A genomic timescale for the origin of eukaryotes

BMC Evolutionary Biology

Volumn 1, Issue , 2001, Pages

  Hedges, S Blair ^a   Chen, Hsiong ^a   Kumar, Sudhir ^b   Wang, Daniel Y C ^a   Thompson, Amanda S ^a   Watanabe, Hidemi ^c  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

^c RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); CYANOBACTERIA; EUKARYOTA; GIARDIA; PROKARYOTA;

EID: 1642534172     PISSN: 14712148     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2148-1-4     Document Type: Article

References (53)

1. Rivera MC, Jain R, Moore JE, Lake JA: Genomic evidence for two functionally distinct gene classes Proc Natl Acad Sci USA 1998, 95:6239-6244
2. Margulis L: Origin of Eukaryotic Cells New Haven, Connecticut, Yale University Press 1970
3. Margulis L: Archael-eubacterial mergers in the origin of Eukarya: Phylogenetic classification of life Proc Natl Acad Sci USA 1996, 93:1071-1076
4. Golding GB, Gupta R: Protein-based phylogenies support a chimeric origin of the eukaryotic genome Mol Biol Evol 1995, 12:1-6
5. Feng D-F, Cho G, Doolittle RF: Determining divergence times with a protein clock: Update and reevaluation Proc Natl Acad Sci USA 1997, 94:13028-13033
6. Gupta RS: Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes Micro Mol Biol Rev 1998, 62:1435-1491
7. Doolittle WF: A paradigm gets shifty Nature 1998, 392:15-16
8. Doolittle WF: Phylogenetic classification and the universal tree Science 1999, 284:2124-2128
9. Lang DF, Gray MW, Burger G: Mitochondrial genome evolution and the origin of eukaryotes Annu Rev Genet 1999, 33:351-397
10. DesMarais DJ: When did photosynthesis emerge on earth? Science 2000, 289:1703-1705
11. Brocks JJ, Logan GA, Buick R, Summons RE: Archean molecular fossils and the early rise of eukaryotes Science 1999, 285:1033-1036
12. Han T-M, Runnegar B: Megascopic eukaryotic algae from the 2.1 billion-year-old Negaunee iron-formation, Michigan Science 1992, 257:232-235
13. Schopf JW: Microfossils of the early Archean apex chert: New evidence of the antiquity of life Science 1993, 260:640-646
14. Knoll AH: A new molecular window on early life Science 1999, 285:1025-1027
15. Summons RE, Jahnke LL, Hope JM, Logan GA: 2-methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis Nature 1999, 400:554-557
16. Rohmer M, Bisseret P, Neunlist S: The hopanoids, prokaryotic triterpenoids and precursors of ubiquitous molecular fossils In: Biological Markers in Sediments and Petroleum: A Tribute to Wolfgang K Seifert (Edited by Moldowan JM, Albrecht P, Philp RP) Englewood Cliffs, New Jersey, Prentice Hall 19921-17
17. Rohmer M: The biosynthesis of triterpenoids of the hopane series in the Eubacteria: A mine of new enzyme reactions Pure Appl Chem 1993, 65:1293-1298
18. Ohmoto H: When did the earth's atmosphere become oxic? The Geochemical News 1997, 93:12-26
19. Watanabe Y, Martini JEJ, Ohmoto H: Geochemical evidence for terrestrial ecosystems 2.6 billion years ago Nature 2000, 408:574-578
20. Widdel F, Schnell S, Heising S, Ehrenreich A, Assmus B: Ferrous iron oxidation by anoxygenic phototrophic bacteria Nature 1993, 362:834-838
21. Doolittle RF, Feng D-F, Tsang S, Cho G, Little E: Determining divergence times of the major kingdoms of living organisms with a protein clock Science 1996, 271:470-477
22. Hasegawa M, Fitch WM: Dating the cenancestor of organisms Science 1996, 274:1750
23. Kollman JM, Doolittle RF: Determining the relative rates of change for prokaryotic and eukaryotic proteins with anciently duplicated paralogs J Mol Evol 2000, 51:173-181
24. Rivera MC, Lake JA: Evidence that eukaryotes and eocyte prokaryotes are immediate relatives Science 1992, 257:74-76
25. Andersson SGE, Zomorodipour A, Andersson JO, Sicheritz-Ponten T, Alsmark UCM, Podowski RM, Naslund AK, Eriksson A-S, Winkler HH, Kurland CG: The genome sequence of Rickettsia prowazekii and the origin of mitochondria Nature 1998, 396:133-140
