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.author Brunstein, Adriana [UNIFESP]
dc.contributor.author Varuzza, Leonardo
dc.contributor.author Sanson, Gerdine F. O. [UNIFESP]
dc.contributor.author Briones, Marcelo Ribeiro da Silva [UNIFESP]
dc.date.accessioned 2015-06-14T13:30:15Z
dc.date.available 2015-06-14T13:30:15Z
dc.date.issued 2004-01-01
dc.identifier http://dx.doi.org/10.1590/S1415-47572004000400026
dc.identifier.citation Genetics and Molecular Biology. Sociedade Brasileira de Genética, v. 27, n. 4, p. 632-636, 2004.
dc.identifier.issn 1415-4757
dc.identifier.uri http://repositorio.unifesp.br/handle/11600/1957
dc.description.abstract To 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.sponsorship Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.description.sponsorship Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
dc.format.extent 632-636
dc.language.iso eng
dc.publisher Sociedade Brasileira de Genética
dc.relation.ispartof Genetics and Molecular Biology
dc.rights Acesso aberto
dc.subject molecular evolution en
dc.subject experimental phylogenetics en
dc.subject neutral theory en
dc.subject mathematical models of nucleotide substitutions en
dc.title Changes in G+C content of a neutrally evolving gene under a non-reversible dynamics measured by computer simulations based on experimental evolution data en
dc.type Artigo
dc.contributor.institution Universidade Federal de São Paulo (UNIFESP)
dc.contributor.institution Universidade de São Paulo (USP)
dc.description.affiliation Universidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Departamento de Microbiologia, Imunologia e Parasitologia
dc.description.affiliation Universidade de São Paulo Instituto de Matemática e Estatística Departamento de Ciência da Computação
dc.description.affiliationUnifesp UNIFESP, EPM, Depto. de Microbiologia, Imunologia e Parasitologia
dc.identifier.file S1415-47572004000400026.pdf
dc.identifier.scielo S1415-47572004000400026
dc.identifier.doi 10.1590/S1415-47572004000400026
dc.description.source SciELO
dc.identifier.wos WOS:000226583400026



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