Ancient Phylogenetic Relationships

Theoretical Population Biology

Volumn 61, Issue 4, 2002, Pages 391-408

  Gribaldo, Simonetta ^a   Philippe, Hervé ^a  

^a SORBONNE UNIVERSITÉ   (France)

Author keywords

Molecular phylogeny; Tree of life; Tree reconstruction artifacts

Indexed keywords

AMINO ACID SEQUENCE; ANIMAL; HUMAN; MOLECULAR GENETICS; PHYLOGENY; REVIEW; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE HOMOLOGY, AMINO ACID;

ARTIFACT; PHYLOGENETICS; PHYLOGENY; RECONSTRUCTION;

ARCHEZOA; BACTERIA (MICROORGANISMS); EUKARYOTA; THUJA;

EID: 0036593395     PISSN: 00405809     EISSN: None     Source Type: Journal    
DOI: 10.1006/tpbi.2002.1593     Document Type: Article

References (152)

1. Adachi J., Hasegawa M. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28:1996;1-150.
2. Aguinaldo A. M., Turbeville J. M., Linford L. S., Rivera M. C., Garey J. R., Raff R. A., Lake J. A. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 387:1997;489-493.
3. Aravind L., Tatusov R. L., Wolf Y. I., Walker D. R., Koonin E. V. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14:1998;442-444.
4. Archibald J. M., Roger A. J. Gene duplication and gene conversion shape the evolution of archaeal chaperonins. J. Mol. Biol. 3l6:2002;1041-1050.
5. Arisue N., Hashimoto T., Lee J. A., Moore D. V., Gordon P., Sensen C. W., Gaasterland T., Hasegawa M., Müller M. The phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1a and EF-2. J. Eukaryot. Microbiol. 49:2002a;1-10.
6. Arisue N., Hasshimoto T., Yoshikawa H., Nakamura Y., Nakamura G., Nakamura F., Yano T.-A., Hasegawa M. Phylogenetic position of Blastocystis hominis and of stramenopiles inferred from multiple molecular sequence data. J. Eukaryot. Microbiol. 49:2002b;42-53.
7. Baldauf S. L., Palmer J. D. Animals and fungi are each other's closest relatives: Congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA. 90:1993;11, 558-11, 562.
8. Baldauf S. L., Roger A. J., Wenk-Siefert I., Doolittle W. F. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science. 290:2000;972-977.
9. Bapteste E., Brinkmann H., Lee J. A., Moore D. V., Sensen C. W., Gordon P., Durufle L., Gaasterland T., Lopez P., Muller M., Philippe H. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. USA. 99:2002;1414-1419.
10. Bapteste E., Philippe H. The potential value of indels as phylogenetic markers: Position of trichomonads as a case study. Mol. Biol. Evol. 19:2002;972-977.
11. Boore J. L., Brown W. M. Big trees from little genomes: Mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev. 8:1998;668-674.
12. Brinkmann H., Philippe H. Archaea sister group of Bacteria Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol. 16:1999;817-825.
13. Brochier C., Bapteste E., Moreira D., Philippe H. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 18:2002;1-5.
14. Brochier C., Philippe H. Phylogeny: A non-hyperthermophilic ancestor for Bacteria. Nature. 417:2002;244.
15. Brochier C., Philippe H., Moreira D. The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome. Trends Genet. 16:2000;529-533.
16. Brown J. R., Doolittle W. F. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. USA. 92:1995;2441-2445.
17. Brown J. R., Douady C. J., Italia M. J., Marshall W. E., Stanhope M. J. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28:2001;281-285.
18. Brown J. R., Robb F. T., Weiss R., Doolittle W. F. Evidence for the early divergence of tryptophanyl- and tyrosyl-tRNA synthetases. J. Mol. Evol. 45:1997;9-16.
19. Budin K., Philippe H. New insights into the phylogeny of eukaryotes based on ciliate Hsp70 sequences. Mol. Biol. Evol. 15:1998;943-956.
20. Bull J. J., Huelsenbeck J. P., Cunningham C. W., Swofford D. L., Wadell P. J. Partitioning and combining characters in phylogenetic analysis. Syst. Biol. 42:1993;384-397.