26. Cavalier-Smith T: Kingdom protozoa and its 18 phyla Microbiol Rev 1993, 57:953-994
27. Sogin ML, Gunderson JH, Elwood HJ, Alonso RA, Peattie DA: Phylogenetic meaning of the kingdom concept: An unusual ribosomal RNA from G iardia lamblia Science 1989, 243:75-77
28. Embley TM, Hirt RP: Early branching eukaryotes? Curr Opin Genet Dev 1998, 8:624-629
29. Martin W, Müller M: The hydrogen hypothesis for the first eukaryote Nature 1998, 392:37-41
30. Roger AJ, Svard SG, Tovar J, Clark CG, Smith MW, Gillin FD, Sogin ML: A mitochondrial-like chaperonin 60 gene in G iardia lamblia : Evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria Proc Natl Acad Sci USA 1998, 95:229-234
31. Mojzsis SJ, Arrhenius G, McKeegan KD, Harrison TM, Nutman AP, Friend CRL: Evidence for life on Earth before 3,800 million years ago Nature 1996, 384:55-59
32. Gupta RS, Mukhtar T, Singh B: Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): Implications regarding the origin of photosynthesis Mol Microbiol 1999, 32:893-906
33. Xiong J, Fischer WM, Inoue K, Nakahara M, Bauer CE: Molecular evidence for the early evolution of photosynthesis Science 2000, 289:1724-1730
34. Kirschvink JL, Gaidos EJ, Bertani LE, Beukes NJ, Gutzmer J, Maepa LN, Steinberger RE: Paleoproterozoic snowball Earth: Extreme climatic and geochemical global change and its biological consequences Proc Natl Acad Sci USA 2000, 97:1400-1405
35. Pavlov AA, Kasting JF, Brown LL: Greenhouse warming by CH4 in the atmosphere of early Earth J Geophys Res 2000, 105:11981-11990
36. Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H: The genome sequence of Buchnera sp. APS, an endocellular bacterial symbiont of aphids Nature 2000, 407:81-86
37. Thompson JD, Higgins DG, Gibson TJ: ClustalW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22:4673-4680
38. Wang DY-C, Kumar S, Hedges SB: Divergence time estimates for the early history of animal phyla and the origin of plants, animals, and fungi Proc R Soc Lond B 1999, 266:163-171
39. Sogin ML: History assignment: When was the mitochondrion founded? Curr Opin Genet Dev 1997, 7:792-799
40. Kumar S, Hedges SB: A molecular timescale for vertebrate evolution Nature 1998, 392:917-920
41. Hedges SB, Parker PH, Sibley CG, Kumar S: Continental breakup and the ordinal diversification of birds and mammals Nature 1996, 381:226-229
42. Fitch WM: Molecular evolutionary clocks In: Molecular Evolution (Edited by Ayala FJ) Sunderland, MA, Sinauer Associates 1976160-178
43. Gu X: Early metazoan divergence was about 830 million years ago J Mol Evol 1998, 47:369-371
44. Lynch M: The age and relationships of the major animal phyla Evolution 1999, 53:319-325
45. Yang Z: Paml: A program package for phylogenetic analysis by maximum likelihood CABIOS 1997, 13:555-556
46. Fitch WM, 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 1970, 4:579-593
47. Takezaki N, Rzhetsky A, Nei M: Phylogenetic test of the molecular clock and linearized trees Mol Biol Evol 1995, 12:823-833
48. Kumar S: Phyltest: A program for testing phylogenetic hypotheses University Park, Pennsylvania, Institute of Molecular Evolutionary Genetics, Pennsylvania State University 1996
49. Saitou N, Nei M: The neighbor-joining method: A new method for reconstructing phylogenetic trees Mol Biol Evol 1987, 4:406-425
50. Adachi J, Hasegawa M: Molphy version 2.3: Programs for molecular phylogenetics based on maximum likelihood Tokyo, Institute of Statistical Mathematics 1996
51. Kumar S, Tamura K, Nei M: Mega: Molecular evolutionary genetic analysis University Park, Pennsylvania State University 1993
52. Holland HD: Early proterozoic atmosphere change In: Early life on Earth (Edited by Bengston S) New York, Columbia University Press 1994237-244
53. Ohmoto H: Evidence in pre - 2.2 Ga paleosols for the early evolution of atmospheric oxygen and terrestrial biota Geology 1996, 24:1135