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TH E ADAPTIVE LANDSCAPE in Evolutionary Biology CHAPTER17 :H and the Liutionary TH E ADAPTIVE LANDSCAPE in Evolutionary Biology CHAPTER17 :h and the liutionary )id forest High-Dimensional Adaptive ed butter­ osophicai Landscapes Facilitate Evolutionary Sciences, Innovation hoiogicai Andreas Wagner f Popuia­ iutionary 'go,IL. 17.1 Introduction one peak to the next, one needs to cross a mal­ adaptive valley-the valley of death, if you will­ The Adaptive Landscape is one of the most influen­ with no detour around this valley. This changes in tial concepts in evolutionary biology (Wright 1932, higher dimensional landscapes, where, counterin­ Futuyma 1998, see also Chapter 2 of this volume). It tuitively, "extra dimensional bypasses" around mal­ is commonly visualized as a surface of rolling hills adaptive valleys exist (Conrad 1990). Through such or rugged mountains in a three-dimensional space. bypasses, one can h'avel from peak to peak while Two of the three dimensions represent allele fre­ avoiding valleys of death. Gavrilets pointed out quencies or-relevant for my purpose-genotypes. that this principle has implications for the evolu­ The third dimension represents fitness. The land­ tion of reproductive isolation (Gavrilets 1997, 2005). scape's peaks represent adaptive trait combinations I here explain that it also has implications for how or genotypes. The Adaptive Landscape concept biological systems llU1ovate. has been highly successful, so much so that it has hU1ovations in evolving biological systems are spawned multiple variants in the h~nds of differ­ qualitatively new and beneficial new phenotypes. ent authors, including holey landscapes (Gavrilets High-dimensional Adaptive Landscapes can facil­ 1997) and phenotype landscapes. The variant I itate such llU1ovations. In the next section I dis­ emphasize here can be viewed as a phenotype land­ cuss evidence for this assertion for three classes scape (see also Chapter 18 of this volume for differ­ of systems important for evolutionary llU1ovation. ent kinds of phenotype landscapes). These are metabolic networks, gene regulation cir­ I view the Adaptive Landscape as a metaphor cuits, as well as protein and RNA macromolecules. for the evolutionary process. It is an abstraction Detailed studies of the high-dimensional genotype derived from an immensely complex reality. Such spaces of these systems have demonstrated the abstraction is necessary for all human understand­ existence of vast genotype networks. These are ing of the world around us. Yet like all abstractions, connected sets of genotypes with the same phe­ it also has limitations. Several of these limitations notype that extend far through genotype space. are caused by the high dimensionality of geno­ Genotype networks are important for the abil­ type spaces. This high dimensionality has already ity of biological systems to explore many novel been appreciated by Sewall Wright, the creator phenotypes. Genotype networks can be viewed of the Adaptive Landscape concept (Wright 1932). as a consequence of the high-dimensionality of Its consequences have been shldied at least since genotype spaces. I will begin illustrating this fea­ the late 1980s (Kauffman and Levin 1987; Con­ ture in some detail with metabolic networks, and rad 1990; Gavrilets 1997). One important such con­ then discuss the other system classes more briefly. sequence regards a basic geometric intuition we Table 17.1 summarizes some of the concepts I will derive from three-dimensional space. To get from introduce. 271 272 PART V DEVELOPMENT, FORM, AND FUNCTION Table 17.1 Important concepts for the three system classes discussed in this chapter. Genotype Neighbors Genotype space Phenotype Metabolic Network DNA encoding all metabolic Networks that differ in All possible metabolic Ability to synthesize biomass or enzymes/reactions in a one enzyme (reaction) networks other important molecules from a metabolism given spectrum of nutrients Regulatory circuit DNA encoding regulatory Circuits that differ in one All possible regul atory Gene expression or molecular interactions among molecules regulatory interaction circuits activity of all ci rcuit molecules Macromolecule Amino acid or nucleotide Polymers that differ in a All possible amino Tertiary structure (fold) and (protein/RNA) polymers single monomer acid/nucleotide polymers biochemical activity 17.2 Metabolic network space possible metabolic networks and their biosynthetic Metabolic networks are comprised of hundreds abilities. To do so, it is necessary to define a space , to thousands of chemical reactions-catalyzed by of possible metabolic genotypes. The metabolic r enzymes that are encoded by genes-which synthe­ genotype of anyone organism is the part of (. size all small molecules in biomass from environ­ the organism's genome that encodes the enzymes mental nutrients. In addition, they produce energy which catalyze metabolic reactions. Although this 1 and many important secondary metabolites. Such genotype is a string of DNA, it is useful to represent t networks are involved in many innovations, from it in a more compact way as follows. Consider the