21. Burger G., Saint-Louis D., Gray M. W., Lang B. F. Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea. Cyanobacterial introns and shared ancestry of red and green algae. Plant Cell. 11:1999;1675-1694.
22. Cavalier-Smith T. Eukaryotes with no mitochondria. Nature. 326:1987;332-333.
23. Cavalier-Smith T. Principles of protein and lipid targeting in secondary symbiogenesis: Euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J. Eukaryot. Microbiol. 46:1999;347-366.
24. Charlebois R. L., Sensen C. W., Doolittle W. F., Brown J. R. Evolutionary analysis of the hisCGABdFDEHI gene cluster from the archaeon Sulfolobus solfataricus P2. J. Bacteriol. 179:1997;4429-4432.
25. Chase M. W., Fay M. F. Ancient flowering plants: DNA sequences and angiosperm classification. Genome Biol. 2:2001.
26. Daubin V., Gouy M. Bacterial molecular phylogeny using supertree approach. Genome. Inform. Ser. Workshop Genome Inform. 12:2001;155-164.
27. Deckert G., Warren P. V., Gaasterland T., Young W. G., Lenox A. L., Graham D. E., Overbeek R., Snead M. A., Keller M., Aujay M., Huber R., Feldman R. A., Short J. M., Olsen G. J., Swanson R. V. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 392:1998;353-358.
28. Doolittle W. F. Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes. Technical comment on M. Huynen et al. Science. 286:1999a;1443.
29. Doolittle W. F. Lateral genomics. Trends Cell Biol. 9:1999b;M5-8.
30. Dolittle W. F. Phylogenetic classification and the universal tree. Science. 284:1999c;2124-2129.
31. Edlind T. D., Li J., Visvesvara G. S., Vodkin M. H., McLaughlin G. L., Katiyar S. K. Phylogenetic analysis of beta-tubulin sequences from amitochondrial protozoa. Mol. Phylogenet. Evol. 5:1996;359-367.
32. Embley T. M., Hirt R. P. Early branching eukaryotes? Curr. Opin. Genet. Dev. 8:1998;624-629.
33. Fast N. M., Kissinger J. C., Roos D. S., Keeling P. J. Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol. Biol. Evol. 18:2001;418-426.
34. Fast N. M., Xue L., Bingham S., Keeling P. J. Re-examining alveolate evolution using multiple protein molecular phylogenies. J. Eukaryot. Microbiol. 49:2002;30-37.
35. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:1978;401-410.
36. Felsenstein J. Taking variation of evolutionary rates between sites into account in inferring phylogenies. J. Mol. Evol. 53:2001;447-455.
37. Fitch W. M. The nonidentity of invariable positions in the cytochromes c of different species. Biochem. Genet. 5:1971;231-241.
38. Fitch W. M., Markowitz E. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4:1970;579-593.
39. Fitz-Gibbon S. T., House C. H. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27:1999;4218-4222.
40. Forterre P. Thermoreduction, a hypothesis for the origin of prokaryotes. C. R. Acad. Sci. III. 318:1995;415-422.
41. Forterre P., Bouthier De La Tour C., Philippe H., Duguet M. Reverse gyrase from hyperthermophiles: Probable transfer of a thermoadaptation trait from archaea to bacteria. Trends Genet. 16:2000;152-154.
42. Forterre P., Philippe H. The last universal common ancestor (LUCA), simple or complex? Biol. Bull. 196:1999a;373-375.
43. Forterre P., Philippe H. Where is the root of the universal tree of life? BioEssays. 21:1999b;871-879.
44. Foster P. G., Hickey D. A. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 48:1999;284-290.
45. Fuerst J. A. The planctomycetes: Emerging models for microbial ecology, evolution and cell biology. Microbiology. 141:1995;1493-1506.
46. Galtier N. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18:2001;866-873.
47. Galtier N., Gouy M. Inferring phylogenies from DNA sequences of unequal base compositions. Proc. Natl. Acad. Sci. USA. 92:1995;11, 317-11, 321.
48. Galtier N., Lobry J. R. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 44:1997;632-636.
49. Galtier N., Tourasse N., Gouy M. A nonhyperthermophilic common ancestor to extant life forms. Sciences. 283:1999;220-221.
