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. Schemes for Increasing Complexity I The Basis of Progressive Evolution (1969) Self-replicating molecules Prokaryotes Increasing complexity Single-celled eukaryotes Multicelled eukaryotes with cellular differentiation Organisms with differentiated tissues and organs Organisms with well-developed limbs and nervous systems G. Ledyard Stebbins Homeotherms Human beings
  • 4. Schemes for Increasing Complexity II Major Transitions in Evolution (1995) Increasing complexity Replicating molecules --> Populations of molecules in compartments Independent replicators --> Chromosomes RNA as gene and enzyme --> DNA + protein Prokaryotes --> Eurkaryotes Asexual clones --> Sexual populations Protists --> Animals, plants, fungi (cell differentiation) Solitary individuals --> Colonies (non-reproductive castes) Primate societies --> Human societies (language) Maynard Smith and Szathmáry
  • 5. Schemes for Increasing Complexity III Megatrajectory Sequence Increasing complexity Increase in efficency of life processes Prokaryote diversification Unicellular eukaryote diversification Aquatic multicellularity Invasion of the land Intelligence Knoll & Bambach 2000
  • 6. The Problem“Complexity is hard to define or measure…” Maynard Smith and Szathmáry, 1995
  • 7. Segmentation and Complexity I Differentiation of centrum length in vertebrates Increasing complexity (from McShea 1992)
  • 8. Segmentation and Complexity II Functional differentiation in arthropod limbs Increasing complexity (from Cisne 1974)
  • 9. Segmentation and Complexity III Increasing complexity Differentiation of segment length in centipedes (from Fusco and Minelli 2000
  • 10. Fractals and Complexity Fractal dimension in ammonoids Increasing complexity (from Boyiajian & Lutz 1992)
  • 11. Cell Number and Complexity Increasing complexity (from Valentine et al. 1994)
  • 12. Genome Size and the Scala Naturae Increasing complexity (from Gregory 2005)
  • 13. Proteome Size and the Scala Naturae ?
  • 14. Protein Structural DomainsFolding
  • 15. Protein Domain Classification IFoldSuperfamily(1445)Family(2598)Domain
  • 16. 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
  • 17. http://supfam.org Protein Domain Database I
  • 18. Protein Domain Database II238 Bacteria 26 Basal 53 Fungi 8 Arthropods Eukaryotes27 Archaea 9 Plants 5 Invertebrates 19 Chordates (excl. Arthropods)
  • 19. Superfamily Number and the Scala Naturae
  • 20. Family Number and the Scala Naturae
  • 21. Architecture Number and the Scala Naturae
  • 22. The Tree of Life I ArchitecturesSuperfamilies Families
  • 23. The Tree of Life II
  • 24. The Tree of Life III
  • 25. The Tree of Life IV
  • 26. Protein Space
  • 27. Protein SpacePrincipal Coordinate Analysis – A Very BriefIntroduction PC1 Variable 2 PC 2 Variable 1
  • 28. Protein SpacePrincipal Coordinate Analysis – A Very BriefIntroduction
  • 29. Protein SpacePrincipal Coordinate Analysis – A Very BriefIntroduction
  • 30. Protein Space - Superfamilies
  • 31. Protein Space - Families
  • 32. Protein Space - Architectures
  • 33. Tempo and Protein Evolution
  • 34. Tempo and Protein Evolution Tempo and mode of evolution in a character complex (from Westoll 1949)
  • 35. Tempo and Protein Evolution Tempo and mode of cell type evolution I Increasing complexity (from Valentine et al. 1994)
  • 36. Tempo and Protein Evolution Tempo and mode of cell type evolution IIIncreasing complexity (from Hedges et al. 2004)
  • 37. Tempo and Protein Evolution - SuperfamiliesLUCA
  • 38. Tempo and Protein Evolution - FamiliesLUCA
  • 39. Tempo and Protein Evolution - ArchitecturesLUCA
  • 40. 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