Protein phylogenies robustly resolve the deep-level relationships within Euglenozoa

Molecular Phylogenetics and Evolution

Volumn 30, Issue 1, 2004, Pages 201-212

  Simpson, Alastair G B ^a   Roger, Andrew J ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Algae; Euglena; Heat shock protein; Kinetoplast; Protists; Protozoa; Secondary symbiosis; Trypanosomes

Indexed keywords

ALGAE; DIPLONEMIDA; EUGLENA; EUGLENA GRACILIS; EUGLENIDA; EUGLENOZOA; HETEROLOBOSEA; KINETOPLASTIDA; PROTISTA; PROTOZOA;

EID: 0345832217     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(03)00177-5     Document Type: Article

References (63)

1. Andersson, J.O., Roger, A.J., 2002. A cyanobacterial gene in nonphotosynthetic protists - an early chloroplast acquisition in eukaryotes? Curr. Biol. 12, 115-119.
2. Archibald, J.M., Cavalier-Smith, T., Maier, U., Douglas, S., 2001. Molecular chaperones encoded by a reduced nucleus: the cryptomonad nucleomorph. J. Mol. Evol. 52, 490-501.
3. Archibald, J.M., Keeling, P.J., 2002. Recycled plastids: a 'green movement' in eukaryotic evolution. Trends Genet. 18, 577-584.
4. Atkins, M.S., Teske, A.P., Anderson, O.R., 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.
5. Baldauf, S.L., Doolittle, W.F., 1997. Origin and evolution of the slime molds (Mycetozoa). Proc. Natl. Acad. Sci. USA 94, 12007-12012.
6. Baldauf, S.L., Roger, A.J., Wenk-Siefert, I., Doolittle, W.F., 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972-977.
7. Bapteste, E., Brinkmann, H., Lee, J.A., Moore, D.V., Sensen, C.W., 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.
8. Blom, D., de Haan, A., van den Berg, M., Sloof, P., Jirku, M., Lukes, J., Benne, R., 1998. RNA editing in the free-living bodonid Bodo saltans. Nucleic Acids Res. 26, 1205-1213.
9. Bonen, L., 1993. Trans-splicing of pre-mRNA in plants, animals and protists. FASEB J. 7, 40-46.
10. Brugerolle, G., 1985. Des trichocystes chez les bodonides, un caractère phylogénétique supplémentaire entre Kinetoplastida et Euglenida. Protistologica 21, 339-348.
11. 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.
12. Busse, I., Preisfeld, A., 2003. Systematics of primary osmotrophic euglenids: a molecular approach to the phylogeny of Distigma and Astasia. Int. J. Syst. Evol. Microbiol. 53, 617-624.
13. Callahan, H., Litaker, R.W., Noga, E.J., 2002. Molecular taxonomy of the suborder Bodonina (Order Kinetoplastida), including the important fish parasite, Ichthyobodo necator. J. Eukaryot. Microbiol. 49, 119-128.
14. Cavalier-Smith, T., 1995. Zooflagellate phylogeny and classification. Tsitologia 37, 1010-1029.
15. Cavalier-Smith, T., 1998. A revised six-kingdom system of life. Biol. Rev. 73, 203-266.
16. Cavalier-Smith, T., 1999. Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryotic family tree. J. Eukaryot. Microbiol. 46, 347-366.
17. Cavalier-Smith, T., 2000. Flagellate megaevolution: the basis for eukaryote diversification. In: Leadbeater, B.S.C., Green, J.C. (Eds.), The Flagellates; Unity, Diversity and Evolution. Taylor and Francis, London, pp. 361-390.
18. Dawson, N.S., Walne, P.L., 1994. Evolutionary trends in euglenoids. Arch. Protistenkd. 144, 221-225.
19. Dolezel, D., Jirku, M., Maslov, D.A., Lukes, J., 2000. Phylogeny of the bodonid flagellates (Kinetoplastida) based on small-subunit rRNA gene sequences. Int. J. Syst. Evol. Microbiol. 50, 1943-1951.
20. Elbrächter, M., Schnepf, E., Balzer, I., 1996. Hemistasia phaeocysticola (Scherffel) comb. nov., redescription of a free-living, marine phagotrophic kinetoplastid flagellate. Arch. Protistenkd. 147, 125-136.