50. Germot A., Philippe H. Critical analysis of eukaryotic phylogeny: A case study based on the HSP70 family. J. Eukaryot. Microbiol. 46:1999;116-124.
51. Germot A., Philippe H., Le Guyader H. Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Mol. Biochem. Parasitol. 87:1997;159-168.
52. Gogarten J. P., Kibak H., Dittrich P., Taiz L., Bowman E. J., Bowman B. J., Manolson M. F., Poole R. J., Date T., Oshima T., Konishi J., Denda K., Yoshida M. Evolution of the vacuolar H+-ATPase: Implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. USA. 86:1989;6661-6665.
53. Gogarten-Boekels M., Hilario E., Gogarten J. P. The effects of heavy meteorite bombardment on the early evolution - The emergence of the three domains of life. Orig. Life Evol. Biosph. 25:1995;251-264.
54. Gribaldo S., Cammarano P. The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery. J. Mol. Evol. 47:1998;508-516.
55. Gribaldo S., Lumia V., Creti R., de Macario E. C., Sanangelantoni A., Cammarano P. Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein. J. Bacteriol. 181:1999;434-443.
56. Guindon S., Perriere G. Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes. Mol. Biol. Evol. 18:2001;1838-1840.
57. Gupta R. S. What are archaebacteria: Life's third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol. Microbiol. 229:1998;695-708.
58. Gupta R. S., Johari V. Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the deinococcus-thermus group and cyanobacteria. J. Mol. Evol. 46:1998;716-720.
59. Gupta R. S., Singh B. Phylogenetic analysis of 70kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Curr. Biol. 4:1994;1104-1114.
60. Hannaert V., Brinkmann H., Nowitzki U., Lee J. A., Albert M.-A., Sensen C. W., Gaasterland T., Müller M., Michels P., Martin W. Enolase from Trypanosoma brucei, from the amitochondriate protist Mastigamoeba balamuthi, and from the chloroplast and cytosol of Euglena gracilis: Pieces in the evolutionary puzzle of the eukaryotic glycolytic pathway. Mol. Biol. Evol. 17:2000;989-1000.
61. Hasegawa M., Hashimoto T. Ribosomal RNA trees misleading? Nature. 361:1993;23.
62. Hashimoto T., Hasegawa M. Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1alpha/Tu and 2/G. Adv. Biophys. 32:1996;73-120.
63. Hashimoto T., Sanchez L. B., Shirakura T., Muller M., Hasegawa M. Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. Proc. Natl. Acad. Sci. USA. 95:1998;6860-6865.
64. Hendy M., Penny D. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:1989;297-309.
65. Henze K., Horner D. S., Suguri S., Moore D. V., Sánchez L. B., Müller M., Embley T. M. Unique phylogenetic relationships of glucokinase and glucosephosphate isomerase of the amitochondriate eukaryotes Giardia intestinalis, Spironucleus barkhanus and Trichomonas vaginalis. Gene. 281:2001;123-131.
66. Hillis D. M. Inferring complex phylogenies. Nature. 383:1996;130-131.
67. Hirt R. P., Logsdon J. M. Jr., Healy B., Dorey M. W., Doolittle W. F., Embley T. M. Microsporidia are related to fungi: Evidence from the largest subunit of RNA polymerase II and other proteins. Proc. Natl. Acad. Sci. USA. 96:1999;580-585.
68. Imai E., Honda H., Hatori K., Brack A., Matsuno K. Elongation of oligopeptides in a simulated submarine hydrothermal system. Science. 283:1999;831-833.
69. Iwabe N., Kuma K., Hasegawa M., Osawa S., Miyata T. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA. 86:1989;9355-9359.
70. Jain R., Rivera M. C., Lake J. A. Horizontal gene transfer among genomes: The complexity hypothesis. Proc. Natl. Acad. Sci. USA. 96:1999;3801-3806.
71. Jenkins C., Fuerst J. A. Phylogenetic analysis of evolutionary relationships of the planctomycete division of the domain bacteria based on amino acid sequences of elongation factor tu. J. Mol. Evol. 52:2001;405-418.
72. Jukes T. H., Cantor C. R. Evolution of protein molecules. Munro H. N. Mammalian Protein Metabolism. 1969;21-132 Academic Press, New York.
