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Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints

Various characteristics of complex gene regulatory networks (GRNs) have been discovered during the last decade, e.g., redundancy, exponential indegree distributions, scale-free outdegree distributions, mutational robustness, and evolvability. Although progress has been made in this field, it is not...

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Detalles Bibliográficos
Autores principales: Tsuda, Masaki E., Kawata, Masakado
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916849/
https://www.ncbi.nlm.nih.gov/pubmed/20700492
http://dx.doi.org/10.1371/journal.pcbi.1000873
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author Tsuda, Masaki E.
Kawata, Masakado
author_facet Tsuda, Masaki E.
Kawata, Masakado
author_sort Tsuda, Masaki E.
collection PubMed
description Various characteristics of complex gene regulatory networks (GRNs) have been discovered during the last decade, e.g., redundancy, exponential indegree distributions, scale-free outdegree distributions, mutational robustness, and evolvability. Although progress has been made in this field, it is not well understood whether these characteristics are the direct products of selection or those of other evolutionary forces such as mutational biases and biophysical constraints. To elucidate the causal factors that promoted the evolution of complex GRNs, we examined the effect of fluctuating environmental selection and some intrinsic constraining factors on GRN evolution by using an individual-based model. We found that the evolution of complex GRNs is remarkably promoted by fixation of beneficial gene duplications under unpredictably fluctuating environmental conditions and that some internal factors inherent in organisms, such as mutational bias, gene expression costs, and constraints on expression dynamics, are also important for the evolution of GRNs. The results indicate that various biological properties observed in GRNs could evolve as a result of not only adaptation to unpredictable environmental changes but also non-adaptive processes owing to the properties of the organisms themselves. Our study emphasizes that evolutionary models considering such intrinsic constraining factors should be used as null models to analyze the effect of selection on GRN evolution.
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spelling pubmed-29168492010-08-10 Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints Tsuda, Masaki E. Kawata, Masakado PLoS Comput Biol Research Article Various characteristics of complex gene regulatory networks (GRNs) have been discovered during the last decade, e.g., redundancy, exponential indegree distributions, scale-free outdegree distributions, mutational robustness, and evolvability. Although progress has been made in this field, it is not well understood whether these characteristics are the direct products of selection or those of other evolutionary forces such as mutational biases and biophysical constraints. To elucidate the causal factors that promoted the evolution of complex GRNs, we examined the effect of fluctuating environmental selection and some intrinsic constraining factors on GRN evolution by using an individual-based model. We found that the evolution of complex GRNs is remarkably promoted by fixation of beneficial gene duplications under unpredictably fluctuating environmental conditions and that some internal factors inherent in organisms, such as mutational bias, gene expression costs, and constraints on expression dynamics, are also important for the evolution of GRNs. The results indicate that various biological properties observed in GRNs could evolve as a result of not only adaptation to unpredictable environmental changes but also non-adaptive processes owing to the properties of the organisms themselves. Our study emphasizes that evolutionary models considering such intrinsic constraining factors should be used as null models to analyze the effect of selection on GRN evolution. Public Library of Science 2010-08-05 /pmc/articles/PMC2916849/ /pubmed/20700492 http://dx.doi.org/10.1371/journal.pcbi.1000873 Text en Tsuda, Kawata. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Tsuda, Masaki E.
Kawata, Masakado
Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints
title Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints
title_full Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints
title_fullStr Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints
title_full_unstemmed Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints
title_short Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints
title_sort evolution of gene regulatory networks by fluctuating selection and intrinsic constraints
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916849/
https://www.ncbi.nlm.nih.gov/pubmed/20700492
http://dx.doi.org/10.1371/journal.pcbi.1000873
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