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Sélection indirecte en évolution Darwinienne : Mécanismes et implications

David Parsons 1, 2
2 BEAGLE - Artificial Evolution and Computational Biology
LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : The Aevol model is an in silico experimental evolution model that was specifically developped by Carole Knibbe to study the evolution of the structure of the genome. Using Aevol, a very strong second-order selective pressure towards a specific level of mutational variability of the phenotype was revealed: it was shown that since the survival of a lineage on the long term is conditionned to its ability to produce beneficial mutations while not loosing those previously found, a specific trade-off between robustness and evolvability is indirectly selected. A consequence of this indirect selective pressure is the central role played by the spontaneous rate of chromosomal rearrangements in determining the structure of the genome. More specifically, it was shown that because some rearrangements (large duplications and large deletions) have an impact not only arround their breakpoints but on the whole sequence between them, non-coding sequences are actually mutagenic for the coding sequences they surround. The consequence is a clear trend for organisms having evolved under high rearrangement rates to have very short genomes with hardly any non-coding sequences while organisms evolving in the context of low rearrangement rates have huge, mostly non-coding genomes. Here, we modified the Aevol model to introduce an explicit regulation of gene expression as well as a sensitivity to sequence similarity in DNA recombination events. We observed that the effects of the second-order pressure mentioned above are very robust to modelling choices: they are similarly observed when gene regulation is made available, when rearrangements occur preferentially between similar sequences and even when a biologically plausible process of horizontal transfer is allowed. Moreover, the effects of this second-order selective pressure are not limited to the genomic level: high rearrangement rates usually lead to genomes that have many polycistronic RNAs, almost no non-coding RNAs and very simple regulation networks. On the contrary, at low rearrangement rates organisms have most of their genes transcribed on monocistronic RNAs, they own a huge number of coding RNAs and present very complex and intricate regulation networks. These astounding effects at different levels of organization can account for many features found on real organisms. Thus, the indirect selective pressure that was identified thanks to the Aevol model allows to reproduce a large panel of known biological properties by changing the sole spontaneous rearrangement rate, making this pressure a good candidate for explaining these observations on real organisms.
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David Parsons. Sélection indirecte en évolution Darwinienne : Mécanismes et implications. Sciences agricoles. INSA de Lyon, 2011. Français. ⟨NNT : 2011ISAL0140⟩. ⟨tel-00715781⟩

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