The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10400.7/319 |
Resumo: | The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal interference - the competition of clones carrying different beneficial mutations - which leads to the loss of many small effect mutations and fixation of large effect ones. If interference is abundant, then mechanisms for horizontal transfer of genes, which allow the immediate combination of beneficial alleles in a single background, are expected to evolve. However, the relevance of interference in natural complex environments, such as the gut, is poorly known. To address this issue, we studied the invasion of beneficial mutations responsible for Escherichia coli's adaptation to the mouse gut and demonstrate the pervasiveness of clonal interference. The observed dynamics of change in frequency of beneficial mutations are consistent with soft sweeps, where a similar adaptive mutation arises repeatedly on different haplotypes without reaching fixation. The genetic basis of the adaptive mutations revealed a striking parallelism in independently evolving populations. This was mainly characterized by the insertion of transposable elements in both coding and regulatory regions of a few genes. Interestingly in most populations, we observed a complete phenotypic sweep without loss of genetic variation. The intense clonal interference during adaptation to the gut environment, here demonstrated, may be important for our understanding of the levels of strain diversity of E. coli inhabiting the human gut microbiota and of its recombination rate. |
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The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweepsQuantitative Biology - Populations and EvolutionCloningThe accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal interference - the competition of clones carrying different beneficial mutations - which leads to the loss of many small effect mutations and fixation of large effect ones. If interference is abundant, then mechanisms for horizontal transfer of genes, which allow the immediate combination of beneficial alleles in a single background, are expected to evolve. However, the relevance of interference in natural complex environments, such as the gut, is poorly known. To address this issue, we studied the invasion of beneficial mutations responsible for Escherichia coli's adaptation to the mouse gut and demonstrate the pervasiveness of clonal interference. The observed dynamics of change in frequency of beneficial mutations are consistent with soft sweeps, where a similar adaptive mutation arises repeatedly on different haplotypes without reaching fixation. The genetic basis of the adaptive mutations revealed a striking parallelism in independently evolving populations. This was mainly characterized by the insertion of transposable elements in both coding and regulatory regions of a few genes. Interestingly in most populations, we observed a complete phenotypic sweep without loss of genetic variation. The intense clonal interference during adaptation to the gut environment, here demonstrated, may be important for our understanding of the levels of strain diversity of E. coli inhabiting the human gut microbiota and of its recombination rate.Howard Hughes Medical Institute (HHMI-55007436), LAO/ITQB, FCT Grants: FRH/BD/80257/2011 and SFRH/BPD/14299/2003.PLOSARCAJoão Barroso-BatistaAna SousaMarta LourençoMarie-Louise BergmanJocelyne DemengeotKarina B. XavierIsabel Gordo2015-09-28T16:38:13Z2014-03-062014-03-06T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.7/319engBarroso-Batista J, Sousa A, Lourenço M, Bergman M-L, Sobral D, Demengeot J, et al. (2014) The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps. PLoS Genet 10(3): e1004182. doi:10.1371/journal.pgen.100418210.1371/journal.pgen.1004182info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2022-11-29T14:34:43Zoai:arca.igc.gulbenkian.pt:10400.7/319Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T16:11:38.273926Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps |
title |
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps |
spellingShingle |
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps João Barroso-Batista Quantitative Biology - Populations and Evolution Cloning |
title_short |
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps |
title_full |
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps |
title_fullStr |
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps |
title_full_unstemmed |
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps |
title_sort |
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps |
author |
João Barroso-Batista |
author_facet |
João Barroso-Batista Ana Sousa Marta Lourenço Marie-Louise Bergman Jocelyne Demengeot Karina B. Xavier Isabel Gordo |
author_role |
author |
author2 |
Ana Sousa Marta Lourenço Marie-Louise Bergman Jocelyne Demengeot Karina B. Xavier Isabel Gordo |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
ARCA |
dc.contributor.author.fl_str_mv |
João Barroso-Batista Ana Sousa Marta Lourenço Marie-Louise Bergman Jocelyne Demengeot Karina B. Xavier Isabel Gordo |
dc.subject.por.fl_str_mv |
Quantitative Biology - Populations and Evolution Cloning |
topic |
Quantitative Biology - Populations and Evolution Cloning |
description |
The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal interference - the competition of clones carrying different beneficial mutations - which leads to the loss of many small effect mutations and fixation of large effect ones. If interference is abundant, then mechanisms for horizontal transfer of genes, which allow the immediate combination of beneficial alleles in a single background, are expected to evolve. However, the relevance of interference in natural complex environments, such as the gut, is poorly known. To address this issue, we studied the invasion of beneficial mutations responsible for Escherichia coli's adaptation to the mouse gut and demonstrate the pervasiveness of clonal interference. The observed dynamics of change in frequency of beneficial mutations are consistent with soft sweeps, where a similar adaptive mutation arises repeatedly on different haplotypes without reaching fixation. The genetic basis of the adaptive mutations revealed a striking parallelism in independently evolving populations. This was mainly characterized by the insertion of transposable elements in both coding and regulatory regions of a few genes. Interestingly in most populations, we observed a complete phenotypic sweep without loss of genetic variation. The intense clonal interference during adaptation to the gut environment, here demonstrated, may be important for our understanding of the levels of strain diversity of E. coli inhabiting the human gut microbiota and of its recombination rate. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-03-06 2014-03-06T00:00:00Z 2015-09-28T16:38:13Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10400.7/319 |
url |
http://hdl.handle.net/10400.7/319 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Barroso-Batista J, Sousa A, Lourenço M, Bergman M-L, Sobral D, Demengeot J, et al. (2014) The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps. PLoS Genet 10(3): e1004182. doi:10.1371/journal.pgen.1004182 10.1371/journal.pgen.1004182 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
PLOS |
publisher.none.fl_str_mv |
PLOS |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799130572128256000 |