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The Relationship Between Robustness and Evolution 1 1,2 1,2,3,4 2 Pengyao Jiang , Martin Kreitman , John Reinitz

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The Relationship Between Robustness and Evolution 1 1,2 1,2,3,4 2 Pengyao Jiang , Martin Kreitman , John Reinitz bioRxiv preprint doi: https://doi.org/10.1101/268862; this version posted February 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 The relationship between robustness and evolution 1 1,2 1,2,3,4 2 Pengyao Jiang , Martin Kreitman , John Reinitz 3 1 Department of Ecology & Evolution, University of Chicago, IL 60637, USA 4 2 Institute for Genomics & Systems Biology, Chicago, IL 60637, USA 5 3 Department of Statistics, University of Chicago, IL 60637, USA 6 4 Department of Molecular Genetics and Cell Biology, University of Chicago, IL 60637, 7 USA 8 Keywords 9 canalization; adaptation; Boolean model; Wright-Fisher; population simulations; perceptron; 10 evolutionary capacitor 1 bioRxiv preprint doi: https://doi.org/10.1101/268862; this version posted February 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 11 Abstract 12 Developmental robustness (canalization) is a common attribute of traits in multi-cellular 13 organisms. High robustness ensures the reproducibility of phenotypes in the face of envi- 14 ronmental and developmental noise, but it also dampens the expression of genetic mutation, 15 the fuel for adaptive evolution. A reduction in robustness may therefore be adaptive under 16 certain evolutionary scenarios. To better understand how robustness influences phenotypic 17 evolution, and to decipher conditions under which canalization itself evolves, a genetic model 18 was constructed in which phenotype is explicitly represented as a collection of traits, calcu- 19 lated from genotype, and the degree of robustness can be explicitly controlled. The genes 20 were subjected to mutation, altering phenotype and fitness. We then simulated the dynamics 21 of a population evolving under two classes of initial conditions, one in which the popula- 22 tion is at a fitness optimum and one in which it is far away. The model is formulated with 23 two robustness parameters in the genotype to phenotype map, controlling robustness over 24 a tight (γ) or a broad (α) range of values. Within the robustness range determined by γ, 25 high robustness results in a equilibrium population fitness closer to the optimal fitness value 26 than low robustness. High robustness should be favored, therefore, under a constant optimal 27 environment. This situation reverses when populations are challenged to evolve to a new 28 phenotype optimum. In this situation, low robustness populations adapt faster than high 29 robustness populations and reach higher equilibrium mean fitness. A larger set of phenotypes 30 are accessable by mutation when robustness is low, in part explaining why low robustness is 31 favored under this condition. A larger range of robustness could be sampled by varying α, 32 revealing a complex relationship between robustness and both the initial rate of phenotypic 33 adaptation as well as the final equilibrium population mean fitness. Intermediate values of α 34 produced a bifurcation in evolutionary trajectories, with some populations remaining at low 35 population mean fitness, and others escaping to achieve high population mean fitness. We 36 then allowed robustness itself to be encoded by a mutable genetic locus that could co-evolve 37 along with the phenotype under selection. Low robustness genotypes are initially favored 2 bioRxiv preprint doi: https://doi.org/10.1101/268862; this version posted February 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 38 when adapting to a new optimal phenotype. A high robustness genotype then replaces it, 39 well before maximum fitness is achieved, and moreover appears to prevent further invasion 40 into the population of a low-robustness genotype. This phenomenon was dependent on hav- 41 ing tight linkage (and sufficiently low mutation rate) between the robustness locus and the 42 loci encoding phenotype. 3 bioRxiv preprint doi: https://doi.org/10.1101/268862; this version posted February 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 43 Introduction 44 Phenotypes display a spectrum of sensitivities to environmental cues. At one extreme are 45 highly plastic traits, for which specific environmental or physiological signals induce alterna- 46 tive optimal phenotypes. At the other extreme are invariant, i.e., canalized or robust, traits 47 for which the influence of the external environment has been attenuated. Natural selection 48 can establish setpoints along this spectrum of environmental sensitivity to optimize popu- 49 lations to specific environmental regimes [Ancel, 1999, Stewart et al., 2012, Ehrenreich and 50 Pfennig, 2015, Palacio-L´opez et al., 2015]. 