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Book club on "Origins of Evolutionary Innovations" by A. Wagner

Book club on "Origins of Evolutionary Innovations" by A. Wagner

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    Wagner chapter 1 Wagner chapter 1 Presentation Transcript

    • 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