21. Estévez, A.M., Simpson, L., 1999. Uridine insertion/deletion RNA editing in trypanosome mitochondria: a review. Gene 240, 247-260.
22. Felsenstein, J., 2000. PHYLIP (Phylogeny inference package), version 3.6a. Seattle: Distributed by the author, University of Washington.
23. Frantz, C., Ebel, C., Paulus, F., Imbault, P., 2000. Characterization of trans-splicing in Euglenoids. Curr. Genet. 37, 349-355.
24. Gibbs, S.P., 1978. The chloroplasts of Euglena may have evolved from symbiotic green algae. Can. J. Bot. 56, 2883-2889.
25. Hannaert, V., Saavedra, E., Duffieux, F., Szikora, J.-P., Rigden, D.J., Michels, P.A.M., Opperdoes, F.R., 2003. Plant-like traits associated with metabolism of Trypanosoma parasites. Proc. Natl. Acad. Sci. USA 100, 1067-1071.
26. Inagaki, Y., Hayashi-Ishimaru, Y., Ehara, M., Igarashi, I., Ohama, T., 1997. Algae or protozoa: phylogenetic position of euglenophytes and dinoflagellates as inferred from mitochondrial sequences. J. Mol. Evol. 45, 295-300.
27. Keeling, P.J., Doolittle, W.F., 1996. Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Mol. Biol. Evol. 13, 1297-1305.
28. Kent, M.L., Elston, R.A., Nerad, T.A., Sawyer, T.K., 1987. An Isonema-like flagellate (Protozoa: Mastigophora) infection in larval geoduck clams, Panope abrupta. J. Invertebr. Pathol. 50, 221-229.
29. Kivic, P.A., Walne, P.L., 1984. An evaluation of a possible phylogenetic relationship between the Euglenophyta and Kinetoplastida. Orig. Life 13, 269-288.
30. Larsen, J., Patterson, D.J., 1990. Some flagellates (Protista) from tropical marine sediments. J. Nat. Hist. 24, 801-937.
31. Leander, B.S., Triemer, R.E., Farmer, M.A., 2001. Character evolution in heterotrophic euglenids. Eur. J. Protistol. 37, 337-356.
32. Leedale, G.F., 1978. Phylogenetic criteria in euglenoid flagellates. BioSystems 10, 183-187.
33. Leedale, G.F., Vickerman, K., 2000. Phylum Euglenozoa. In: Lee, J.J., Leedale, G.F., Bradbury, P. (Eds.), The Illustrated Guide to the Protozoa, second ed. Society of Protozoologists, Lawrence, Kansas, pp. 1135-1185.
34. Lipscomb, D.L., 1989. Relationships among the eukaryotes. In: Fernholm, B., Bremer, K., Jörnvall, H. (Eds.), The Hierarchy of Life. Elsevier Science Publishers, Amsterdam, pp. 161-178.
35. López-Garcia, P., Philippe, H., Gail, F., Moreira, D., 2003. Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge. Proc. Natl. Acad. Sci. USA 100, 697-702.
36. Maslov, D.A., Yasuhira, S., Simpson, L., 1999. Phylogenetic affinities of Diplonema within the Euglenozoa as inferred from the SSU rRNA gene and partial CO1 protein sequences. Protist 150, 33-42.
37. Montegut-Felkner, A.E., Triemer, R.E., 1992. Phylogenetic placement of Diplonema ambulator inferred from small subunit rRNA analysis. J. Phycol. 28 (Suppl.), 12.
38. Montegut-Felkner, A.E., Triemer, R.E., 1994. Phylogeny of Diplonema ambulator (Larsen and Patterson). 1. Homologies of the flagellar apparatus. Eur. J. Protistol. 30, 227-237.
39. Montegut-Felkner, A.E., Triemer, R.E., 1996. Phylogeny of Diplonema ambulator (Larsen and Patterson). 2. Homologies of the feeding apparatus. Eur. J. Protistol. 32, 64-76.
40. Moreira, D., Lopez-Garcia, P., Rodriguez-Valera, F., 2001. New insights on the phylogenetic position of diplonemids: GC content bias, differences of evolutionary rate, and a new environmental sequence. Int. J. Syst. Evol. Microbiol. 51, 2211-2219.
41. Myler, P., Audleman, L., deVos, T., Hixson, G., Kiser, P., Lemly, C., Magness, C., Rickel, E., Sisk, E., Sunkin, S., Swartzell, S., Westlake, T., Bastien, P., Fu, G., Ivens, A., Stuart, K., 1999. Leishmania major Friedlin chromosome 1 has an unusual distribution of protein-coding genes. Proc. Natl. Acad. Sci. USA 96, 2902-2906.
