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

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

Author Brunstein, Adriana Autor UNIFESP Google Scholar
Varuzza, Leonardo Google Scholar
Sanson, Gerdine F. O. Autor UNIFESP Google Scholar
Briones, Marcelo Ribeiro da Silva Autor UNIFESP Google Scholar
Institution Universidade Federal de São Paulo (UNIFESP)
Universidade de São Paulo (USP)
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.
Keywords molecular evolution
experimental phylogenetics
neutral theory
mathematical models of nucleotide substitutions
Language English
Sponsor Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Date 2004-01-01
Published in Genetics and Molecular Biology. Sociedade Brasileira de Genética, v. 27, n. 4, p. 632-636, 2004.
ISSN 1415-4757 (Sherpa/Romeo, impact factor)
Publisher Sociedade Brasileira de Genética
Extent 632-636
Origin http://dx.doi.org/10.1590/S1415-47572004000400026
Access rights Open access Open Access
Type Article
Web of Science ID WOS:000226583400026
SciELO ID S1415-47572004000400026 (statistics in SciELO)
URI http://repositorio.unifesp.br/handle/11600/1957

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