notes on the diagnosis of the genus Cochliopodium (Hertwig and Lesser, 1874) Bark, 1973. Protistology 1:66-71. 

Kühn S, Lange M, Medlin LK (2000) Phylogenetic position of Cryothecomonas inferred from nuclear-encoded small subunit ribosomal RNA. Protist 151:337-345.

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. Microbiol. 53:1735-1739. Download PDF

Longet D, Burki F, Flakowski J, Berney C, Polet S, Fahrni J, Pawlowski J (2004) Multigene evidence for close evolutionary relations between Gromia and Foraminifera. Acta Protozool. (in press).

Margulis L, McKhann HI, Olendzenski L (1993) Illustrated Glossary of the Protoctista. Jones and Bartlett Publishers International.

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 11:131-139.

Nikolaev SI, Berney C, Fahrni J, Mylnikov AP, Aleshin VV, Petrov NB, Pawlowski J (2003) Gymnophrys cometa and Lecythium sp. are core Cercozoa: evolutionary implications. Acta Protozool. 42:183-190. Download PDF

Nikolaev SI, Berney C, Fahrni JF, Bolivar B, Polet S, Mylnikov AP, Aleshin VV, Petrov NB, Pawlowski, J (2004) The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid Eukaryotes. Proc. Natl. Acad. Sci. USA 101:8066-8071. Download PDF

Nikolaev SI., Petrov NB, Mylnikov AP, Berney C, Fahrni J, Pawlowski J (2004) Phylogenetic position of Multicilia marina and the evolution of Amoebozoa. Protist (submitted).

Olive LS (1975) The Mycetozoans. Academic Press, New York.

Page FC (1983) Marine Gymnamoebae. Institute of Terr. Ecology, Cambridge.

Page FC (1987) The classification of 'naked' amoebae (Phylum Rhizopoda). Arch. Protistenkd. 133:199-217.

Page FC (1988) A new key to freshwater and soil Gymnamoebia. Freshwater Biol. Ass., Ambleside, Cumbria.

Page FC, Blakey SM (1979) Cell surface structure as a taxonomic character in the Thecamoebidae (Protozoa: Gymnamoebia). Zool. J. Linn. Soc. 66:113-135.

Page FC, Willumsen NBS (1983) A light- and electron-microscopical study of Paraflabellula reniformis (Schmoller, 1964), type species of a genus of amoebae (Amoebida, Flabellulidae) with subpseudopodia. Protistologica 19:567-575.

Peglar MT, Amaral Zettler LA, Anderson OR, Nerad TA, Gillevet PM, Mullen TE, Frasca Jr S, Silberman JD, O'Kelly CJ, Sogin ML (2003) Two new small-subunit ribosomal RNA gene lineages within the subclass Gymnamoebia. J. Eukaryot. Microbiol. 50:224-232.

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. Download PDF

Simpson AGB, Roger AJ (2002) Eukaryotic evolution: getting to the root of the problem. Curr. Biol. 12:R691-R693.

Smirnov A, Brown S (2004) Guide to the study and identification of soil amoebae. Protistology 3:148-190.

Smirnov AV (1999a) An illustrated survey of gymnamoebae - Euamoebida and Leptomyxida (Rhizopoda, Lobosea), isolated from anaerobic sediments of the Nivaa Bay (Baltic Sea, The Sound). Ophelia 50:113-148.

Smirnov AV (1999b) Korotnevella diskophora n.sp. (Gymnamoebia, Paramoebidae) - small freshwater amoeba with peculiar scales. Protistology 1:30-33.

Smirnov AV, Goodkov AV (1999) An illustrated list of the basic morphotypes of Gymnamoebia (Rhizopoda, Lobosea). Protistology 1:20-29.

Smirnov AV, Nassonova ES, Berney C, Fahrni J, Bolivar I, Pawlowski J (2004) Small-subunit ribosomal RNA gene phylogeny and morphological classification of the Gymnamoebia. Protist (submitted).

Stechmann A, Cavalier-Smith T (2003) The root of the eukaryotic tree pinpointed. Curr. Biol. 13:R665-R666.

Stothard DR, Schroeder-Diedrich JM, Awwad MH, Gast RJ, Ledee DR, Rodriguez-Zaragoza S, Dean CL, Fuerst PA, Byers TJ (1998) The evolutionary history of the genus Acanthamoeba and the identification of eight new 18S rRNA gene sequence types. J. Eukaryot. Microbiol. 45:45-54.

Vickerman K, Le Ray D, Hoef-Emdan K, De Jonckheere J (2002) The soil flagellate Proleptomonas faecicola: cell organisation and phylogeny suggest that the only described free-living trypanosomatid is not a kinetoplastid but has cercomonas affinities. Protist 153:9-24.

Visvesvara GS, Schuster FL, Martinez AJ (1993) Balamuthia mandrillaris, n. g., n. sp., agent of amebic meningoencephalitis in humans and other animals.  J. Eukaryot. Microbiol. 40:504-514.

Wylezich C, Meisterfeld R, Meisterfeld S, Schlegel M (2002) 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.

 

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