73. Keeling P. J. Foraminifera and Cercozoa are related in actin phylogeny: Two orphans find a home? Mol. Biol. Evol. 18:200la;1551-1557.
74. Keeling P. J. Parasites go the full monty. Nature. 414:2001b;401-402.
75. Keeling P. J., Palmer J. D. Parabasalian flagellates are ancient eukaryotes. Nature. 405:2000;635-637.
76. Keeling P. J., Palmer J. D. Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase. Proc. Natl. Acad. Sci. 98:2001;10, 745-10, 750.
77. Koonin E. V., Makarova K. S., Aravind L. Horizontal gene transfer in prokaryotes: Quantification and classification. Annu. Rev. Microbiol. 55:2001;709-742.
78. Korbel J. O., Snel B., Huynen M. A., Bork P. SHOT: A web server for the construction of genome phytogenies. Trends Genet. 18:2002;158-162.
79. Koski L. B., Golding G. B. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52:2001;540-542.
80. Koski L. B., Morton R. A., Golding G. B. Codon bias and base composition are poor indicators of horizontally transferred genes. Mol. Biol. Evol. 18:2001;404-412.
81. Kuma K., Nikoh N., Iwabe N., Miyata T. Phylogenetic position of Dictyostelium inferred from multiple protein data sets. J. Mol. Evol. 41:1995;238-246.
82. Lawrence J. G., Ochman H. Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10:2002;1-4.
83. Lawson F. S., Charlebois R. L., Dillon J. A. Phylogenetic analysis of carbamoylphosphate synthetase genes: Complex evolutionary history includes an internal duplication within a gene which can root the tree of life. Mol. Biol. Evol. 13:1996;970-977.
84. Lecointre G., Philippe H., Le H. L. V., Le Guyader H. Species sampling has a major impact on phylogenetic inference. Mol. Phylogenet. Evol. 2:1993;205-224.
85. Lin J., Gerstein M. Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels. Genome Res. 10:2000;808-818.
86. Lockhart P., Steel M., Hendy M., Penny D. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:1994;605-612.
87. Lockhart P. J., Larkum A. W., Steel M., Waddell P. J., Penny D. Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. USA. 93:1996;1930-1934.
88. Lockhart P. J., Steel M. A., Barbrook A. C., Huson D., Charleston M. A., Howe C. J. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol. Biol. Evol. 15:1998;1183-1188.
89. Loomis W. F., Smith D. W. Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison. Proc. Natl. Acad. Sci. USA. 87:1990;9093-9097.
90. Lopez P., Casane D., Philippe H. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19:2002;1-7.
91. Lopez P., Forterre P., Philippe H. The root of the tree of life in the light of the covarion model. J. Mol. Evol. 49:1999;496-508.
92. Lynch M., Conery J. S. The evolutionary fate and consequences of duplicate genes. Science. 290:2000;1151-1155.
93. Madsen O., Scally M., Douady C. J., Kao D. J., DeBry R. W., Adkins R., Amrine H. M., Stanhope M. J., de Jong W. W., Springer M. S. Parallel adaptive radiations in two major clades of placental mammals. Nature. 409:2001;610-614.
94. Mai Z., Ghosh S., Frisardi M., Rosenthal B., Rogers R., Samuelson J. Hsp60 is targeted to a cryptic mitochondrion-derived organelle ("crypton") in the microaerophilic protozoan parasite Entamoeba histolytica. Mol. Cell. Biol. 19:1999;2198-2205.
95. Margulis L. Archaeal-eubacterial mergers in the origin of Eukarya: Phylogenetic classification of life. Proc. Natl. Acad. Sci. USA. 93:1996;1071-1076.
96. Martin W. Mosaic bacterial chromosomes: A challenge en route to a tree of genomes. Bioessays. 21:1999;99-104.
97. Matte-Tailliez O., Brochier C., Forterre P., Philippe H. Archaeal phylogeny based on ribosomal proteins. Mol. Biol. Evol. 19:2002;631-639.
98. Mayr E. Two empires or three? Proc. Natl. Acad. Sci. USA. 95:1998;9720-9723.
99. Moreira D., Kervestin S., Jean-Jean O., Philippe H. Evolution of eukaryotic translation elongation and termination factors: Variations of evolutionary rate and genetic code deviations. Mol. Biol. Evol. 19:2002;189-200.
