wagner chapter 1

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