The influence of the bottleneck protocol on the adaptation rate and predictability

Detalhes bibliográficos
Ano de defesa: 2021
Autor(a) principal: SILVA JÚNIOR, Osmar Freitas da
Orientador(a): CAMPOS, Paulo Roberto de Araújo
Banca de defesa: Não Informado pela instituição
Tipo de documento: Dissertação
Tipo de acesso: Acesso aberto
Idioma: eng
Instituição de defesa: Universidade Federal de Pernambuco
Programa de Pós-Graduação: Programa de Pos Graduacao em Fisica
Departamento: Não Informado pela instituição
País: Brasil
Palavras-chave em Português:
Física Teórica e Computacional
Bottleneck
Previsibilidade
Link de acesso: https://repositorio.ufpe.br/handle/123456789/40779
Resumo: SILVA JÚNIOR, Osmar Freitas da, também é conhecido em citações bibliográficas por: FREITAS, Osmar
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spelling SILVA JÚNIOR, Osmar Freitas dahttp://lattes.cnpq.br/3410425385594168http://lattes.cnpq.br/5468845680173423CAMPOS, Paulo Roberto de Araújo2021-08-05T12:04:12Z2021-08-05T12:04:12Z2021-04-16SILVA JÚNIOR, Osmar Freitas da. The influence of the bottleneck protocol on the adaptation rate and predictability. 2021. Dissertação (Mestrado em Física) – Universidade Federal de Pernambuco, Recife, 2021.https://repositorio.ufpe.br/handle/123456789/40779SILVA JÚNIOR, Osmar Freitas da, também é conhecido em citações bibliográficas por: FREITAS, OsmarBottlenecks are evolutionary events that reduce the population size. In experimental evolution, the cultivation of microorganisms in laboratory conditions follows a serial passaging protocol in which periodic bottlenecks are an inherent aspect. In this work, we study a computational model of microbial evolution to understand the influence of the bottleneck protocol on the rate of adaptation and predictability of the population. To address these questions, evolutionary simulations are run using a standard Wright-Fisher model integrated with a bottleneck regime, and the implementation of a fitness landscape with varying ruggedness. The rate of adaptation is analyzed as a function of bottleneck and population sizes at different time units. It is found that the rate of adaptation depends monotonically on bottleneck size when time is expressed per generation, but is maximal at intermediate bottleneck size for times expressed per bottleneck and per birth. Additionally, fitness landscapes allow to register the change in the population’s genetic composition as trajectories over the genotypic space. Under this path-dependent perspective, an ensemble of trajectories is generated in many independent runs, for which statistical and computational measurements of predictability are inferred. Irrespective of the timing of population bottlenecks, we find that predictability increases with population size. We also find that predictability of the adaptive pathways increases in increasingly rugged fitness landscapes.CAPESCNPqGargalos, ou bottlenecks, são eventos evolutivos que reduzem o tamanho de uma população. Em experimentos evolutivos, o protocolo para o cultivo de microrganismos em laboratório costuma impor estas amostragens de maneira regular e periódica. Neste trabalho, estudamos um modelo computacional de evolução microbiana para entender como este protocolo pode influenciar a taxa de adaptação de uma população e sua previsibilidade. Para abordar essas questões, simulamos uma população que evolui sob este protocolo usando o modelo de Wright-Fisher e um relevo de adaptação com epistasia regulável. A taxa de adaptação é medida em função da severidade do bottleneck em diferentes unidades de tempo. Verificamos que a taxa de adaptação depende monotonicamente do tamanho do bottleneck quando o tempo é expresso por geração, mas apresenta um máximo em tamanhos intermediários quando os tempos são expressos em unidades por bottleneck e por nascimento. A adoção de um relevo de adaptação permite registrar a mudança na composição genética da população, e obter um ensemble das trajetórias evolutivas no espaço de genótipos. Utilizamos medidas estatísticas e computacionais para inferir o grau de previsibilidade destas trajetórias. Destacamos que a previsibilidade aumenta com o tamanho da população, independentemente do tamanho da amostragem. Também observamos que a previsibilidade das trajetórias evolutivas aumenta em função da epistasia do relevo de adaptação.engUniversidade Federal de PernambucoPrograma de Pos Graduacao em FisicaUFPEBrasilhttp://creativecommons.org/licenses/by-nc-nd/3.0/br/info:eu-repo/semantics/openAccessFísica