The tree of one percent

Genome Biology

Volumn 7, Issue 10, 2006, Pages

  Dagan, Tal ^a   Martin, William ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA; SMALL NUCLEOLAR RNA;

ARTICLE; CELL NUCLEUS; CELL ORGANELLE; CHLOROPLAST; COMPARATIVE GENE MAPPING; ENDOSYMBIOSIS; EUKARYOTE EVOLUTION; FLAGELLUM; GENE STRUCTURE; GENE TRANSFER; HORIZONTAL GENE TRANSFER; HUMAN; INTRON; MICROBIAL GENETICS; MITOCHONDRION; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; PROKARYOTE; RNA PROCESSING; RNA SEQUENCE; SEQUENCE HOMOLOGY; ANIMAL; ARCHAEBACTERIUM; BACTERIAL GENE; BACTERIUM; BIOLOGICAL MODEL; DECISION TREE; FUNGAL GENE; GENE; GENETICS; SYMBIOSIS;

EUKARYOTA; PROKARYOTA;

ANIMALS; ARCHAEA; BACTERIA; DECISION TREES; EVOLUTION, MOLECULAR; GENES, BACTERIAL; GENES, FUNGAL; GENES, PROTOZOAN; MODELS, GENETIC; SYMBIOSIS;

EID: 33750810896     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2006-7-10-118     Document Type: Article

References (70)

