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PMID: 17261804 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Pattern pluralism and the Tree of Life hypothesis.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 104 ·No. 7 ·2007-02-13 ·Pages 2043-9

Doolittle WF, Bapteste E

Abstract

Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.

MeSH Terms
Animals Biological Evolution Gene Transfer, Horizontal Genetic Variation Humans Models, Genetic Phylogeny
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Doolittle W Ford
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5. ford@dal.ca
Bapteste Eric
References (74)
74 references, click to expand
  1. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
    Nature. 1999 May 27;399(6734):323-9 PMID: 10360571
  2. Phylogenetic classification and the universal tree.
    Science. 1999 Jun 25;284(5423):2124-9 PMID: 10381871
  3. Whole genome-based phylogenetic analysis of free-living microorganisms.
    Nucleic Acids Res. 1999 Nov 1;27(21):4218-22 PMID: 10518613
  4. Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels.
    Genome Res. 2000 Jun;10(6):808-18 PMID: 10854412
  5. Genomics. Are there bugs in our genome?
    Science. 2001 Jun 8;292(5523):1848-50 PMID: 11358998
  6. Universal trees based on large combined protein sequence data sets.
    Nat Genet. 2001 Jul;28(3):281-5 PMID: 11431701
  7. Recombination and the population structures of bacterial pathogens.
    Annu Rev Microbiol. 2001;55:561-90 PMID: 11544367
  8. Species, rules and meaning: the politics of language and the ends of definitions in 19th century natural history.
    Stud Hist Philos Sci. 1996 Dec;27(4):473-519 PMID: 11614120
  9. Eubacterial phylogeny based on translational apparatus proteins.
    Trends Genet. 2002 Jan;18(1):1-5 PMID: 11750686
  10. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores.
    J Bacteriol. 2002 Apr;184(8):2072-80 PMID: 11914337
  11. Using homolog groups to create a whole-genomic tree of free-living organisms: an update.
    J Mol Evol. 2002 Apr;54(4):539-47 PMID: 11956692
  12. On the evolution of cells.
    Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8742-7 PMID: 12077305
  13. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history.
    Genome Res. 2002 Jul;12(7):1080-90 PMID: 12097345
  14. The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea.
    J Mol Microbiol Biotechnol. 2002 Jul;4(4):453-61 PMID: 12125824
  15. Genome trees and the tree of life.
    Trends Genet. 2002 Sep;18(9):472-9 PMID: 12175808
  16. Recycled plastids: a 'green movement' in eukaryotic evolution.
    Trends Genet. 2002 Nov;18(11):577-84 PMID: 12414188
  17. Prokaryotic evolution in light of gene transfer.
    Mol Biol Evol. 2002 Dec;19(12):2226-38 PMID: 12446813
  18. Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans.
    Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7678-83 PMID: 12777624
  19. Horizontal gene transfer: a critical view.
    Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):9658-62 PMID: 12902542
  20. Phylogenetics and the cohesion of bacterial genomes.
    Science. 2003 Aug 8;301(5634):829-32 PMID: 12907801
  21. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria.
    PLoS Biol. 2003 Oct;1(1):E19 PMID: 12975657
  22. Lateral gene transfer and the origins of prokaryotic groups.
    Annu Rev Genet. 2003;37:283-328 PMID: 14616063
  23. On the conceptual difficulties in rooting the tree of life.
    Trends Microbiol. 2004 Jan;12(1):9-13 PMID: 14700546
  24. From a phylogenetic tree to a reticulated network.
    J Comput Biol. 2004;11(1):195-212 PMID: 15072696
  25. Genome phylogenetic analysis based on extended gene contents.
    Mol Biol Evol. 2004 Jul;21(7):1401-8 PMID: 15084675
  26. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise.
    J Mol Evol. 2004 May;58(5):527-39 PMID: 15170256
  27. Phylogenomics of eukaryotes: impact of missing data on large alignments.
    Mol Biol Evol. 2004 Sep;21(9):1740-52 PMID: 15175415
  28. A new biology for a new century.
    Microbiol Mol Biol Rev. 2004 Jun;68(2):173-86 PMID: 15187180
  29. Phylogenetic reconstruction and lateral gene transfer.
    Trends Microbiol. 2004 Sep;12(9):406-11 PMID: 15337161
  30. The ring of life provides evidence for a genome fusion origin of eukaryotes.
    Nature. 2004 Sep 9;431(7005):152-5 PMID: 15356622
  31. Computing prokaryotic gene ubiquity: rescuing the core from extinction.
    Genome Res. 2004 Dec;14(12):2469-77 PMID: 15574825
  32. Frequent recombination in a saltern population of Halorubrum.
    Science. 2004 Dec 10;306(5703):1928-9 PMID: 15591201
  33. Does a tree-like phylogeny only exist at the tips in the prokaryotes?
    Proc Biol Sci. 2004 Dec 22;271(1557):2551-8 PMID: 15615680
  34. Phylogeny determined by protein domain content.
    Proc Natl Acad Sci U S A. 2005 Jan 11;102(2):373-8 PMID: 15630082
  35. Genomic insights that advance the species definition for prokaryotes.
    Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2567-72 PMID: 15701695
  36. Fuzzy species among recombinogenic bacteria.
    BMC Biol. 2005 Mar 07;3:6 PMID: 15752428
  37. Lateral gene transfer in eukaryotes.
    Cell Mol Life Sci. 2005 Jun;62(11):1182-97 PMID: 15761667
  38. Evolutionary origins of genomic repertoires in bacteria.
    PLoS Biol. 2005 May;3(5):e130 PMID: 15799709
  39. Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement.
    BMC Evol Biol. 2005 Apr 08;5:27 PMID: 15819979
  40. Phylogenomics and the reconstruction of the tree of life.
    Nat Rev Genet. 2005 May;6(5):361-75 PMID: 15861208
  41. Do orthologous gene phylogenies really support tree-thinking?
    BMC Evol Biol. 2005 May 24;5:33 PMID: 15913459
  42. An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences.
    BMC Evol Biol. 2005 Jun 02;5:36 PMID: 15932645
  43. The net of life: reconstructing the microbial phylogenetic network.
    Genome Res. 2005 Jul;15(7):954-9 PMID: 15965028
  44. Reconstructing reticulate evolution in species-theory and practice.
    J Comput Biol. 2005 Jul-Aug;12(6):796-811 PMID: 16108717
  45. Horizontal gene transfer, genome innovation and evolution.
    Nat Rev Microbiol. 2005 Sep;3(9):679-87 PMID: 16138096
  46. Genome trees and the nature of genome evolution.
    Annu Rev Microbiol. 2005;59:191-209 PMID: 16153168
  47. Highways of gene sharing in prokaryotes.
    Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14332-7 PMID: 16176988
  48. The microbial pan-genome.
    Curr Opin Genet Dev. 2005 Dec;15(6):589-94 PMID: 16185861
  49. Application of phylogenetic networks in evolutionary studies.
    Mol Biol Evol. 2006 Feb;23(2):254-67 PMID: 16221896
  50. Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes.
    Mol Ecol. 2005 Nov;14(13):4033-50 PMID: 16262857
  51. Insights on biology and evolution from microbial genome sequencing.
    Genome Res. 2005 Dec;15(12):1603-10 PMID: 16339357
  52. Ancient gene duplications and the root(s) of the tree of life.
    Protoplasma. 2005 Dec;227(1):53-64 PMID: 16389494
  53. Phylogenetic networks from multi-labelled trees.
    J Math Biol. 2006 May;52(5):613-32 PMID: 16463187
  54. Phylogenomics: the beginning of incongruence?
    Trends Genet. 2006 Apr;22(4):225-31 PMID: 16490279
  55. 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
  56. Toward automatic reconstruction of a highly resolved tree of life.
    Science. 2006 Mar 3;311(5765):1283-7 PMID: 16513982
  57. Sex and virulence in Escherichia coli: an evolutionary perspective.
    Mol Microbiol. 2006 Jun;60(5):1136-51 PMID: 16689791
  58. The evolution of supertrees.
    Trends Ecol Evol. 2004 Jun;19(6):315-22 PMID: 16701277
  59. Reconstructing reticulate evolutionary histories of plants.
    Trends Plant Sci. 2006 Aug;11(8):398-404 PMID: 16839803
  60. Reciprocal illumination in the gene content tree of life.
    Syst Biol. 2006 Jun;55(3):441-53 PMID: 16861208
  61. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.
    Genome Res. 2006 Sep;16(9):1099-108 PMID: 16899658
  62. Maximum likelihood of phylogenetic networks.
    Bioinformatics. 2006 Nov 1;22(21):2604-11 PMID: 16928736
  63. Reconstructing an ultrametric galled phylogenetic network from a distance matrix.
    J Bioinform Comput Biol. 2006 Aug;4(4):807-32 PMID: 17007069
  64. Genomics and the bacterial species problem.
    Genome Biol. 2006;7(9):116 PMID: 17020593
  65. The tree of one percent.
    Genome Biol. 2006;7(10):118 PMID: 17081279
  66. Early evolution and the origin of eukaryotes.
    Curr Opin Genet Dev. 1991 Dec;1(4):457-63 PMID: 1822277
  67. Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts.
    Science. 1978 Jan 27;199(4327):395-403 PMID: 202030
  68. Bacterial evolution.
    Microbiol Rev. 1987 Jun;51(2):221-71 PMID: 2439888
  69. Problems in the development of an explicit hypothetical phylogeny of the lower eukaryotes.
    Biosystems. 1978 Apr;10(1-2):67-89 PMID: 418828
  70. Tempo and mode in the macroevolutionary reconstruction of Darwinism.
    Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):6764-71 PMID: 8041695
  71. A comparison of the nucleotide sequences of the adk and recA genes of pathogenic and commensal Neisseria species: evidence for extensive interspecies recombination within adk.
    J Mol Evol. 1996 Dec;43(6):631-40 PMID: 8995060
  72. A molecular view of microbial diversity and the biosphere.
    Science. 1997 May 2;276(5313):734-40 PMID: 9115194
  73. The hydrogen hypothesis for the first eukaryote.
    Nature. 1998 Mar 5;392(6671):37-41 PMID: 9510246
  74. Genome phylogeny based on gene content.
    Nat Genet. 1999 Jan;21(1):108-10 PMID: 9916801
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.0610699104
Email
ford@dal.ca
Published
2007-02-13
Epub
2007-00-29
Pages
2043-9
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC1892968
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.0610699104 PMC Full Text View journal details
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