100. Moreira D., Le Guyader H., Philippe H. Unusually high evolutionary rate of the elongation factor 1 alpha genes from the Ciliophora and its impact on the phylogeny of eukaryotes. Mol. Biol. Evol. 16:1999;234-245.
101. Moreira D., Le Guyader H., Philippe H. The origin of red algae: Implications for the evolution of chloroplasts. Nature. 405:2000;69-72.
102. Murphy W. J., Eizirik E., Johnson W. E., Zhang Y. P., Ryder O. A., O'Brien S. J. Molecular phylogenetics and the origins of placental mammals. Nature. 409:2001;614-618.
103. Nelson K. E., Clayton R. A., Gill S. R., Gwinn M. L., Dodson R. J., Haft D. H., Hickey E. K., Peterson J. D., Nelson W. C., Ketchum K. A., McDonald L., Utterback T. R., Malek J. A., Linher K. D., Garrett M. M., Stewart A. M., Cotton M. D., Pratt M. S., Phillips C. A., Richardson D., Heidelberg J., Sutton G. G., Fleischmann R. D., Eisen J. A., Fraser C. M. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 399:1999;323-329.
104. Nikaido M., Harada M., Cao Y., Hasegawa M., Okada N. Monophyletic origin of the order chiroptera and its phylogenetic position among mammalia, as inferred from the complete sequence of the mitochondrial DNA of a Japanese megabat, the ryukyu flying fox (Pteropus dasymallus) [In Process Citation]. J. Mol. Evol. 51:2000;318-328.
105. Nikoh N., Hayase N., Iwabe N., Kuma K., Miyata T. Phylogenetic relationship of the kingdoms Animalia, Plantae, and Fungi, inferred from 23 different protein species. Mol. Biol. Evol. 11:1994;762-768.
106. Nisbet E. G., Sleep N. H. The habitat and nature of early life. Nature. 409:2001;1083-1091.
107. Ochman H., Lawrence J. G., Groisman E. A. Lateral gene transfer and the nature of bacterial innovation. Nature. 405:2000;299-304.
108. Olsen G. Earliest phylogenetic branching: Comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harb. Symp. Quant. Biol. 1987.
109. Olsen G. J., Woese C. R., Overbeek R. The winds of (evolutionary) change: Breathing new life into microbiology. J. Bacteriol. 176:1994;1-6.
110. Pace N. R. Origin of life - facing up to the physical setting. Cell. 65:1991;531-533.
111. Page R. D., Charleston M. A. From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7:1997;231-240.
112. Pawlowski J., Bolivar I., Fahrni J. F., de Vargas C., Gouy M., Zaninetti L. Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record. Mol. Biol. Evol. 14:1997;498-505.
113. Pennisi E. Genome data shake tree of life. Science. 280:1998;672-674.
114. Penny D., McComish B. J., Charleston M. A., Hendy M. D. Mathematical elegance with biochemical realism: The covarion model of molecular evolution. J. Mol. Evol. 53:2001;711-723.
115. Penny D., Poole A. The nature of the last universal common ancestor. Curr. Opin. Genet. Dev. 9:1999;672-677.
116. Philippe H. Long branch attraction and protist phylogeny. Protist. 51:2000;307-316.
117. Philippe H., Adoutte A. The molecular phylogeny of Eukaryota: Solid facts and uncertainties. Coombs G., Vickerman K., Sleigh M., Warren A. Evolutionary Relationships Among Protozoa. 1998;25-56 Kluwer, Dordrecht.
118. Philippe H., Budin K., Moreira D. Horizontal transfers confuse the prokaryotic phylogeny based on the HSP70 protein family. Mol. Microbiol. 31:1999;1007-1009.
119. Philippe H., Douzery E. The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships. J. Mammalian Evol. 2:1994;133-152.
120. Philippe H., Forterre P. The rooting of the universal tree of life is not reliable. J. Mol. Evol. 49:1999;509-523.
121. Philippe H., Germot A. Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution. Mol. Biol. Evol. 17:2000;830-834.
122. Philippe H., Laurent J. How good are deep phylogenetic trees? Curr. Opin. Genet. Dev. 8:1998;616-623.
