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On the role of sparseness in the evolution of modularity in gene regulatory networks
Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major fa...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5979046/ https://www.ncbi.nlm.nih.gov/pubmed/29775459 http://dx.doi.org/10.1371/journal.pcbi.1006172 |
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author | Espinosa-Soto, Carlos |
author_facet | Espinosa-Soto, Carlos |
author_sort | Espinosa-Soto, Carlos |
collection | PubMed |
description | Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases. |
format | Online Article Text |
id | pubmed-5979046 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-59790462018-06-16 On the role of sparseness in the evolution of modularity in gene regulatory networks Espinosa-Soto, Carlos PLoS Comput Biol Research Article Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases. Public Library of Science 2018-05-18 /pmc/articles/PMC5979046/ /pubmed/29775459 http://dx.doi.org/10.1371/journal.pcbi.1006172 Text en © 2018 Carlos Espinosa-Soto http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://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 Espinosa-Soto, Carlos On the role of sparseness in the evolution of modularity in gene regulatory networks |
title | On the role of sparseness in the evolution of modularity in gene regulatory networks |
title_full | On the role of sparseness in the evolution of modularity in gene regulatory networks |
title_fullStr | On the role of sparseness in the evolution of modularity in gene regulatory networks |
title_full_unstemmed | On the role of sparseness in the evolution of modularity in gene regulatory networks |
title_short | On the role of sparseness in the evolution of modularity in gene regulatory networks |
title_sort | on the role of sparseness in the evolution of modularity in gene regulatory networks |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5979046/ https://www.ncbi.nlm.nih.gov/pubmed/29775459 http://dx.doi.org/10.1371/journal.pcbi.1006172 |
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