Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions

Proceedings of the Royal Society B: Biological Sciences

Volumn 267, Issue 1449, 2000, Pages 1213-1221

  Philippe, Hervé ^a   Lopez, Philippe ^a   Brinkmann, Henner ^a   Budin, Karine ^a   Germot, Agnès ^a   Laurent, Jacqueline ^a   Moreira, David ^a   Müller, Miklós ^b   Le Guyader, Hervé ^a  

^a CNRS   (France)

^b ROCKEFELLER UNIVERSITY   (United States)

Author keywords

Early branching organisms; Eukaryotes; Long branch attraction artefact; Loss of function; Molecular phylogeny

Indexed keywords

NUCLEOTIDE; RIBOSOME RNA;

EVOLUTIONARY BIOLOGY; PHYLOGENY;

AMINO ACID SUBSTITUTION; ARTICLE; CELL LINEAGE; EUKARYOSIS; GENETIC MARKER; HUMAN; MITOCHONDRION; MOLECULAR EVOLUTION; MOLECULAR MODEL; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE;

EID: 0034702256     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2000.1130     Document Type: Article

References (54)

1. Adachi, J. & Hasegawa, M. 1996 MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28, 1-150.
2. Ayala, F. J. 1997 Vagaries of the molecular clock. Proc. Natl Acad. Sci. USA 94, 7776-7783.
3. Baldauf, S. L. & Doolittle, W. F. 1997 Origin and evolution of the slime molds (Mycetozoa). Proc. Natl Acad. Sci. USA 94, 12007-12012.
4. Baldauf, S. L. & Palmer, J. D. 1993 Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc. Natl Acad. Sci. USA 90, 11 558-11 562.
5. Brinkmann, H. & Philippe, H. 1999 Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol. 16, 817-825.
6. Budin, K. & Philippe, H. 1998 New insights into the phylogeny of eukaryotes based on ciliate hsp70 sequences. Mol. Biol. Evol. 15, 943-956.
7. Cao, Y., Waddell, P. J., Okada, N. & Hasegawa, M. 1998 The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates. Mol. Biol. Evol. 15, 1637-1646.
8. Cavalier-Smith, T. 1987 The origin of eukaryotic and archae-bacterial cells. Ann. NY Acad. Sci. 503, 17-54.
9. Embley, T. M. & Hirt, R. P. 1998 Early branching eukaryotes? Curr. Opin. Genet. Devel. 8, 624-629.
10. Farris, J. 1969 A successive approximations approach to character weighting. Syst. Zool. 18, 371-385.
11. Felsenstein, J. 1978 Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-410.
12. Field, K. G., Olsen, G. J., Lane, D. J., Giovannoni, S. J., Ghiselin, M. T., Raff, E. C., Pace, N. R. & Raff, R. A. 1988 Molecular phylogeny of the animal kingdom. Science 239, 748-753.
13. Fitch, W. M. & Markowitz, E. 1970 An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4, 579-593.
14. Galtier, N. & Gouy, M. 1995 Inferring phylogenies from DNA sequences of unequal base compositions. Proc. Natl Acad. Sci. USA 92, 11 317-11 321.
15. Germot, A. & Philippe, H. 1999 Critical analysis of eukaryotic phylogeny: a case study based on the hsp70 family. J. Eukaryot. Microbiol. 46, 116-124.
16. Goldman, N., Thorne, J. L. & Jones, D. T. 1998 Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149, 445-458.
17. Gray, M. W., Burger, G. & Lang, B. F. 1999 Mitochondrial evolution. Science 283, 1476-1481.
18. Hasegawa, M. & Fujiwara, M. 1993 Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny. Mol. Phylogenet. Evol. 2, 1-5.
19. Hasegawa, M. & Hashimoto, T. 1993 Ribosomal RNA trees misleading? Nature 361, 23.
20. Heard, S. 1992 Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees. Evolution 46, 1818-1826.
21. Hirt, R. P., Logsdon Jr, J. M., Healy, B., Dorey, M. W., Doolittle, W. F. & Embley, T. M. 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.
22. Kamaishi, T., Hashimoto, T., Nakamura, Y., Masuda, Y., Nakamura, F., Okamoto, K., Shimizu, M. & Hasegawa, M. 1996 Complete nucleotide sequences of the genes encoding translation elongation factors 1 alpha and 2 from a microsporidian parasite, Glugea plecoglossi: implications for the deepest branching of eukaryotes. J. Biochem. (Tokyo) 120, 1095-1103.
23. Knoll, A. H. 1992 The early evolution of eukaryotes: a geological perspective. Science 256, 622-627.
24. + of Hexamita inflata and the quest for the first branch in the eukaryotic tree. Mol. Biochem. Parasitol. 59, 41-48.
25. Lockhart, P., Steel, M., Hendy, M. & Penny, D. 1994 Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11, 605-612.