123. Philippe H., Lopez P., Brinkmann H., Budin K., Germot A., Laurent J., Moreira D., Müller M., Le Guyader H. Early branching or fast evolving eukaryotes? An answer based on slowly evolving positions. Philos. Trans. R. Soc. Lond. B Biol. Sci. 267:2000;1213-1221.
124. Philippe H., Sörhannus U., Baroin A., Perasso R., Gasse F., Adoutte A. Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record. J. Evol. Biol. 7:1994;247-265.
125. Poe S., Swofford D. L. Taxon sampling revisited. Nature. 398:1999;299-300.
126. Posada D., Crandall K. A. The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54:2002;396-402.
127. Ragan M. A. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201:2001;187-191.
128. Roger A. J., Sandblom O., Doolittle W. F., Philippe H. An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes. Mol. Biol. Evol. 16:1999;218-233.
129. Rokas A., Holland P. W. H. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15:2000;454-459.
130. Ruepp A., Graml W., Santos-Martinez M. L., Koretke K. K., Volker C., Mewes H. W., Frishman D., Stocker S., Lupas A. N., Baumeister W. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature. 407:2000;508-513.
131. Schwartz R. M., Dayhoff M. O. Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts. Science. 199:1978;395-403.
132. Sogin M. L. Early evolution and the origin of eukaryotes. Curr. Opin. Genet. Dev. 1:1991;457-463.
133. Stetter K. O. Hyperthermophiles in the history of life. Ciba Found. Symp. 202:1996;1-10.
134. Strous M., Fuerst J. A., Kramer E. H., Logemann S., Muyzer G., van de Pas-Schoonen K. T., Webb R., Kuenen J. G., Jetten M. S. Missing lithotroph identified as new planctomycete. Nature. 400:1999;446-449.
135. Swofford D. L., Olsen G. J., Waddell P. J., Hillis D. M. Phylogenetic inference. Hillis D. M., Moritz C., Mable B. K. Molecular Systematics. 1996;407-514 Sinauer Associates, Sunderland.
136. Tekaia F., Lazcano A., Dujon B. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9:1999;550-557.
137. Tovar J., Fischer A., Clark C. G. The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica. Mol. Microbiol. 32:1999;1013-1021.
138. Van de Peer Y., Ben Ali A., Meyer A. Microsporidia: Accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi. Gene. 246:2000;1-8.
139. Venkatesh B., Ning Y., Brenner S. Late changes in spliceosomal introns define clades in vertebrate evolution. Proc. Natl. Acad. Sci. USA. 96:1999;10, 267-10, 271.
140. Vossbrinck C. R., Maddox J. V., Friedman S., Debrunner-Vossbrinck B. A., Woese C. R. Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes. Nature. 326:1987;411-414.
141. Wang B. Limitations of compositional approach to identifying horizontally transferred genes. J. Mol. Evol. 53:2001;244-250.
142. Weisburg W. G., Giovannoni S. J., Woese C. R. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst. Appl. Microbiol. 11:1989;128-134.
143. Woese C. R. Bacterial evolution. Microbiol. Rev. 51:1987;221-271.
144. Woese C. R. Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. USA. 97:2000;8392-8396.
145. Woese C. R., Achenbach L., Rouviere P., Mandelco L. Archaeal phylogeny: Reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst. Appl. Microbiol. 14:1991;364-371.
146. Woese C. R., Fox G. E. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. USA. 74:1977;5088-5090.
147. Woese C. R., Kandler O., Wheelis M. L. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA. 87:1990;4576-4579.
148. Woese C. R., Olsen G. J., Ibba M., Soll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64:2000;202-236.
149. Wolf Y. I., Rogozin I. B., Grishin N. V., Tatusov R. L., Koonin E. V. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1:2001;8.
150. Yang Z. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11:1996a;367-370.
151. Yang Z. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:1996b;587-596.
152. Zuckerkandl E., Pauling L. Molecules as documents of evolutionary history. J. Theor. Biol. 8:1965;357-366.