Book club on "Origins of Evolutionary Innovations" by A. Wagner http://bioinfoblog.it/

1. Book club
Andreas Wagner,
The Origins of Evolutionary Innovations
Chapter 1
Book club presented by G. Dall'Olio, IBE-CEXS

2. Contents of Chapter 1
1)What is an “Evolutionary Innovation”?
2)Definition of “Genotype Space” and “Genotype
Network”

3. Evolutionary Innovations
 An Evolutionary Innovation is a new trait that
introduces something “revolutionary” in
evolution
 The definition is quite broad... think that any
phenotype has been an evolutionary innovation
when it first appeared
 Let's see some notable examples

4. Examples of Evolutionary
Innovation
 In Metabolic networks:
 Microbes that evolve the ability to metabolize
xenobiotics (waste compounds produced by
humans)
 Urea Cycle
 Oxygen as an electron acceptor

5. Examples of Evolutionary
Innovation
 In Regulatory networks:
 Eye­like spots on butterflies' wings (Distal­less gene)
 Lenses of marine animals' eyes
 Plants' leaves (Knox genes)

6. Examples of Evolutionary
Innovation
 As novel molecules:
 Enzymes that obtain the ability to catalyze
completely different reactions after a mutation
 E.coli's L­Ru5P, that acquired aldolase activity after a
mutation
 IDH (citric cycle) and IMDH (leucine synthesis)
 Evolution of anti­freeze proteins

7. Examples of Evolutionary
Innovation
 Paper published today (Jan 27th 2012)
 A phage evolved the ability to infect a novel strain
of E.coli

8. Evolutionary Innovations
resume
 In general, the aim of this book is to describe how
novel phenotypes are discovered

9. Contents of Chapter 1
1)What is an “Evolutionary Innovation”?
2)Definition of “Genotype Space” and “Genotype
Network”

10. Definition of
Genotype Space
 The genotype space is the set of all possible
genotypes
 Let's represent it as a matrix where two neighbor
genotypes differ only for one position:
AAAAA AAAAC AAAAG AAAAT AAATT
AAACA AAACC AAACG AAACT AAATC
AACCA AACCC AACCG AACCT …..
ACCCA ACCCC ACCCG ACCCT …..
CCCCA CCCCC CCCCG CCCCT …..
….. ….. ….. ….. …..

11. Example of Genotype Space
 The genotype space is the set of all possible
genotypes
 Let's represent it as a matrix where two neighbor
genotypes differ only for one position:
Only one
AAAAA AAAAC AAAAG AAAAT AAATT difference
between
AAACA AAACC AAACG AAACT AAATC neighbor
AACCA AACCC AACCG AACCT ….. points
ACCCA ACCCC ACCCG ACCCT …..
CCCCA CCCCC CCCCG CCCCT …..
….. ….. ….. ….. …..

12. Example of Genotype Space
 The genotype space is the set of all possible
genotypes
 Let's represent it as a matrix where two neighbor
genotypes differ only for one position:
Only one
AAAAA AAAAC AAAAG AAAAT AAATT difference
between
AAACA AAACC AAACG AAACT AAATC neighbor
AACCA AACCC AACCG AACCT ….. points
ACCCA ACCCC ACCCG ACCCT …..
CCCCA CCCCC CCCCG CCCCT …..
….. ….. ….. ….. …..
Here, genotypes are represented as sequences, but they
can be other things (will be discussed later)

13. Genotype network
 A genotype network is a set of genotypes that have the same
phenotype, and are connected by single pairwise differences
 Let's assume that the marked genotypes have the same
phenotype:
AAAAA AAAAC AAAAG AAAAT AAATT
AAACA AAACC AAACG AAACT AAATC
AACCA AACCC AACCG AACCT …..
ACCCA ACCCC ACCCG ACCCT …..
CCCCA CCCCC CCCCG CCCCT …..
….. ….. ….. ….. …..
 → Yellow genotypes represent a genotype network

14. Genotype networks
resume
 The concept of Genotype networks allows us to
study how much a genotype can vary, without
changing the phenotype
 This is important to get to the final aim of this
book: understand how new innovative phenotypes
are discovered

15. Exploring genotype
networks
AAAAA AAAAC AAAAG AAAAT AAATT
AAACA AAACC AAACG AAACT AAATC
AACCA AACCC AACCG AACCT …..
ACCCA ACCCC ACCCG ACCCT …..
CCCCA CCCCC CCCCG CCCCT …..
….. ….. ….. ….. …..
 How big can a genotype network be?
 How can a population explore a genotype network?
 ….. many answers in the next chapters of the book

16. Exploring Genotype
networks
 AAAAA and ACCCT have the same phenotype (they are in the
same genotype network)
 Do their neighbors (e.g. AAACA and CCCT) have similar
phenotype?
AAAAA AAAAC AAAAG AAAAT AAATT
AAACA AAACC AAACG AAACT AAATC
AACCA AACCC AACCG AACCT …..
ACCCA ACCCC ACCCG ACCCT …..
CCCCA CCCCC CCCCG CCCCT …..
….. ….. ….. ….. …..

