Root of the Eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data

Molecular Biology and Evolution

Volumn 22, Issue 3, 2005, Pages 409-420

  Arisue, Nobuko ^a,b,e   Hasegawa, Masami ^a,b   Hashimoto, Tetsuo ^a,b,c,d  

^a GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^c ROCKEFELLER UNIVERSITY   (United States)

^d UNIVERSITY OF TSUKUBA   (Japan)

^e OSAKA UNIVERSITY   (Japan)

Author keywords

Combined phylogeny; Diplomonadida; Eukaryote evolution; Maximum likelihood; Parabasala; Root

Indexed keywords

RIBOSOME RNA; TUBULIN;

ARTICLE; DATA ANALYSIS; EUKARYOTE EVOLUTION; FLAGELLATE; GENETIC VARIABILITY; GENOME; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENY; RED ALGA;

ANIMALS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 14544283723     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi023     Document Type: Article

References (64)

1. Adachi, J., and M. Hasegawa. 1996. MOLPHY version 2.3: program for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monographs No. 28, The Institute of Statistical Mathematics, Tokyo.
2. Aldritt, S. M., P. Tien, and C. C. Wang. 1985. Pyrimidine salvage in Giardia lamblia. J. Exp. Med. 161:437-445.
3. Annoura, T., T. Nara, T. Makiuchi, T. Hashimoto, and T. Aoki. 2004. The origin of dihydroorotate dehydrogenase genes of kinetoplastids, with special reference to their biological significance and adaptation to anaerobic, parasitic conditions. J. Mol. Evol. in press.
4. Archibald, J. M., D. Longet, J. Pawlowski, and P. J. Keeling. 2003. A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol. 20:62-66.
5. Arisue, N., T. Hashimoto, J. A. Lee, D. V. Moore, P. Gordon, C. W. Sensen, T. Gaasterland, M. Hasegawa, and M. Müller. 2002a. The phylogenetic position of the peleobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1α and EF-2. J. Eukaryot. Microbiol. 49:1-10.
6. Arisue, N., T. Hashimoto, H. Yoshikawa, Y. Nakamura, G. Nakamura, F. Nakamura, T. Yano, and M. Hasegawa. 2002b. Phylogenetic position of Blastocystis hominis and of stramenopiles inferred from multiple molecular sequence data. J. Eukaryot. Microbiol. 49:42-53.
7. Arisue, N., Y. Maki, H. Yoshida, A. Wada, L. B. Sánchez, M. Müller, and T. Hashimoto. 2004. Comparative analysis of the ribosomal components of the hydrogenosome-containing protist, Trichomonas vaginalis. J. Mol. Evol. 59:59-71.
8. Baldauf, S. L. 2003. The deep roots of eukaryotes. Science 300:1703-1706.
9. 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.
10. Bapteste, E., H. Brinkmann, J. A. Lee, D. V. Moore, C. W. Sensen, P. Gordon, L. Duruflé, T. Gaasterland, P. Lopez, M. Müller, and H. Philippe. 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.
11. Cavalier-Smith, T. 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. 52:297-354.
12. Cavalier-Smith, T., and E. E. Chao. 2003a. Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution. J. Mol. Evol. 56:540-563.
13. Cavalier-Smith, T., and E. E. Chao. 2003b. Phylogeny and classification of phylum Cercozoa (Protozoa). Protist 154:341-358.
14. Cavalier-Smith, T. 2004. Only six kingdoms of life. Proc R. Soc. Lond. Ser. B 271:1251-1262.
15. Dacks, J. B., and W. F. Doolittle. 2001. Reconstructing/deconstructing the earliest eukaryotes: how comparative genomics can help. Cell 107:419-425.
16. Dacks, J. B., J. D. Silberman, A. G. B. Simpson, S. Moriya, T. Kudo, M. Ohkuma, and R. J. Redfield. 2001. Oxymonads are closely related to the excavate taxon Trimastix. Mol. Biol. Evol. 18:1034-1044.
17. Dacks, J. B., A. Marinets, W. F. Doolittle, T. Cavalier-Smith, and J. M. Logsdon Jr. 2002. Analyses of RNA polymerase II genes from free-living protists: phylogeny, long branch attraction, and the eukaryotic big bang. Mol. Biol. Evol. 19:830-840.
18. Edgcomb, V. P., A. J. Roger, A. G. B. Simpson, D. T. 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.
19. Embley, T. M., M. van der Giezen, D. S. Horner, P. L. Dyal, and P. Foster. 2003. Mitochondria and hydrogenosomes are two forms of the same fundamental organelle. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358:191-201.
20. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
21. Gribaldo, S., and H. Philippe. 2002. Ancient phylogenetic relationships. Theoret. Popul. Biol. 61:391-408.
22. Hasegawa, M., and H. Kishino. 1994. Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree. Mol. Biol. Evol. 11:142-145.
23. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
24. Hashimoto, T., L. B. Sánchez, 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.
25. Hashimoto, T., Y. Nakamura, T. Kamaishi, and M. Hasegawa. 1997. Early evolution of eukaryotes inferred from protein phylogenies of translation elongation factors 1α and 2. Arch. Protistenkd. 148:287-295.
26. Hirt, R. P., J. M. Logsdon Jr., 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.
27. 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.
28. Hughey, R, and A. Krogh. 1996. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput. Appl. Biosci. 12:95-107.