microbes to higher organisms. Examples include known "universe" of enzyme-catalyzed chemical A the ability of microbes to grow on synthetic antibi­ reactions. This muverse currently comprises more y' otics or other toxic xenobiotic compounds, such . than 5000 reactions and the associated enzymes. II as polychlorinated biphenyls, chlorobenzenes, or Write the names of these reactions or their stoicluo­ Fe pentachlorophenol, in some cases using them as metric equations as a list. For anyone organism, 2( their sole carbon source (Cline et al. 1989; van write a one next to the reaction in this list if its 111 der Meer 1995; van der Meer et al. 1998; Copley genome encodes an enzyme catalyzing this reac­ 2000; Dantas et al. 2008; Rehmann and Daugulis tion, and a zero if it does not. The result will be a hE 2008). They also include the urea cycle, a metabolic long string of ones and zeroes that can represent the all innovation of land-living animals that allows them metabolic genotype of the organism (Rodrigues and nl: to convert toxic ammonia into urea for excretion. Wagner 2009). ad Novel metabolic traits often involve new combina­ In tlus representation, a metabolic genotype can po tions of chemical reactions (enzymes) in an organ­ be viewed as a single point in a vast metabolic CaJ ism that already exist separately elsewhere. For genotype space, a space of possible metabolic net­ thE example, a novel metabolic pathway to degrade works. This space contains all possible pres­ an. pentachlorophenol involves four steps that its host ence/absence combinations of enzyme-catalyzed tat organism assembled- probably through horizontal reactions. Each such combination constitutes a are gene transfer- from enzymes processing naturally metabolic network. For a universe of 5000 reactions, ChE occurring chlorinated chemicals, as well as from there are 25000 such metabolic networks, a hyper­ wh an enzyme involved in tyrosine metabolism (Cop­ astronomical number, many more than could be frQ] ley 2000). Similarly, the urea cycle arose when four realized in organisms on earth. Metabolic genotype can widespread enzymatic reactions involved in argi­ space can also be viewed as the set of all binary gell nine biosynthesis combined with arginase, a reac­ strings of length 5000. Yet anotl1er, geometric rep­ T tion involved in arginine degradation (Takiguchi resentation is that of a 5000-dimensional hypercube qua et al. 1989). graph. Tlus is a graph whose vertices-the vertices Thi.: To study innovation in metabolic networks sys­ of an n-dimensional cube-are the individual geno­ ablE tematically, one needs to be able to represent all types. Two genotypes are connected by an edge if pan HIGH-DIMENS IONAL ADAPTIVE LANDSCAP ES FAC ILITATE EVOLUTIONARY INNOVATION 27 3 they are (I-mutant) neighbors, that is, if they differ metabolic phenotype. For example, one could list in a single chemical reaction. the essential biomass molecules that a metabolic This genotype space is a prototypical exam­ network is able to synthesize iI1 anyone chemical mthesize biomass or ple of a high-dimensional space. Each of its axes environment. However, unless a metabolic network nant molecules from a (reactions) corresponds to one dimension. In con­ can synthesize all essential molecules, it may not rum of nutrients h'ast to our low-dimensional Euclidean space, it be able to sustain life. This definition is therefore ssion or molecular is a discrete and not a continuous space, con­ of liInited use. To study metabolic umovations, and " circuit molecules taining an enumerable number of elements. It is especially umovations that allow survival on novel Icture (fold) and thus quite different from Euclidean space. How­ I activity sources of energy and carbon, the followu1g defini­ ever, it also shares some similarities with this space. tion is more useful. This definition focuses on car­ The most important of them is that in genotype bon, because carbon is a central element u1life, and space intuitive measures of the distance between because umovations involving carbon metabolism two metabolic genotypes exists. One such mea­ are thus especially important. Howevel~ what I ir biosynthetic sure is simply the fraction of metabolic reactions in describe also applies to other metabolic iImovations define a space which two genotypes differ. In mathematical terms, (Rodrigues and Wagner 2011). ['he metabolic metabolic genotype space is thus a metric space Consider a minimal chemical environment that : the part of (Searcoid 2007). contau1S a small number of molecules which can ; the enzymes serve as a source of all necessary elements except Although this carbon. For u1stance, U1 the case of E. coli, this 17.3 From metabolic genotype ~ to represent environment comprises only six different kinds to phenotype Consider the of molecules. Now make a list of many different ·zed chemical A free-living organism such as Escherichia coli or potential sources of carbon and energy, such as glu­ mprises more yeast needs to synthesize some 50 essential biomass cose, ethanol, glycerol, and so forth. For the sake ted enzymes. molecules to grow and divide (Forster et al.
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