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

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  • 1. Adventures in protein world revealthe Tree of Life and the evolution of complexityGraeme T. Lloyd, Philip C. J. Donoghue and Julian Gough
  • 2. Scala Naturae
  • 3. The Problem“Complexity is hard to define or measure…” Maynard Smith and Szathmáry, 1995
  • 4. Genome Size and the Scala Naturae (from Gregory 2005)
  • 5. Cell Number and the Scala Naturae (from Valentine et al. 1994)
  • 6. Proteome Size and the Scala Naturae ?
  • 7. Protein Structural DomainsFolding
  • 8. Protein Domain Classification IFoldSuperfamily(1445)Family(2598)Domain
  • 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. http://supfam.org Protein Domain Database I
  • 11. Protein Domain Database II238 Bacteria 26 Basal 53 Fungi 8 Arthropods Eukaryotes27 Archaea 9 Plants 5 Invertebrates 19 Chordates (excl. Arthropods)
  • 12. Superfamily Number and the Scala Naturae
  • 13. Family Number and the Scala Naturae
  • 14. Architecture Number and the Scala Naturae
  • 15. The Tree of Life I ArchitecturesSuperfamilies Families
  • 16. The Tree of Life II
  • 17. The Tree of Life III
  • 18. The Tree of Life IV
  • 19. Protein Space I
  • 20. Protein Space IIPrincipal Coordinate Analysis – A Very Brief Introduction PC1 Variable 2 PC 2 Variable 1
  • 21. Protein Space III - Superfamilies
  • 22. Protein Space IV - Families
  • 23. Protein Space V - Architectures
  • 24. Tempo and Protein Evolution I
  • 25. Tempo and Protein Evolution II - SuperfamiliesLUCA
  • 26. Tempo and Protein Evolution III - FamiliesLUCA
  • 27. Tempo and Protein Evolution IV - ArchitecturesLUCA
  • 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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