Changes in G+C content of a neutrally evolving gene under a non-reversible dynamics measured by computer simulations based on experimental evolution data

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dc.contributor.authorBrunstein, Adriana [UNIFESP]
dc.contributor.authorVaruzza, Leonardo
dc.contributor.authorSanson, Gerdine F. O. [UNIFESP]
dc.contributor.authorBriones, Marcelo Ribeiro da Silva [UNIFESP]
dc.contributor.institutionUniversidade Federal de São Paulo (UNIFESP)
dc.contributor.institutionUniversidade de São Paulo (USP)
dc.date.accessioned2015-06-14T13:30:15Z
dc.date.available2015-06-14T13:30:15Z
dc.date.issued2004-01-01
dc.description.abstractTo evaluate the effects of non-reversibility on compositional base changes and the distribution of branch lengths along a phylogeny, we extended, by means of computer simulations, our previous sequential PCR in vitro evolution experiment. In that study a 18S rRNA gene evolved neutrally for 280 generations and a homogeneous non-stationary model of base substitution based on a non-reversible dynamics was built from the in vitro evolution data to describe the observed pattern of nucleotide substitutions. Here, the process was extended to 840 generations without selection, using the model parameters calculated from the in vitro evolution experiment. We observed that under a non-reversible model the G+C content of the sequences significantly increases when compared to simulations with a reversible model. The values of mean and variance of the branch lengths are reduced under a non-reversible dynamics although they follow a Poisson distribution. We conclude that the major implication of non-reversibility is the overall decrease of branch lengths, although no transition from a stochastic to an ordered process is observed. According to our model the result of this neutral process will be the increase in the G+C content of the descendant sequences with an overall decrease in the frequency of substitutions.en
dc.description.affiliationUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Departamento de Microbiologia, Imunologia e Parasitologia
dc.description.affiliationUniversidade de São Paulo Instituto de Matemática e Estatística Departamento de Ciência da Computação
dc.description.affiliationUnifespUNIFESP, EPM, Depto. de Microbiologia, Imunologia e Parasitologia
dc.description.sourceSciELO
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.description.sponsorshipConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
dc.format.extent632-636
dc.identifierhttp://dx.doi.org/10.1590/S1415-47572004000400026
dc.identifier.citationGenetics and Molecular Biology. Sociedade Brasileira de Genética, v. 27, n. 4, p. 632-636, 2004.
dc.identifier.doi10.1590/S1415-47572004000400026
dc.identifier.fileS1415-47572004000400026.pdf
dc.identifier.issn1415-4757
dc.identifier.scieloS1415-47572004000400026
dc.identifier.urihttp://repositorio.unifesp.br/handle/11600/1957
dc.identifier.wosWOS:000226583400026
dc.language.isoeng
dc.publisherSociedade Brasileira de Genética
dc.relation.ispartofGenetics and Molecular Biology
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectmolecular evolutionen
dc.subjectexperimental phylogeneticsen
dc.subjectneutral theoryen
dc.subjectmathematical models of nucleotide substitutionsen
dc.titleChanges in G+C content of a neutrally evolving gene under a non-reversible dynamics measured by computer simulations based on experimental evolution dataen
dc.typeinfo:eu-repo/semantics/article
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