17. Example of Genotype
network taken from the
book (fig. 2.6)
 The lines corresponds to genotypes in a genotype network
 G1 and G2 have the same phenotype
 White spaces correspond to genotypes that don't have the
phenotype analyzed in this genotype network

18. Extending the definition of
“genotype”
 Depending what we want to study, we can use
different definitions of “genotype” and
“phenotype”
 For example, in a metabolic network, the genotype
can be the set of reactions that an organism can
catalize

19. Example of alternative
definition of “genotype”
MGAT1 functional MGAT1 functional MGAT1 functional MGAT1 functional
MGAT2 functional MGAT2 not functional MGAT2 not functional MGAT2 not functional
MGAT3 functional MGAT3 functional MGAT3 not functional MGAT3 not functional
MGAT4 functional MGAT4 functional MGAT4 functional MGAT4 not functional
MGAT5 functional MGAT5 functional MGAT5 functional MGAT5 functional
MGAT1 not functional MGAT1 not functional MGAT1 not functional MGAT1 not functional
MGAT2 functional MGAT2 not functional MGAT2 not functional MGAT2 not functional
MGAT3 functional MGAT3 functional MGAT3 not functional MGAT3 not functional
MGAT4 functional MGAT4 functional MGAT4 functional MGAT4 not functional
MGAT5 functional MGAT5 functional MGAT5 functional MGAT5 functional
MGAT1 not functional MGAT1 not functional MGAT1 not functional ….
MGAT2 not functional MGAT2 not functional MGAT2 not functional
MGAT3 functional MGAT3 functional MGAT3 functional
MGAT4 functional MGAT4 not functional MGAT4 not functional
MGAT5 functional MGAT5 functional MGAT5 functional
MGAT1 not functional MGAT1 functional MGAT1 not functional …..
MGAT2 not functional MGAT2 not functional MGAT2 not functional
MGAT3 not functional MGAT3 not functional MGAT3 not functional
MGAT4 functional MGAT4 functional MGAT4 functional
MGAT5 functional MGAT5 functional MGAT5 not functional

20. Example of alternative
definition of “genotype”
 All the yellow cells have the same phenotype (e.g.
they can produce glycosylation)
MGAT1 functional MGAT1 functional MGAT1 functional MGAT1 functional
MGAT2 functional MGAT2 not functional MGAT2 not functional MGAT2 not functional
MGAT3 functional MGAT3 functional MGAT3 not functional MGAT3 not functional
MGAT4 functional MGAT4 functional MGAT4 functional MGAT4 not functional
MGAT5 functional MGAT5 functional MGAT5 functional MGAT5 functional
MGAT1 not functional MGAT1 not functional MGAT1 not functional MGAT1 not functional
MGAT2 functional MGAT2 not functional MGAT2 not functional MGAT2 not functional
MGAT3 functional MGAT3 functional MGAT3 not functional MGAT3 not functional
MGAT4 functional MGAT4 functional MGAT4 functional MGAT4 not functional
MGAT5 functional MGAT5 functional MGAT5 functional MGAT5 functional
MGAT1 not functional MGAT1 not functional MGAT1 not functional ….
MGAT2 not functional MGAT2 not functional MGAT2 not functional
MGAT3 functional MGAT3 functional MGAT3 functional
MGAT4 functional MGAT4 not functional MGAT4 not functional
MGAT5 functional MGAT5 functional MGAT5 functional
MGAT1 not functional MGAT1 functional MGAT1 not functional …..
MGAT2 not functional MGAT2 not functional MGAT2 not functional
MGAT3 not functional MGAT3 not functional MGAT3 not functional
MGAT4 functional MGAT4 functional MGAT4 functional
MGAT5 functional MGAT5 functional MGAT5 not functional

21. Take home messages
 Genotype network != biological pathways
 Genotype network: set of possible genotypes
sharing the same phenotype, and connected
 Evolutionary Innovation: any novel phenotype
 Theory of Innovation: studies how populations can
explore the genotype space, the properties of
genotype networks, and how innovative
phenotypes can be found