Evolutionary history of "early-diverging" eukaryotes: The excavate taxon Carpediemonas is a close relative of Giardia

Molecular Biology and Evolution

Volumn 19, Issue 10, 2002, Pages 1782-1791

  Simpson, Alastair G B ^a   Roger, Andrew J ^a   Silberman, Jeffrey D ^b,c   Leipe, Detlef D ^b,c   Edgcomb, Virginia P ^d   Jermiin, Lars S ^e   Patterson, David J ^e   Sogin, Mitchell L ^d  

^a DALHOUSIE UNIVERSITY   (Canada)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d MARINE BIOLOGICAL LABORATORY   (United States)

^e UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Archezoa; Diplomonads; Eukaryote evolution; Jakobids; Mitochondria; Protists

Indexed keywords

ALPHA TUBULIN; BETA TUBULIN; RIBOSOME RNA;

ARTICLE; CELL ORGANELLE; CLADISTICS; EUKARYOTE EVOLUTION; EUKARYOTIC CELL; FLAGELLATE; GENETIC VARIABILITY; GIARDIA; MAXIMUM LIKELIHOOD METHOD; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA GENE; TAXON;

ARCHEZOA; CARPEDIEMONAS; DIPLOMONADIDA; EUGLENOZOA; EUKARYOTA; GIARDIA; JAKOBIDAE; MASTIGOPHORA (FLAGELLATES); PARABASALIDEA; PROTISTA; PROTOZOA; RETORTAMONADIDAE;

EID: 0036791132     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004000     Document Type: Article

References (51)