51 Here we address questions concerning phenotypes that fall at one end of the spectrum— 52 canalized traits—and how they evolve. First brought to our attention by C. H. Waddington 53 [Waddington, 1942], canalization involves not only the attenuation of environmental variabil- 54 ity, but also the insensitivity to genetic mutation and developmental noise. Canalization is 55 widely recognized as a general feature in developmental processes, due both to the structural 56 properties of developmental networks as well as to evolution of traits governed by stabilizing 57 selection [Siegal and Bergman, 2002, Barkai and Leibler, 1997, Meiklejohn and Hartl, 2002, 58 F´elixand Barkoulas, 2015]. Recent studies investigating gene regulatory networks have also 59 found support for Waddington’s classical idea of canalization being governed by attractor 60 states in the epigenetic landscape [Manu et al., 2009a,b, Moris et al., 2016, Huang, 2012]. 61 The high reproduciblity of a strongly canalized trait attenuates heritable phenotypic 62 variation, thus reducing the rate of adaptation [Fisher, 1930]. Yet canalized traits evolve 63 adaptively over phylogenetic time. Scutellar bristle number in Drosophila, for example, 64 is highly canalized [Rendel, 1959, Wheeler, 1987]; but also differs characteristically within 65 family Drosophilidae [Wheeler, 1987], making it a useful taxonomic feature in species clas- 66 sification. Under what circumstances, then, can canalized traits evolve? Early conceptual 67 models invoke gene-environmental interactions upon specific environmental stimuli to release 68 phenotypic variation on which natural selection can act [Waddington, 1942, 1953, Simpson, 69 1953]. This process involves environmental factors interacting with existing genetic variation 4 bioRxiv preprint doi: https://doi.org/10.1101/268862; this version posted February 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 70 to create novel phenotypes [Scharloo, 1991, Gibson and Hogness, 1996, Gibson and Dworkin, 71 2004]. 72 Mutation can also release otherwise suppressed phenotypic variation. The number of 73 vibrissae is typically nineteen in the house mouse, but in Tabby mutants this number can 74 vary [Dun and Fraser, 1958]. Similarly in Drosophila, the number of scutellar bristles varies 75 in a scute mutant but not wildtype [Rendel, 1965]. Release of phenotypic variation is not 76 restricted to mutation in genetic components regulating a specific phenotype. There may also 77 be genetic factors that act as global regulators of robustness, sometimes called “evolutionary 78 capacitors”. Rutherford and Lindquist [1998] proposed that Hsp90, a chaperone involved 79 in protein folding, is one such factor, buffering phenotypic variation under non-stressed 80 environmental conditions but releasing this variation at opportune times in response to 81 specific environmental stressors [Gibson, 2009, Masel, 2005, Paaby and Rockman, 2014, 82 Masel and Siegal, 2009]. Additional regulators have been found in a genetic screen for them 83 in yeast [Levy and Siegal, 2008]. But evidence for the existence of genetic capacitors that 84 contribute to adaptation remains under debate [Masel and Siegal, 2009, Meiklejohn and 85 Hartl, 2002, Levy and Siegal, 2008, Masel, 2005]. The strongest support for this hypothesis 86 comes from a study that found directionality of eye size change upon Hsp90 induction in 87 the cavefish, a phenotype that is otherwise stabilized by Hsp90 in the ancestral surface 88 populations [Rohner et al., 2013]. More recently, however, Geiler-Samerotte et al. [2016] 89 found a destabilizing effect of Hsp90 on de novo mutations, indicating that the buffering 90 effect of Hsp90 on standing population variation involves a selective sieve against destabilized 91 mutants. 92 The largest gap in our understanding of how canalized traits evolve, however, does not 93 revolve around uncertainly about the specific molecular mechanisms of canalization that 94 contribute to adaptation (such as Hsp90). Rather, it revolves around theoretical issues: the 95 degree of robustness that can be maintained in the population under stabilizing selection, 96 and the extent to which a lowering of robustness is required when adapting to a novel 5 bioRxiv preprint doi: https://doi.org/10.1101/268862; this version posted February 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 97 environment. Here we summarize key findings about robustness against mutation.
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