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. 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 Domains
Folding

8. Protein Domain Classification I
Fold
Superfamily
(1445)
Family
(2598)
Domain

9. Protein Domain Classification II
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

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

11. Protein Domain Database II
238 Bacteria 26 Basal 53 Fungi 8 Arthropods
Eukaryotes
27 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
Architectures
Superfamilies 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 II
Principal 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 -
Superfamilies
LUCA

26. Tempo and Protein Evolution III -
Families
LUCA

27. Tempo and Protein Evolution IV -
Architectures
LUCA

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