1. Adventures in protein world reveal
the Tree of Life and the evolution of
complexity
Graeme 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 Domains
Folding

15. SCOP Protein Domain Classification
Classes
(7)
Folds
(48)
Superfamily
(1445)
Family
(2598)
Domain
(75930)

16. Protein Domain Classification
A B C D
Protein 1: Architecture = A,A,C
Protein 2: Architecture = D,B
Protein 3: Architecture = B
Protein 4: Architecture = C,A,A
Protein 5: Architecture = D,B,C

17. http://supfam.org Protein Domain Database I

18. Protein Domain Database II
238 Bacteria 26 Basal 53 Fungi 8 Arthropods
Eukaryotes
27 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
Architectures
Superfamilies Families

23. The Tree of Life II

24. The Tree of Life III

25. The Tree of Life IV

26. Protein Space

27. Protein Space
Principal Coordinate Analysis – A Very Brief
Introduction
PC1
Variable 2
PC
2
Variable 1

28. Protein Space
Principal Coordinate Analysis – A Very Brief
Introduction

29. Protein Space
Principal Coordinate Analysis – A Very Brief
Introduction

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 II
Increasing complexity
(from Hedges et al. 2004)

37. Tempo and Protein Evolution -
Superfamilies
LUCA

38. Tempo and Protein Evolution -
Families
LUCA

39. Tempo and Protein Evolution -
Architectures
LUCA

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