Home LiteratureArticle Details
PMID: 17081279 Published · ppublish English Journal Article

The tree of one percent.

Genome biology ·Vol. 7 ·No. 10 ·2006-00-00 ·Pages 118

Dagan T, Martin W

Abstract

Two significant evolutionary processes are fundamentally not tree-like in nature--lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes. To incorporate such processes into the bigger picture of early evolution, biologists need to depart from the preconceived notion that all genomes are related by a single bifurcating tree.

MeSH Terms
Animals Archaea/genetics Bacteria/genetics Decision Trees Evolution, Molecular Genes, Bacterial Genes, Fungal Genes, Protozoan Models, Genetic Symbiosis
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Dagan Tal
Institute of Botany, University of Düsseldorf, D-40225 Düsseldorf, Germany. tal.dagan@uni-duesseldorf.de
Martin William
References (62)
62 references, click to expand
  1. Fun with genealogy.
    Proc Natl Acad Sci U S A. 1997 Nov 25;94(24):12751-3 PMID: 9398070
  2. 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 Jan 6;3:2 PMID: 12515582
  3. The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists.
    Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):6954-9 PMID: 10860956
  4. The simultaneous symbiotic origin of mitochondria, chloroplasts, and microbodies.
    Ann N Y Acad Sci. 1987;503:55-71 PMID: 3304084
  5. The origin of eukaryotic and archaebacterial cells.
    Ann N Y Acad Sci. 1987;503:17-54 PMID: 3113314
  6. Evolutionary origins of genomic repertoires in bacteria.
    PLoS Biol. 2005 May;3(5):e130 PMID: 15799709
  7. Testing the exon theory of genes: the evidence from protein structure.
    Science. 1994 Jul 8;265(5169):202-7 PMID: 8023140
  8. Genomic evidence for two functionally distinct gene classes.
    Proc Natl Acad Sci U S A. 1998 May 26;95(11):6239-44 PMID: 9600949
  9. The ring of life provides evidence for a genome fusion origin of eukaryotes.
    Nature. 2004 Sep 9;431(7005):152-5 PMID: 15356622
  10. Phylogenetic classification and the universal tree.
    Science. 1999 Jun 25;284(5423):2124-9 PMID: 10381871
  11. On the prokaryotic nature of red algal chloroplasts.
    Proc Natl Acad Sci U S A. 1975 Jun;72(6):2310-4 PMID: 1056032
  12. Introns and the origin of nucleus-cytosol compartmentalization.
    Nature. 2006 Mar 2;440(7080):41-5 PMID: 16511485
  13. The biology of intron gain and loss.
    Trends Genet. 2006 Jan;22(1):16-22 PMID: 16290250
  14. Archaebacteria (Archaea) and the origin of the eukaryotic nucleus.
    Curr Opin Microbiol. 2005 Dec;8(6):630-7 PMID: 16242992
  15. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.
    Nat Genet. 2005 Dec;37(12):1372-5 PMID: 16311593
  16. Ancient horizontal gene transfer.
    Nat Rev Genet. 2003 Feb;4(2):121-32 PMID: 12560809
  17. Horizontal gene transfer, genome innovation and evolution.
    Nat Rev Microbiol. 2005 Sep;3(9):679-87 PMID: 16138096
  18. The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica.
    Mol Microbiol. 1999 Jun;32(5):1013-21 PMID: 10361303
  19. Toward automatic reconstruction of a highly resolved tree of life.
    Science. 2006 Mar 3;311(5765):1283-7 PMID: 16513982
  20. Time for a change.
    Nature. 2006 May 18;441(7091):289 PMID: 16710401
  21. Where is the root of the universal tree of life?
    Bioessays. 1999 Oct;21(10):871-9 PMID: 10497338
  22. The universal ancestor.
    Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6854-9 PMID: 9618502
  23. Evolution of intraflagellar transport from coated vesicles and autogenous origin of the eukaryotic cilium.
    Bioessays. 2006 Feb;28(2):191-8 PMID: 16435301
  24. Eukaryotic evolution, changes and challenges.
    Nature. 2006 Mar 30;440(7084):623-30 PMID: 16572163
  25. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.
    PLoS Biol. 2005 Oct;3(10):e316 PMID: 16122348
  26. Using consensus networks to visualize contradictory evidence for species phylogeny.
    Mol Biol Evol. 2004 Jul;21(7):1459-61 PMID: 15084681
  27. The net of life: reconstructing the microbial phylogenetic network.
    Genome Res. 2005 Jul;15(7):954-9 PMID: 15965028
  28. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.
    Proc Natl Acad Sci U S A. 1989 Dec;86(23):9355-9 PMID: 2531898
  29. Interpreting the universal phylogenetic tree.
    Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8392-6 PMID: 10900003
  30. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes.
    Proc Natl Acad Sci U S A. 1989 Sep;86(17):6661-5 PMID: 2528146
  31. Relics from the RNA world.
    J Mol Evol. 1998 Jan;46(1):18-36 PMID: 9419222
  32. Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes.
    Microbiol Mol Biol Rev. 1998 Dec;62(4):1435-91 PMID: 9841678
  33. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4 PMID: 15608248
  34. Phylogenetic super-networks from partial trees.
    IEEE/ACM Trans Comput Biol Bioinform. 2004 Oct-Dec;1(4):151-8 PMID: 17051697
  35. Was the nucleus the first endosymbiont?
    Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):2880-1 PMID: 8159671
  36. Phylogenetics and the cohesion of bacterial genomes.
    Science. 2003 Aug 8;301(5634):829-32 PMID: 12907801
  37. 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 Jan 29;358(1429):39-57; discussion 57-8 PMID: 12594917
  38. Mitochondrion-derived organelles in protists and fungi.
    Int Rev Cytol. 2005;244:175-225 PMID: 16157181
  39. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.
    Int J Syst Evol Microbiol. 2002 Mar;52(Pt 2):297-354 PMID: 11931142
  40. A mitochondrial remnant in the microsporidian Trachipleistophora hominis.
    Nature. 2002 Aug 22;418(6900):865-9 PMID: 12192407
  41. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny.
    Mol Biol Evol. 2006 May;23(5):848-55 PMID: 16280536
  42. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes.
    Mol Biol Evol. 2004 Sep;21(9):1643-60 PMID: 15155797
  43. The nature of the last universal common ancestor.
    Curr Opin Genet Dev. 1999 Dec;9(6):672-7 PMID: 10607605
  44. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes.
    Nat Rev Genet. 2004 Feb;5(2):123-35 PMID: 14735123
  45. Genomics and the irreducible nature of eukaryote cells.
    Science. 2006 May 19;312(5776):1011-4 PMID: 16709776
  46. On the origin of mitosing cells
    J Theor Biol. 1967 Mar;14(3):255-74 PMID: 11541392
  47. Horizontal gene transfer: a critical view.
    Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):9658-62 PMID: 12902542
  48. Thermoreduction, a hypothesis for the origin of prokaryotes.
    C R Acad Sci III. 1995 Apr;318(4):415-22 PMID: 7648354
  49. Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria.
    Mol Biol Evol. 2006 May;23(5):1019-30 PMID: 16495350
  50. Cell evolution and Earth history: stasis and revolution.
    Philos Trans R Soc Lond B Biol Sci. 2006 Jun 29;361(1470):969-1006 PMID: 16754610
  51. Genomes in flux: the evolution of archaeal and proteobacterial gene content.
    Genome Res. 2002 Jan;12(1):17-25 PMID: 11779827
  52. The origin of nuclei and of eukaryotic cells.
    Nature. 1975 Aug 7;256(5517):463-8 PMID: 808732
  53. Origin and evolution of the peroxisomal proteome.
    Biol Direct. 2006 Mar 23;1:8 PMID: 16556314
  54. Early evolution: prokaryotes, the new kids on the block.
    Bioessays. 1999 Oct;21(10):880-9 PMID: 10497339
  55. The origin of eukaryotes is suggested as the symbiosis of pyrococcus into gamma-proteobacteria by phylogenetic tree based on gene content.
    J Mol Evol. 2004 Nov;59(5):606-19 PMID: 15693617
  56. Determining divergence times with a protein clock: update and reevaluation.
    Proc Natl Acad Sci U S A. 1997 Nov 25;94(24):13028-33 PMID: 9371794
  57. Patterns of bacterial gene movement.
    Mol Biol Evol. 2004 Jul;21(7):1294-307 PMID: 15115802
  58. Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation.
    Nature. 2003 Nov 13;426(6963):172-6 PMID: 14614504
  59. Application of phylogenetic networks in evolutionary studies.
    Mol Biol Evol. 2006 Feb;23(2):254-67 PMID: 16221896
  60. On the evolution of cells.
    Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8742-7 PMID: 12077305
  61. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
    Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576-9 PMID: 2112744
  62. The hydrogenosome.
    J Gen Microbiol. 1993 Dec;139(12):2879-89 PMID: 8126416
Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
Published
2006-00-00
Epub
2006-00-01
Pages
118
Language
English
Region
England
NLM ID
100960660
PMCID
PMC1794558
Subset
IM
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com