26. Lockhart, P. J., Larkum, A. W., Steel, M., Waddell, P. J. & Penny, D. 1996 Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc. Natl Acad. Sci. USA 93, 1930-1934.
27. Lockhart, P. J., Steel, M. A., Barbrook, A. C., Huson, D., Charleston, M. A. & Howe, C. J. 1998 A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol. Biol. Evol. 15, 1183-1188.
28. Loomis, W. F. & Smith, D. W. 1990 Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison. Proc. Natl Acad. Sci. USA 87, 9093-9097.
29. Lopez, P., Forterre, P. & Philippe, H. 1999 The root of the tree of life in the light of the covarion model. J. Mol. Evol. 49, 496-508.
30. Lwoff, A. 1943 L'Évolution physiologique. Étude des pertes de fonctions chez les microorganismes. Paris: Hermann et Cie.
31. Miyamoto, M. M. & Fitch, W. M. 1995 Testing the covarion hypothesis of molecular evolution. Mol. Biol. Evol. 12, 503-513.
32. Moreira, D., Le Guyader, H. & Philippe, H. 2000 The origin of red algae: implications for the evolution of chloroplasts. Nature. (In the press.)
33. Naylor, G. J. P. & Brown, W. M. 1998 Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst. Biol. 47, 61-76.
34. Patterson, D. & Sogin, M. 1992 Eukaryote origins and protistan diversity. In The origin and evolution of the cell (ed. H. Hartman & K. Matsuno), pp. 13-46. Singapore: World Scientific.
35. Pawlowski, J., Bolivar, I., Fahrni, J. F., De Vargas, C., Gouy, M. & Zaninetti, L. 1997 Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record. Mol. Biol. Evol. 14, 498-505.
36. Peyretaillade, E., Biderre, C., Peyret, P., Dufficux, F., Metenier, G., Gouy, M., Michot, B. & Vivares, C. P. 1998 Microsporidian Encephalitozoon cuniculi, a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core. Nucl. Acids Res. 26, 3513-3520.
37. Philippe, H. 1993 MUST, a computer package of management utilities for sequences and trees. Nucl. Acids Res. 21, 5264-5272.
38. Philippe, H. 1997 Rodent monophyly: pitfalls of molecular phytogenies. J. Mol. Evol. 45, 712-715.
39. Philippe, H. & Adoutte, A. 1998 The molecular phytogeny of Eukaryota: solid facts and uncertainties. In Evolutionary relationships among Protozoa (ed. G. Coombs, K. Vickerman, M. Sleigh & A. Warren), pp. 25-56. London: Chapman & Hall.
40. 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.
41. Philippe, H. & Laurent, J. 1998 How good are deep phylogenetic trees? Curr. Opin. Genet. Devel. 8, 616-623.
42. Philippe, H., Chenuil, A. & Adoutte, A. 1994 Can the Cambrian explosion be inferred through molecular phylogeny? Development 120 (Suppl.), 15-25.
43. Sogin, M. 1997 History assignment: when was the mitochondrion founded? Curr. Opin. Genet. Devel. 7, 792-799.
44. Sogin, M. L. & Silberman, J. D. 1998 Evolution of the protists and protistan parasites from the perspective of molecular systematics. Int. J. Parasitol. 28, 11-20.
45. Sogin, M. L., Gunderson, J. H., Elwood, H. J., Alonso, R. A. & Peattie, D. A. 1989 Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science 243, 75-77.
46. Stiller, J. & Hall, B. 1999 Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol. Biol. Evol. 16, 1270-1279.
47. Sullivan, J. & Swofford, D. L. 1997 Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mamm. Evol. 4, 77-86.
48. Swofford, D. L. 1993 PAUP: phylogenetic analysis using parsimony, version 3.1.1. Champaign, IL: Illinois Natural History Survey.
49. Tuffley, C. & Steel, M. 1998 Modeling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147, 63-91.
50. Wheeler, W. 1990 Nucleic acid sequence phylogeny and random outgroups. Cladistics 6, 363-367.
51. Woese, C. R. & Fox, G. E. 1977 Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl Acad. Sci. USA 74, 5088-5090.
52. Woese, C., Achenbach, L., Rouviere, P. & Mandelco, L. 1991 Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst. Appl. Microbiol. 14, 364-371.
53. Yang, Z. 1996 Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11, 367-370.
54. Yang, Z. 1997 Phylogenetic analysis by maximum likelihood (PAML), version 1.3. Berkeley, CA: Department of Integrative Biology, University of California at Berkeley.