Adventures in protein world revealthe Tree of Life and the evolution of             complexityGraeme T. Lloyd, Philip C. J...
Scala Naturae
The Problem“Complexity is hard to define or measure…”            Maynard Smith and Szathmáry, 1995
Genome Size and the Scala Naturae                           (from Gregory 2005)
Cell Number and the Scala Naturae                         (from Valentine et al. 1994)
Proteome Size and the Scala Naturae               ?
Protein Structural DomainsFolding
Protein Domain Classification IFoldSuperfamily(1445)Family(2598)Domain
Protein Domain Classification II             A   B   C   DProtein 1:                   Architecture = A,A,CProtein 2:     ...
http://supfam.org   Protein Domain Database I
Protein Domain Database II238 Bacteria    26 Basal         53 Fungi        8 Arthropods               Eukaryotes27 Archaea...
Superfamily Number and the Scala             Naturae
Family Number and the Scala Naturae
Architecture Number and the Scala              Naturae
The Tree of Life I                                     ArchitecturesSuperfamilies      Families
The Tree of Life II
The Tree of Life III
The Tree of Life IV
Protein Space I
Protein Space IIPrincipal Coordinate Analysis – A Very Brief Introduction                                             PC1 ...
Protein Space III - Superfamilies
Protein Space IV - Families
Protein Space V - Architectures
Tempo and Protein Evolution I
Tempo and Protein Evolution II -       SuperfamiliesLUCA
Tempo and Protein Evolution III -          FamiliesLUCA
Tempo and Protein Evolution IV -        ArchitecturesLUCA
Conclusions• Protein domains can help us reconstruct  the tree of life and offer a promising new  metric for biologic comp...
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Adventures in protein world reveal the Tree of Life and the evolution of complexity

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Adventures in protein world reveal the Tree of Life and the evolution of complexity

  1. 1. Adventures in protein world revealthe Tree of Life and the evolution of complexityGraeme T. Lloyd, Philip C. J. Donoghue and Julian Gough
  2. 2. Scala Naturae
  3. 3. The Problem“Complexity is hard to define or measure…” Maynard Smith and Szathmáry, 1995
  4. 4. Genome Size and the Scala Naturae (from Gregory 2005)
  5. 5. Cell Number and the Scala Naturae (from Valentine et al. 1994)
  6. 6. Proteome Size and the Scala Naturae ?
  7. 7. Protein Structural DomainsFolding
  8. 8. Protein Domain Classification IFoldSuperfamily(1445)Family(2598)Domain
  9. 9. Protein Domain Classification II A B C DProtein 1: Architecture = A,A,CProtein 2: Architecture = D,BProtein 3: Architecture = BProtein 4: Architecture = C,A,AProtein 5: Architecture = D,B,C
  10. 10. http://supfam.org Protein Domain Database I
  11. 11. Protein Domain Database II238 Bacteria 26 Basal 53 Fungi 8 Arthropods Eukaryotes27 Archaea 9 Plants 5 Invertebrates 19 Chordates (excl. Arthropods)
  12. 12. Superfamily Number and the Scala Naturae
  13. 13. Family Number and the Scala Naturae
  14. 14. Architecture Number and the Scala Naturae
  15. 15. The Tree of Life I ArchitecturesSuperfamilies Families
  16. 16. The Tree of Life II
  17. 17. The Tree of Life III
  18. 18. The Tree of Life IV
  19. 19. Protein Space I
  20. 20. Protein Space IIPrincipal Coordinate Analysis – A Very Brief Introduction PC1 Variable 2 PC 2 Variable 1
  21. 21. Protein Space III - Superfamilies
  22. 22. Protein Space IV - Families
  23. 23. Protein Space V - Architectures
  24. 24. Tempo and Protein Evolution I
  25. 25. Tempo and Protein Evolution II - SuperfamiliesLUCA
  26. 26. Tempo and Protein Evolution III - FamiliesLUCA
  27. 27. Tempo and Protein Evolution IV - ArchitecturesLUCA
  28. 28. Conclusions• Protein domains can help us reconstruct the tree of life and offer a promising new metric for biologic complexity• Novel domain families and superfamilies have appeared at a roughly constant rate over the history of life and across different groups• By contrast, novel architectures (new proteins) are acquired at a faster rate in animals, and vertebrates in particular

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