Teórica e ComputacionalBottleneckPrevisibilidadeThe influence of the bottleneck protocol on the adaptation rate and predictabilityinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesismestradoreponame:Repositório Institucional da UFPEinstname:Universidade Federal de Pernambuco (UFPE)instacron:UFPEORIGINALDISSERTAÇÃO Osmar Freitas da Silva Júnior.pdfDISSERTAÇÃO Osmar Freitas da Silva Júnior.pdfapplication/pdf8527933https://repositorio.ufpe.br/bitstream/123456789/40779/1/DISSERTA%c3%87%c3%83O%20Osmar%20Freitas%20da%20Silva%20J%c3%banior.pdfc1ae3c262cd30e68218a9d27855386ecMD51TEXTDISSERTAÇÃO Osmar Freitas da Silva Júnior.pdf.txtDISSERTAÇÃO Osmar Freitas da Silva Júnior.pdf.txtExtracted texttext/plain201480https://repositorio.ufpe.br/bitstream/123456789/40779/4/DISSERTA%c3%87%c3%83O%20Osmar%20Freitas%20da%20Silva%20J%c3%banior.pdf.txt079c0d54eeae60e88956b730a34127b0MD54THUMBNAILDISSERTAÇÃO Osmar Freitas da Silva Júnior.pdf.jpgDISSERTAÇÃO Osmar Freitas da Silva Júnior.pdf.jpgGenerated Thumbnailimage/jpeg1234https://repositorio.ufpe.br/bitstream/123456789/40779/5/DISSERTA%c3%87%c3%83O%20Osmar%20Freitas%20da%20Silva%20J%c3%banior.pdf.jpg6c6489ebcce6851e6783f2b6d4be148eMD55CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; 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dc.title.pt_BR.fl_str_mv The influence of the bottleneck protocol on the adaptation rate and predictability
title The influence of the bottleneck protocol on the adaptation rate and predictability
spellingShingle The influence of the bottleneck protocol on the adaptation rate and predictability
SILVA JÚNIOR, Osmar Freitas da
Física Teórica e Computacional
Bottleneck
Previsibilidade
title_short The influence of the bottleneck protocol on the adaptation rate and predictability
title_full The influence of the bottleneck protocol on the adaptation rate and predictability
title_fullStr The influence of the bottleneck protocol on the adaptation rate and predictability
title_full_unstemmed The influence of the bottleneck protocol on the adaptation rate and predictability
title_sort The influence of the bottleneck protocol on the adaptation rate and predictability
author SILVA JÚNIOR, Osmar Freitas da
author_facet SILVA JÚNIOR, Osmar Freitas da
author_role author
dc.contributor.authorLattes.pt_BR.fl_str_mv http://lattes.cnpq.br/3410425385594168
dc.contributor.advisorLattes.pt_BR.fl_str_mv http://lattes.cnpq.br/5468845680173423
dc.contributor.author.fl_str_mv SILVA JÚNIOR, Osmar Freitas da
dc.contributor.advisor1.fl_str_mv CAMPOS, Paulo Roberto de Araújo
contributor_str_mv CAMPOS, Paulo Roberto de Araújo
dc.subject.por.fl_str_mv Física Teórica e Computacional
Bottleneck
Previsibilidade
topic Física Teórica e Computacional
Bottleneck
Previsibilidade
description SILVA JÚNIOR, Osmar Freitas da, também é conhecido em citações bibliográficas por: FREITAS, Osmar
publishDate 2021
dc.date.accessioned.fl_str_mv 2021-08-05T12:04:12Z
dc.date.available.fl_str_mv 2021-08-05T12:04:12Z
dc.date.issued.fl_str_mv 2021-04-16
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.citation.fl_str_mv SILVA JÚNIOR, Osmar Freitas da. The influence of the bottleneck protocol on the adaptation rate and predictability. 2021. Dissertação (Mestrado em Física) – Universidade Federal de Pernambuco, Recife, 2021.
dc.identifier.uri.fl_str_mv https://repositorio.ufpe.br/handle/123456789/40779
identifier_str_mv SILVA JÚNIOR, Osmar Freitas da. The influence of the bottleneck protocol on the adaptation rate and predictability. 2021. Dissertação (Mestrado em Física) – Universidade Federal de Pernambuco, Recife, 2021.
url https://repositorio.ufpe.br/handle/123456789/40779
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv http://creativecommons.org/licenses/by-nc-nd/3.0/br/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/3.0/br/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Universidade Federal de Pernambuco
dc.publisher.program.fl_str_mv Programa de Pos Graduacao em Fisica
dc.publisher.initials.fl_str_mv UFPE
dc.publisher.country.fl_str_mv Brasil
publisher.none.fl_str_mv Universidade Federal de Pernambuco
dc.source.none.fl_str_mv reponame:Repositório Institucional da UFPE
instname:Universidade Federal de Pernambuco (UFPE)
instacron:UFPE
instname_str Universidade Federal de Pernambuco (UFPE)
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reponame_str Repositório Institucional da UFPE
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