42. Philippe, H., Adoutte, A., 1998. The molecular phylogeny of Eukaryota: solid facts and uncertainties. In: Coombs, G.H., Vickerman, K., Sleigh, M.A., Warren, A. (Eds.), Evolutionary Relationships Among Protozoa. Chapman and Hall, London, pp. 25-56.
43. Preisfeld, A., Busse, I., Klingberg, M., Talke, S., Ruppel, H.G., 2001. Phylogenetic position and inter-relationships of the osmotrophic euglenids based on SSUrDNA data, with emphasis on the Rhabdomonadales (Euglenozoa). Int. J. Syst. Evol. Microbiol. 51, 751-758.
44. Santana, D.M., Lukes, J., Sturm, N.R., Campbell, D.A., 2001. Two sequence classes of kinetoplastid 5S ribosomal RNA gene revealed among bodonid spliced leader RNA gene arrays. FEMS Microbiol. Lett. 204, 233-237.
45. Searle, S., Smith, D.F., 1993. Leishmania major: characterisation and expression of a cytoplasmic stress-related protein. Exp. Parasitol. 77, 43-52.
46. Shimodaira, H., 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51, 492-508.
47. Shimodaira, H., Hasegawa, M., 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246-1247.
48. Simpson, A.G.B., 1997. The identity and composition of the Euglenozoa. Arch. Protistenkd. 148, 318-328.
49. Simpson, A.G.B., Lukes, J., Roger, A.J., 2002. The evolutionary history of kinetoplastids and their kinetoplasts. Mol. Biol. Evol. 19, 2071-2083.
50. Simpson, A.G.B., Roger, A.J., 2002. Eukaryotic evolution: getting to the root of the problem. Curr. Biol. 12, R691-R693.
51. Simpson, A.G.B., van den Hoff, J., Bernard, C., Burton, H.R., Patterson, D.J., 1997. The ultrastructure and systematic position of the euglenozoon Postgaardi mariagerensis Fenchel et al. Arch. Protistenkd. 147, 213-225.
52. Strimmer, K., von Haeseler, A., 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964-969.
53. Sturm, N.R., Maslov, D.A., Grisard, E.C., Campbell, D.A., 2001. Diplonema spp. possess spliced leader RNA genes similar to the kinetoplastids. J. Eukaryot. Microbiol. 48, 325-331.
54. Swofford, D.L., 2000. PAUP*, Phylogenetic Analysis Using Parsimony (*and other methods), version 4. Sunderland, Massachusetts: Sinauer Associates.
55. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882.
56. Thompson, M.D., Zhang, L., Hong, L., Hallick, R.B., 1997. Two new group-II twintrons in the Euglena gracilis chloroplast are absent in basally branching Euglena species. Curr. Genet. 31, 89-95.
57. Triemer, R.E., 1992. Ultrastructure of mitosis in Diplonema ambulator Larsen and Patterson (Euglenozoa). Eur. J. Protistol. 23, 398-404.
58. Triemer, R.E., Farmer, M.A., 1991. An ultrastructural comparison of the mitotic apparatus, feeding apparatus, flagellar apparatus and cytoskeleton in euglenoids and kinetoplastids. Protoplasma 164, 91-104.
59. Vickerman, K., 1976. The diversity of the kinetoplastid flagellates. In: Lumsden, W., Evans, D. (Eds.), Biology of the Kinetoplastida. Academic Press, London, pp. 1-34.
60. Whelan, S., Goldman, N., 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18, 691-699.
61. Wright, A.-D.G., Li, S., Feng, S., Martin, D.S., Lynn, D.H., 1999. Phylogenetic position of the kinetoplastids, Cryptobia bullocki, Cryptobia catostomi, and Cryptobia salmositica and monophyly of the genus Trypanosoma inferred from small subunit ribosomal RNA sequences. Mol. Biochem. Parasitol. 99, 69-76.
62. Yang, Z., 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13, 555-556.
63. Yasuhira, S., Simpson, L., 1997. Phylogenetic affinity of mitochondria of Euglena gracilis and kinetoplastids using cytochrome oxidase I and hsp60. J. Mol. Evol. 44, 341-347.