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Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution
The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene regulatory networks (GRNs) and explore the evolution of mutational robustness and bistability. Living systems have develope...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8803174/ https://www.ncbi.nlm.nih.gov/pubmed/35045068 http://dx.doi.org/10.1371/journal.pcbi.1009796 |
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author | Kaneko, Tadamune Kikuchi, Macoto |
author_facet | Kaneko, Tadamune Kikuchi, Macoto |
author_sort | Kaneko, Tadamune |
collection | PubMed |
description | The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene regulatory networks (GRNs) and explore the evolution of mutational robustness and bistability. Living systems have developed their functions through evolutionary processes. To understand the particularities of this process theoretically, evolutionary simulation (ES) alone is insufficient because the outcomes of ES depend on evolutionary pathways. We need a reference system for comparison. An appropriate reference system for this purpose is an ensemble of the randomly sampled genotypes. However, generating high-fitness genotypes by simple random sampling is difficult because such genotypes are rare. In this study, we used the multicanonical Monte Carlo method developed in statistical physics to construct a reference ensemble of GRNs and compared it with the outcomes of ES. We obtained the following results. First, mutational robustness was significantly higher in ES than in the reference ensemble at the same fitness level. Second, the emergence of a new phenotype, bistability, was delayed in evolution. Third, the bistable group of GRNs contains many mutationally fragile GRNs compared with those in the non-bistable group. This suggests that the delayed emergence of bistability is a consequence of the mutation-selection mechanism. |
format | Online Article Text |
id | pubmed-8803174 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-88031742022-02-01 Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution Kaneko, Tadamune Kikuchi, Macoto PLoS Comput Biol Research Article The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene regulatory networks (GRNs) and explore the evolution of mutational robustness and bistability. Living systems have developed their functions through evolutionary processes. To understand the particularities of this process theoretically, evolutionary simulation (ES) alone is insufficient because the outcomes of ES depend on evolutionary pathways. We need a reference system for comparison. An appropriate reference system for this purpose is an ensemble of the randomly sampled genotypes. However, generating high-fitness genotypes by simple random sampling is difficult because such genotypes are rare. In this study, we used the multicanonical Monte Carlo method developed in statistical physics to construct a reference ensemble of GRNs and compared it with the outcomes of ES. We obtained the following results. First, mutational robustness was significantly higher in ES than in the reference ensemble at the same fitness level. Second, the emergence of a new phenotype, bistability, was delayed in evolution. Third, the bistable group of GRNs contains many mutationally fragile GRNs compared with those in the non-bistable group. This suggests that the delayed emergence of bistability is a consequence of the mutation-selection mechanism. Public Library of Science 2022-01-19 /pmc/articles/PMC8803174/ /pubmed/35045068 http://dx.doi.org/10.1371/journal.pcbi.1009796 Text en © 2022 Kaneko, Kikuchi https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Kaneko, Tadamune Kikuchi, Macoto Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution |
title | Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution |
title_full | Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution |
title_fullStr | Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution |
title_full_unstemmed | Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution |
title_short | Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution |
title_sort | evolution enhances mutational robustness and suppresses the emergence of a new phenotype: a new computational approach for studying evolution |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8803174/ https://www.ncbi.nlm.nih.gov/pubmed/35045068 http://dx.doi.org/10.1371/journal.pcbi.1009796 |
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