Wagner chapter 1

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

Contents of Chapter 11)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 Lets 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.colis 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 11)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 Lets 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 Lets 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 ….. ….. ….. ….. ….. …..

Example of Genotype Space The genotype space is the set of all possible genotypes Lets 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)

Genotype network A genotype network is a set of genotypes that have the same phenotype, and are connected by single pairwise differences Lets 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 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

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

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 dont 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 functional MGAT1 functional MGAT1 functional MGAT1 functionalMGAT2 functional MGAT2 not functional MGAT2 not functional MGAT2 not functionalMGAT3 functional MGAT3 functional MGAT3 not functional MGAT3 not functionalMGAT4 functional MGAT4 functional MGAT4 functional MGAT4 not functionalMGAT5 functional MGAT5 functional MGAT5 functional MGAT5 functionalMGAT1 not functional MGAT1 not functional MGAT1 not functional MGAT1 not functionalMGAT2 functional MGAT2 not functional MGAT2 not functional MGAT2 not functionalMGAT3 functional MGAT3 functional MGAT3 not functional MGAT3 not functionalMGAT4 functional MGAT4 functional MGAT4 functional MGAT4 not functionalMGAT5 functional MGAT5 functional MGAT5 functional MGAT5 functionalMGAT1 not functional MGAT1 not functional MGAT1 not functional ….MGAT2 not functional MGAT2 not functional MGAT2 not functionalMGAT3 functional MGAT3 functional MGAT3 functionalMGAT4 functional MGAT4 not functional MGAT4 not functionalMGAT5 functional MGAT5 functional MGAT5 functionalMGAT1 not functional MGAT1 functional MGAT1 not functional …..MGAT2 not functional MGAT2 not functional MGAT2 not functionalMGAT3 not functional MGAT3 not functional MGAT3 not functionalMGAT4 functional MGAT4 functional MGAT4 functionalMGAT5 functional MGAT5 functional MGAT5 not functional

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

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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Wagner chapter 1

by Giovanni Dall'Olio on Jan 27, 2012

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