Book club
Andreas Wagner,The Origins of Evolutionary Innovations
Chapter 1
Book club presented by G. Dall'Olio, IBE-CEXS
Contents of Chapter 1
1)What is an “Evolutionary Innovation”?
2)Definition of “Genotype Space” and “Genotype Network”
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
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
Examples of Evolutionary Innovation
In Regulatory networks: Eyelike spots on butterflies' wings (Distalless gene) Lenses of marine animals' eyes Plants' leaves (Knox genes)
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
Examples of Evolutionary Innovation
Paper published today (Jan 27th 2012) A phage evolved the ability to infect a novel strain
of E.coli
Evolutionary Innovations resume
In general, the aim of this book is to describe how novel phenotypes are discovered
Contents of Chapter 1
1)What is an “Evolutionary Innovation”?
2)Definition of “Genotype Space” and “Genotype Network”
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 …..
….. ….. ….. ….. …..
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:
AAAAA AAAAC AAAAG AAAAT AAATT
AAACA AAACC AAACG AAACT AAATC
AACCA AACCC AACCG AACCT …..
ACCCA ACCCC ACCCG ACCCT …..
CCCCA CCCCC CCCCG CCCCT …..
….. ….. ….. ….. …..
Only one difference between neighbor points
AAAAA AAAAC AAAAG AAAAT AAATT
AAACA AAACC AAACG AAACT AAATC
AACCA AACCC AACCG AACCT …..
ACCCA ACCCC ACCCG ACCCT …..
CCCCA CCCCC CCCCG CCCCT …..
….. ….. ….. ….. …..
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 difference between neighbor points
Here, genotypes are represented as sequences, but they can be other things (will be discussed later)
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
Genotype networksresume
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
Exploring genotype networks
How big can a genotype network be? How can a population explore a genotype network? ….. many answers in the next chapters of the book
AAAAA AAAAC AAAAG AAAAT AAATT
AAACA AAACC AAACG AAACT AAATC
AACCA AACCC AACCG AACCT …..
ACCCA ACCCC ACCCG ACCCT …..
CCCCA CCCCC CCCCG CCCCT …..
….. ….. ….. ….. …..
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 …..
….. ….. ….. ….. …..
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
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
Example of alternative definition of “genotype”
MGAT1 functionalMGAT2 functionalMGAT3 functionalMGAT4 functionalMGAT5 functional
MGAT1 functionalMGAT2 not functionalMGAT3 functionalMGAT4 functionalMGAT5 functional
MGAT1 functionalMGAT2 not functionalMGAT3 not functionalMGAT4 functionalMGAT5 functional
MGAT1 functionalMGAT2 not functionalMGAT3 not functionalMGAT4 not functionalMGAT5 functional
MGAT1 not functionalMGAT2 functionalMGAT3 functionalMGAT4 functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 functionalMGAT4 functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 not functionalMGAT4 functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 not functionalMGAT4 not functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 functionalMGAT4 functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 functionalMGAT4 not functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 functionalMGAT4 not functionalMGAT5 functional
….
MGAT1 not functionalMGAT2 not functionalMGAT3 not functionalMGAT4 functionalMGAT5 functional
MGAT1 functionalMGAT2 not functionalMGAT3 not functionalMGAT4 functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 not functionalMGAT4 functionalMGAT5 not functional
…..
Example of alternative definition of “genotype”
MGAT1 functionalMGAT2 functionalMGAT3 functionalMGAT4 functionalMGAT5 functional
MGAT1 functionalMGAT2 not functionalMGAT3 functionalMGAT4 functionalMGAT5 functional
MGAT1 functionalMGAT2 not functionalMGAT3 not functionalMGAT4 functionalMGAT5 functional
MGAT1 functionalMGAT2 not functionalMGAT3 not functionalMGAT4 not functionalMGAT5 functional
MGAT1 not functionalMGAT2 functionalMGAT3 functionalMGAT4 functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 functionalMGAT4 functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 not functionalMGAT4 functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 not functionalMGAT4 not functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 functionalMGAT4 functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 functionalMGAT4 not functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 functionalMGAT4 not functionalMGAT5 functional
….
MGAT1 not functionalMGAT2 not functionalMGAT3 not functionalMGAT4 functionalMGAT5 functional
MGAT1 functionalMGAT2 not functionalMGAT3 not functionalMGAT4 functionalMGAT5 functional
MGAT1 not functionalMGAT2 not functionalMGAT3 not functionalMGAT4 functionalMGAT5 not functional
…..
All the yellow cells have the same phenotype (e.g. they can produce glycosylation)
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
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