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.
Highlights
The evolutionary process can be viewed as a consequence of mutations, chance and selection acting on a given population, leading to changes in the genetic scenario
Tests of homogeneity and neutrality of the in vitro evolution PCR process The substitution process along the real phylogeny of the evolutionary process obtained from the PCR evolution method (Sanson et al, 2002) was studied by verifying whether the nucleotide substitutions were homogeneous along the four steps of amplification and cloning by means of comparing the observed substitutions in each step
To verify whether the real phylogeny generated by PCR evolution (Sanson et al, 2002) reflects neutral evolution we determined whether the phylogeny branch lengths fitted a Poisson distribution
Summary
The evolutionary process can be viewed as a consequence of mutations, chance and selection acting on a given population, leading to changes in the genetic scenario. The most commonly used models vary from the simple Jukes and Cantor model (Jukes and Cantor, 1969), to the most general one, the general time reversible model (Rodríguez et al, 1990). These models are approximations of the real process and describe satisfactorily most of them, they all assume reversibility of the substitutions probability matrix, and so are based on an evolutionary process that is independent of time direction. Universidade Federal de São Paulo, Escola Paulista de Medicina, Imunologia e Parasitologia, Departamento de Microbiologia, Rua Botucatu 862, ECB 3 andar, 04023-062 São Paulo, SP, Brazil.
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