1. Andersson, J. O., and A. J. Roger. 2002. A cyanobacterial gene in nonphotosynthetic protists - an early chloroplast acquisition in eukaryotes? Curr. Biol. 12:115-119.
2. Archibald, J. M., C. J. O'kelly, and W. F. Doolittle. 2002. The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolution. Mol. Biol. Evol. 19:422-431.
3. Baldauf, S. L., A. J. Roger, I. Wenk-siefert, and W. F. Doolittle. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977.
4. Bernard, C., A. G. B. Simpson, and D. J. Patterson. 2000. Some free-living flagellates (Protista) from anoxic habitats. Ophelia 52:113-142.
5. Brugerolle, G. 1991. Flagellar and cytoskeletal systems in amitochondrial flagellates: Archamoeba, Metamonada and Parabasala. Protoplasma 164:70-90.
6. Brugerolle, G., and D. J. Patterson. 1997. Ultrastructure of Trimastix convexa Hollande, an amitochondriate anaerobic flagellate with a previously undescribed organization. Europ. J. Protistol. 33:121-130.
7. Cavalier-Smith, T. 1983. A 6-kingdom classification and a unified phylogeny. Pp. 1027-1034 in W. Schwemmler, and H. E. A. Schenk, eds. Endocytobiology. de Gruyter, Berlin.
8. -. 2000. Flagellate megaevolution: the basis for eukaryote diversification. Pp. 361-390 in B. S. C. Leadbeater, and J. C. Green, eds. The flagellates; unity, diversity and evolution. Taylor and Francis, London.
9. -. 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. 52:297-354.
10. Chihade, J. W., J. R. Brown, P. R. Schimmel, and L. Ribas De Pouplana. 2000. Origin of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA synthetase. Proc. Natl. Acad. Sci. USA 97:12153-12157.
11. Dacks, J. B., J. D. Silberman, A. G. B. Simpson, S. Moruya, T. Kudo, M. Ohkuma, and R. Redfield. 2001. Oxymonads are closely related to the excavate taxon Trimastix. Mol. Biol. Evol. 18:1034-1044.
12. Doolittle, W. F. 1998. You are what you eat: a genetic transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet. 14:307-311.
13. Dyall, S. D., and P. J. Johnson. 2000. Origins of hydrogenosomes and mitochondria: evolution and organelle biogenesis. Curr. Opin. Microbiol. 3:404-411.
14. Edgcomb, V. P., A. J. Roger, A. G. B. Simpson, D. Kysela, and M. L. Sogin. 2001. Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies. Mol. Biol. Evol. 18:514-522.
15. Embley, T. M., and R. P. Hirt. 1998. Early branching eukaryotes? Curr. Opin. Genet. Dev. 8:624-629.
16. Felsenstein, J. 2000. PHYLIP (phylogeny inference package). Version 3.6a. Distributed by the author, University of Washington, Seattle.
17. Gillin, F. D., D. S. Reiner, and J. M. McCaffery. 1996. Cell biology of the primitive eukaryote Giardia lamblia. Ann. Rev. Microbiol. 50:679-705.
18. Goldman, N., J. P. Anderson, and A. G. Rodrigo. 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49:652-670.
19. Gray, M. W., G. Burger, B. F. Lang et al. (15 co-authors). 1999. Mitochondrial evolution. Science 283:1476-1481.
20. Gray, M. W., B. F. Lang, R. Cedergren et al. 1998. Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res. 26:865-878.
21. Hashimoto, T., Y. Nakamura, T. Kamaishi, F. Nakamura, J. Adachi, K. Okamoto, and M. Hasegawa. 1995. Phylogenetic place of mitochondrion-lacking protozoan, Giardia lamblia, inferred from amino acid sequences of elongation factor 2. Mol. Biol. Evol. 12:782-793.
22. Hashimoto, T., Y. Nakamura, F. Nakamura, T. Shirakura, J. Adachi, N. Goto, K. Okamoto, and M. Hasegawa. 1994. Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia. Mol. Biol. Evol. 11:65-71.
23. Hashimoto, T., L. B. Sanchez, T. Shirakura, M. Müller, and M. Hasegawa. 1998. Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. Proc. Natl. Acad. Sci. USA 95:6860-6865.
24. Hirt, R. P., J. M. Logsdon, B. Healy, M. W. Dorey, W. F. Doolittle, and T. M. Embley. 1999. Microsporidia are related to fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc. Natl. Acad. Sci. USA 96:580-585.
25. Horner, D. S., and T. M. Embley. 2001. Chaperonin 60 phylogeny provides further evidence for secondary loss of mitochondria among putative early-branching eukaryotes. Mol. Biol. Evol. 18:1970-1975.
26. Keeling, P. J., and W. F. Doolittle. 1997. Evidence that eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin. Proc. Natl. Acad. Sci. USA 94:1270-1275.
27. Lang, B. F., G. Burger, C. J. O'kelly, R. Cedergren, G. B. Golding, C. Lemieux, D. Sankoff, M. Turmel, and M. W. Gray. 1997. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387:493-497.
28. Margulis, L., M. F. Dolan, and R. Guerrero. 2000. The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists. Proc. Natl. Acad. Sci. USA 97:6954-6959.
29. McArthur, A., H. Morrison, J. Nixon et al. (15 co-authors). 2000. The Giardia genome project database. FEMS Microbiol. Lett. 189:271-273.
30. Medlin, L., H. J. Elwood, S. Stickel, and M. L. Sogin. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71:491-499.
31. Morrison, H. G., A. J. Roger, T. G. Nystul, F. D. Gillin, and M. L. Sogin. 2001. Giardia lamblia expresses a protobacterial-like DnaK homolog. Mol. Biol. Evol. 18:530-541.
32. O'Kelly, C. J. 1993. The jakobid flagellates: structural features of Jakoba, Reclinomonas and Histiona and implications for the early diversification of eukaryotes. J. Eukaryot. Microbiol. 40:627-636.
33. O'Kelly, C. J., M. A. Farmer, and T. A. Nerad. 1999. Ultrastructure of Trimastix pyriformis (Klebs) Bernard et al.: similarities of Trimastix species with retortamonad and jakobid flagellates. Protist 150:149-162.
34. Philippe, H., and A. Adoutte. 1998. The molecular phylogeny of Eukaryota: solid facts and uncertainties. Pp. 25-56 in G. H. Coombs, K. Vickerman, M. A. Sleigh, and A. Warren, eds. Evolutionary relationships among protozoa. Chapman and Hall, London.
35. Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
36. Roger, A. J. 1999. Reconstructing early events in eukaryotic evolution. Am. Nat. 154:S146-S163.
37. Roger, A. J., S. G. Svärd, J. Tovar, C. G. Clark, M. W. Smith, F. D. Gillin, and M. L. Sogin. 1998. A mitochondrial-like chaperonin 60 gene in Giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria. Proc. Natl. Acad. Sci. USA 95:229-234.
38. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
39. Siddall, M. E., H. Hong, and S. S. Desser. 1992. Phylogenetic analysis of the Diplomonadida (Wenyon, 1926) Brugerolle, 1975: evidence for heterochrony in protozoa and against Giardia lamblia as a "missing link. " J. Protozool. 39:361-367.
40. Silberman, J. D., A. G. B. Simpson, J. Kulda, I. Cepicka, V. Hampl, P. J. Johnson, and A. J. Roger. 2002. Retortamonad flagellates are closely related to diplomonads- implications for the history of mitochondrial function in eukaryote evolution. Mol. Biol. Evol. 19:777-786.
41. Simpson, A. G. B., C. Bernard, and D. J. Patterson. 2000. The ultrastructure of Trimastix marina Kent, 1880 (Eukaryota), an excavate flagellate. Europ. J. Protistol. 36:229-252.
42. Simpson, A. G. B., and D. J. Patterson. 1999. The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the excavate hypothesis. Europ. J. Protistol. 35:353-370.
43. 2001. On core jakobids and excavate taxa: the ultrastructure of Jakoba incarcerata. J. Eukaryot. Microbiol. 48:480-492.
44. Sogin, M. L. 1997. History assignment: when was the mitochondrion founded? Curr. Opin. Genet. Dev. 7:792-799.
45. Sogin, M. L., J. H. Gunderson, H. J. Elwood, R. A. Alonso, and D. A. Peattie. 1989. Phylogenetic significance of the kingdom concept: an unusual eukaryotic 16S-like ribosomal RNA from Giardia lamblia. Science 243:75-77.
46. Stiller, J. W., and B. D. Hall. 1999. Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol. Biol. Evol. 16:1270-1279.
47. Strimmer, K., and A. Rambaut. 2002. Inferring confidence sets of possibly misspecified gene trees. Proc. R. Soc. Lond. B. 269:137-142.
48. Strimmer, K., and A. Von Haeseler. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
49. Swofford, D. L. 2000. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
50. Tachezy, J. L. B. Sánchez, and M. Müller. 2001. Mitochondrial type iron-sulfur cluster assembly in the amitochondriate eukaryotes Trichomonas vaginalis and Giardia intestinalis, as indicated by the phylogeny of IscS. Mol. Biol. Evol. 18:1919-1928.
51. Van Der Giezen, M., D. J. Slotboom, D. S. Horner, P. L. Dyal, M. Harding, G. P. Xue, T. M. Embley, and E. R. S. Kunji. 2002. Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin for both organelles. EMBO J. 21:572-579.