1. Doolittle WF: If the tree of life fell, would it make a sound? In Microbial Phylogeny and Evolution: Concepts and Controversies. Edited by Sapp J. New York: Oxford University Press; 2004:119-133.
2. Mirkin BG, Fenner TI, Galperin MY, Koonin EV: Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol 2003, 3:2.
3. Snel B, Bork P, Huynen MA: Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res 2002, 12:17-25.
4. Kunin V, Goldovsky L, Darzentas N, Ouzounis CA: The net of life: reconstructing the microbial phylogenetic network. Genome Res 2005, 15:954-959.
5. Ge F, Wang LS, Kim J: The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol 2005, 3:e316.
6. Lerat E, Daubin V, Ochman H, Moran NA: Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 2005, 3:e130.
7. Woese CR: Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 2000, 97:8392-8396.
8. Kurland CG, Canback B, Berg OG: Horizontal gene transfer: a critical view. Proc Natl Acad Sci USA 2003, 100:9658-9662.
9. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P: Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311:1283-1287.
10. Daubin V, Moran NA, Ochman H: Phylogenetics and the cohesion of bacterial genomes. Science 2003, 301:829-832.
11. Gogarten JP, Townsend JP: Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 2005, 3:679-687.
12. Pal C, Papp B, Lercher MJ: Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 2005, 37:1372-1375.
13. Woese CR, Kandler O, Wheelis ML: Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria and Eukarya. Proc Natl Acad Sci USA 1990, 87:4576-4579.
14. Woese CR: The universal ancestor. Proc Natl Acad Sci USA 1998, 95:6854-6859.
15. Woese CR: On the evolution of cells. Proc Natl Acad Sci USA 2002, 99:8742-8747.
16. Pace NR: Time for a change. Nature 2006, 441:289.
17. Iwabe N, Kuma K-I, 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 1989 86:9355-9359.
18. +-ATPase: Implications for the origin of eukaryotes. Proc Natl Acad Sci USA 1989, 86:6661-6665.
19. Kurland CG, Collins LJ, Penny D: Genomics and the irreducible nature of eukaryote cells. Science 2006, 312:1011-1014.
20. Doolittle WF: Genes in pieces: Were they ever together? Nature 1978, 272:581-582.
21. Doolittle WF: Revolutionary concepts in evolutionary cell biology. Trends Biochem Sci 1980, 5:147-149.
22. Doolittle WF: The origin and function of intervening sequences in DNA: a review. Am Nat 1987, 130:915-928.
23. Stoltzfus A, Spencer DF, Zuker M, Logsdon JM Jr, Doolittle WF: Testing the exon theory of genes: the evidence from protein structure. Science 1994, 265:202-207.
24. Forterre P: Thermoreduction, a hypothesis for the origin of prokaryotes. C R Acad Sci III 1995, 318:415-422.
25. Jeffares DC, Poole AM, Penny D: Relics from the RNA world. J Mol Evol 1998, 46:18-36.
26. Poole A, Jeffares D, Penny D: Prokaryotes, the new kids on the block. BioEssays 1999, 21:880-889.
27. Forterre P, Philippe H: Where is the root of the universal tree of life? BioEssays 1999, 21:871-879.
28. Penny D, Poole A: The nature of the last universal common ancestor. Curr Opin Genet Dev 1999, 9:672-677.
29. Jeffares DC, Mourier T, Penny D: The biology of intron gain and loss. Trends Genet 2006, 22:16-22.
30. Cavalier-Smith T: The origin of eukaryote and archaebacterial cells. Ann NY Acad Sci 1987, 503:17-54.
31. Cavalier-Smith T: The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 2002, 52:297-354.
32. Cavalier-Smith T: Cell evolution and Earth history: stasis and revolution. Philos Trans R Soc Lond B Biol Sci 2006, 361:969-1006.
33. Bonen L, Doolittle WF: On the prokaryotic nature of red algal chloroplasts. Proc Natl Acad Sci USA 1975, 72:2310-2314.
34. Cavalier-Smith T: The origin of nuclei and of eukaryotic cells. Nature 1975, 256:463-468.
35. Sagan L: On the origin of mitosing cells. J Theor Biol 1967, 14: 225-274.
36. Margulis L: Origin of Eukaryotic Cells. New Haven, CT: Yale University Press; 1970.
37. Margulis L, Dolan MF, Guerrero R: The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists. Proc Natl Acad Sci USA 2000, 97:6954-6959.
38. Cavalier-Smith T: The simultaneous symbiotic origin of mitochondria, chloroplasts and microbodies. Ann NY Acad Sci 1987, 503:55-71.
39. de Duve C: Singularities. Landmarks on the Pathways of Life. Cambridge, UK: Cambridge University Press; 2005.
40. Lake JA, Rivera MC: Was the nucleus the first endosymbiont? Proc Natl Acad Sci USA 1994, 91:2880-2881.
41. Gupta RS: Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 1998, 62:1435-1491.
42. Horiike T, Hamada K, Miyata D, Shinozawa T: The origin of eukaryotes is suggested as the symbiosis of Pyrococcus into γ-proteobacteria by phylogenetic tree based on gene content. J Mol Evol 2004, 59:606-619.
43. Jekely G, Arendt D: Evolution of intraflagellar transport from coated vesicles and autogenous origin of the eukaryotic cilium. BioEssays 2006, 28:191-198.
44. Gabaldon T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA: Origin and evolution of the peroxisomal proteome. Biol Direct 2006, 1:8.
45. Martin W: Archaebacteria (Archaea) and the origin of the eukaryotic nucleus. Curr Opin Microbiol 2005, 8:630-637.
46. Müller M: The hydrogenosome. J Gen Microbiol 1993, 139:2879-2889.
47. Müller M: Energy metabolism. Part I: Anaerobic protozoa. In Molecular Medical Parasitology. Edited by Marr J. London: Academic Press; 2003: 125-139.
48. Tovar J, Fischer A, Clark CG: The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica. Mol Microbiol 1999, 32:1013-1021.
49. Tovar J, León-Avila G, Sánchez LB, Sutak R, Tachezy J, van der Giezen M, Hernández M, Müller M, Lucocq JM: Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation. Nature 2003, 426:172-176.
50. Williams BA, Hirt RP, Lucocq JM, Embley TM: A mitochondrial remnant in the microsporidian Trachipleistophora hominis. Nature 2002, 418:865-869.
51. van der Giezen M, Tovar J, Clark CG: Mitochondrion-derived organelles in protists and fungi. Int Rev Cytol 2005, 244:175-225.
52. Embley TM, Martin W: Eukaryotic evolution, changes and challenges. Nature 2006, 440:623-630.
53. Martin W, Koonin EV: Introns and the origin of nucleus-cytosol compartmentation. Nature 2006, 440:41-45.
54. Doolittle WF: Phylogenetic classification and the universal tree. Science 1999, 284:2124-2128.
55. Rivera MC, Lake JA: The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 2004, 431:152-155.
56. Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, Gelius-Dietrich G, Henze K, Kretschmann E, Richly E, Leister D, et al.: A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 2004, 21:1643-1660.
57. 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.
58. Timmis JN, Ayliffe MA, Huang CY, Martin W: Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 2004, 5:123-135.
59. Doolittle WF, Boucher Y, Nesbo CL, Douady CJ, Andersson JO, Roger AJ: How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philos Trans R Soc Lond B Biol Sci 2003, 358:39-58.
60. Brown JR: Ancient horizontal gene transfer. Nat Rev Genet 2003, 4:121-132.
61. Martin W: Is something wrong with the tree of life? BioEssays 1996, 18:523-527.
62. Doolittle WF: Fun with genealogy. Proc Natl Acad Sci USA 1997, 94:12751-12753.
63. 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.
64. Holland BR, Jermiin LS, Moulton V: Improved consensus network techniques for genome-scale phylogeny. Mol Biol Evol 2006, 23:848-855.
65. Holland BR, Huber KT, Moulton V, Lockhart PJ: Using consensus networks to visualize contradictory evidence for species phylogeny. Mol Biol Evol 2004, 21:1459-1461.
66. Huson DH, Dezulian T, Klöpper T, Steel MA: Phylogenetic supernetworks from partial trees. IEEE/ACM Trans Comput Biol Bioiform 2004, 1:151-158.
67. Huson DH, Bryant D: Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006, 23:254-267.
68. Hao W, Golding GB: Patterns of bacterial gene movement. Mol Biol Evol 2004, 21:1294-1307.
69. Susko E, Leigh J, Doolittle WF, Bapteste E: Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the γ-proteobacteria. Mol Biol Evol 2006, 23:1019-1030.
70. Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2005, 33: D501-D504.