29. Inagaki, Y., E. Susko, N. M. Fast, and A. J. Roger. 2004. Covarion shifts cause a long-branch attraction artifact that unites Microsporidia and Archaebacteria in EF-1α phylogenies. Mol. Biol. Evol. 21:1340-1349.
30. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
31. Keeling, P. J. 2001. Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Mol. Biol. Evol. 18:1551-1557.
32. Keeling, P. J., and W. F. Doolittle. 1996. Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Mol. Biol. Evol. 13:1297-1305.
33. Kishino, H., T. Miyata, and M. Hasegawa. 1990. Maximum likelihood inference of protein phylogeny, and the origin of chloroplasts. J. Mol. Evol. 31:151-160.
34. nd ed. Society of Protozoologists, Lawrence, Kans.
35. Martin, W., and M. Müller. 1998. The hydrogen hypothesis of the first eukaryote. Nature 392:37-41.
36. Matsuzaki, M., O. Misumi, T. Shin-i et al. (42 co-authors). 2004. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428:653-657.
37. McArthur, A. G., H. G. Morrison, J. E. Nixon et al. (15 co-authors). 2000. The Giardia genome project database. FEMS Microbiol. Lett. 189:271-273.
38. Moreira, D., H. Le Guyader, and H. Philippe. 2000. The origin of red algae and the evolution of chloroplasts. Nature 405:69-72.
39. Nara, T., T. Hashimoto, and T. Aoki. 2000. Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes. Gene 257:209-222.
40. Nozaki, H., M. Matsuzaki, M. Takahara, O. Misumi, H. Kuroiwa, M. Hasegawa, T. Shin-i, Y. Kohara, N. Ogasawara, and T. Kuroiwa. 2003. The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids. J. Mol. Evol. 56:485-497.
41. O'Kelly, C. J., and T. A. Nerad. 1999. Malawimonas jakobiformis n. gen., n. sp. (Malawimonadidae n. fam.): a jakoba-like heterotrophic nanoflagellate with discoidal mitochondrial cristae. J. Eukaryot. Microbiol. 46:522-531.
42. Philippe, H., P. Lopez, H. Brinkmann, K. Budin, A. Germot, J. Laurent, D. Moreira, M. Muller, and H. Le Guyader. 2000. Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proc. R. Soc. Lond. B Biol. Sci. 267:1213-1221.
43. Philippe, H., E. A. Snell, E. Bapteste, P. Lopez, P. W. Holland, and D. Casane. 2004. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol. Biol. Evol. 21:1740-1752.
44. Richards, T. A., R. P. Hirt, B. A. P. Williams, and T. M. Embley. 2003. Horizontal gene transfer and the evolution of parasitic protozoa. Protist 154:17-32.
45. Roger, A. J. 1999. Reconstructing early events in eukaryotic evolution. Am. Nat. 154:S146-S163.
46. Roger, A. J., and J. D. Silberman. 2002. Mitochondria in hiding. Nature 418:827-829.
47. Rotte, C., K. Henze, M. Müller, and W. Martin. 2000. Origins of hydrogenosomes and mitochondria. Curr. Opin. Microbiol. 3:481-486.
48. Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492-508.
49. Shimodaira, H., and M. Hasegawa. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
50. 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.
51. Simpson, A. G. B., and D. J. Patterson. 1999. The ultrastructure of Carpediemonas membranifera: (Eukaryota), with reference to the "excavate hypothesis." Eur. J. Protistol. 35:353-370.
52. Simpson, A. G. B., and A. J. Roger 2002. Eukaryotic evolution: getting to the root of the problem. Curr. Biol. 12:R691-R695.
53. Simpson, A. G. B., A. J. Roger, J. D. Silberman, D. D. Leipe, V. P. Edgcomb, L. S. Jermiin, D. J. Patterson, and M. L. Sogin. 2002. Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia. Mol. Biol. Evol. 19:1782-1791.
54. Sogin, M. L., and J. D. Silberman. 1998. Evolution of the protists and protistan parasites from the perspective of molecular systematics. Int. J. Parasitol. 28:11-20.
55. Stechmann, A., and T. Cavalier-Smith. 2002. Rooting the eukaryote tree by using a derived gene fusion. Science 297:89-91.
56. Stechmann, A., and T. Cavalier-Smith. 2003a. The root of the eukaryote tree pinpointed. Curr. Biol. 13:R665-666.
57. Stechmann, A., and T. Cavalier-Smith. 2003b. Phylogenetic analysis of eukaryotes using heat-shock protein Hsp90. J. Mol. Evol. 57:408-419.
58. Tovar, J., G. Leon-Avila, L. B. Sánchez, R. Sutak, J. Tachezy, M. van der Giezen, M. Hernandez, M. Müller, and J. M. Lucocq. 2003. Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation. Nature 426:172-176.
59. Wang, C. C., R. Verham, S. F. Tzeng, S. Aldritt, and H. W. Cheng. 1983. Pyrimidine metabolism in Tritrichomonas foetus. Proc. Natl. Acad. Sci. USA 80:2564-2568.
60. Wang, C. C., and H. W. Cheng. 1984. Salvage of pyrimidine nucleosides by Trichomonas vaginalis. Mol. Biochem. Parasitol. 10:171-184.
61. Williams, B. A., R. P. Hirt, J. M. Lucocq, and T. M. Embley. 2002. A mitochondrial remnant in the microsporidian Trachipleistophora hominis. Nature 418:865-869.
62. Wuyts, J., P. De Rijk, Y. Van de Peer, T. Winkelmans, and R. De Wachter. 2001. The European Large Subunit Ribosomal RNA database. Nucleic Acids Res. 29:175-177.
63. Wuyts, J., Y. Van de Peer, T. Winkelmans, and R. De Wachter. 2002. The European database on small subunit ribosomal RNA. Nucleic Acids Res. 30:183-185.
64. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.