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. 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. 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. 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. 6. The Problem“Complexity is hard to define or measure…” Maynard Smith and Szathmáry, 1995
  7. 7. Segmentation and Complexity I Differentiation of centrum length in vertebrates Increasing complexity (from McShea 1992)
  8. 8. Segmentation and Complexity II Functional differentiation in arthropod limbs Increasing complexity (from Cisne 1974)
  9. 9. Segmentation and Complexity III Increasing complexity Differentiation of segment length in centipedes (from Fusco and Minelli 2000
  10. 10. Fractals and Complexity Fractal dimension in ammonoids Increasing complexity (from Boyiajian & Lutz 1992)
  11. 11. Cell Number and Complexity Increasing complexity (from Valentine et al. 1994)
  12. 12. Genome Size and the Scala Naturae Increasing complexity (from Gregory 2005)
  13. 13. Proteome Size and the Scala Naturae ?
  14. 14. Protein Structural DomainsFolding
  15. 15. Protein Domain Classification IFoldSuperfamily(1445)Family(2598)Domain
  16. 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. 17. http://supfam.org Protein Domain Database I
  18. 18. Protein Domain Database II238 Bacteria 26 Basal 53 Fungi 8 Arthropods Eukaryotes27 Archaea 9 Plants 5 Invertebrates 19 Chordates (excl. Arthropods)
  19. 19. Superfamily Number and the Scala Naturae
  20. 20. Family Number and the Scala Naturae
  21. 21. Architecture Number and the Scala Naturae
  22. 22. The Tree of Life I ArchitecturesSuperfamilies Families
  23. 23. The Tree of Life II
  24. 24. The Tree of Life III
  25. 25. The Tree of Life IV
  26. 26. Protein Space
  27. 27. Protein SpacePrincipal Coordinate Analysis – A Very BriefIntroduction PC1 Variable 2 PC 2 Variable 1
  28. 28. Protein SpacePrincipal Coordinate Analysis – A Very BriefIntroduction
  29. 29. Protein SpacePrincipal Coordinate Analysis – A Very BriefIntroduction
  30. 30. Protein Space - Superfamilies
  31. 31. Protein Space - Families
  32. 32. Protein Space - Architectures
  33. 33. Tempo and Protein Evolution
  34. 34. Tempo and Protein Evolution Tempo and mode of evolution in a character complex (from Westoll 1949)
  35. 35. Tempo and Protein Evolution Tempo and mode of cell type evolution I Increasing complexity (from Valentine et al. 1994)
  36. 36. Tempo and Protein Evolution Tempo and mode of cell type evolution IIIncreasing complexity (from Hedges et al. 2004)
  37. 37. Tempo and Protein Evolution - SuperfamiliesLUCA
  38. 38. Tempo and Protein Evolution - FamiliesLUCA
  39. 39. Tempo and Protein Evolution - ArchitecturesLUCA
  40. 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

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