Data from: Robustness to noise in gene expression evolves despite epistatic constraints in a model of gene networks

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Draghi, Jeremy; Whitlock, Michael C.; Whitlock, Michael, 2015, "Data from: Robustness to noise in gene expression evolves despite epistatic constraints in a model of gene networks", https://doi.org/10.5683/SP2/RD59UI, Borealis, V1

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Description	Abstract Stochastic noise in gene expression causes variation in the development of phenotypes, making such noise a potential target of stabilizing selection. Here we develop a new simulation model of gene networks to study the adaptive landscape underlying the evolution of robustness to noise. We find that epistatic interactions between the determinants of the expression of a gene and its downstream effect impose significant constraints on evolution, but these interactions do allow the gradual evolution of increased robustness. Despite strong sign epistasis, adaptation rarely proceeds via deleterious intermediate steps, but instead occurs primarily through small beneficial mutations. A simple mathematical model captures the relevant features of the single-gene fitness landscape and explains counterintuitive patterns, such as a correlation between the mean and standard deviation of phenotypes. In more complex networks, mutations in regulatory regions provide evolutionary pathways to increased robustness. These results chart the constraints and possibilities of adaptation to reduce expression noise and demonstrate the potential of a novel modeling framework for gene networks. (2020-06-24) Usage notes Part APart A--use "cat" utility to reassemble into a zipped folder containing the complete code and data files.dryad_files_a Part BPart B--use "cat" utility to reassemble into a zipped folder containing the complete code and data files.dryad_files_b Part CPart C--use "cat" utility to reassemble into a zipped folder containing the complete code and data files.dryad_files_c (2020-06-24)
Subject	Other
Keyword	epistasis, Models/Simulations
Related Publication	Article
Notes	Dryad version number: 1 Version status: submitted Dryad curation status: Published Sharing link: https://datadryad.org/stash/share/iXyVyZF-e3_-bHEaVuUWvTpHHH39RxI5TRHSbChDHaE Storage size: 1830463746 Visibility: public
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Citation Metadata

Persistent Identifier	doi:10.5683/SP2/RD59UI
Publication Date	2021-05-19
Citation Date
Title	Data from: Robustness to noise in gene expression evolves despite epistatic constraints in a model of gene networks
Other Identifier	Dryad: doi:10.5061/dryad.8c81j
Author	Draghi, Jeremy (University of British Columbia) Whitlock, Michael C. (University of British Columbia) Whitlock, Michael (University of British Columbia)
Point of Contact	Use email button above to contact. UBC Library Research Data Team
Description	Abstract Stochastic noise in gene expression causes variation in the development of phenotypes, making such noise a potential target of stabilizing selection. Here we develop a new simulation model of gene networks to study the adaptive landscape underlying the evolution of robustness to noise. We find that epistatic interactions between the determinants of the expression of a gene and its downstream effect impose significant constraints on evolution, but these interactions do allow the gradual evolution of increased robustness. Despite strong sign epistasis, adaptation rarely proceeds via deleterious intermediate steps, but instead occurs primarily through small beneficial mutations. A simple mathematical model captures the relevant features of the single-gene fitness landscape and explains counterintuitive patterns, such as a correlation between the mean and standard deviation of phenotypes. In more complex networks, mutations in regulatory regions provide evolutionary pathways to increased robustness. These results chart the constraints and possibilities of adaptation to reduce expression noise and demonstrate the potential of a novel modeling framework for gene networks. (2020-06-24) Usage notes Part APart A--use "cat" utility to reassemble into a zipped folder containing the complete code and data files.dryad_files_a Part BPart B--use "cat" utility to reassemble into a zipped folder containing the complete code and data files.dryad_files_b Part CPart C--use "cat" utility to reassemble into a zipped folder containing the complete code and data files.dryad_files_c (2020-06-24)
Subject	Other
Keyword	epistasis (Dryad) Models/Simulations (Dryad)
Related Publication	Article doi: https://doi.org/10.1111/evo.12732
Notes	Dryad version number: 1 Version status: submitted Dryad curation status: Published Sharing link: https://datadryad.org/stash/share/iXyVyZF-e3_-bHEaVuUWvTpHHH39RxI5TRHSbChDHaE Storage size: 1830463746 Visibility: public
Distribution Date	2015-07-06
Deposit Date	2020-06-24

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