In silico experimental evolution: a tool to test evolutionary scenariosReport as inadecuate




In silico experimental evolution: a tool to test evolutionary scenarios - Download this document for free, or read online. Document in PDF available to download.

* Corresponding author 1 LIRIS - Laboratoire d-InfoRmatique en Image et Systèmes d-information 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, CarMeN - Laboratoire de recherche en cardiovasculaire, métabolisme, diabétologie et nutrition

Abstract : Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. For instance, some species have undergone a strong reduction of their genome with a drastic reduction of their genic repertoire. Deciphering the causes of these atypical trajectories can be very difficult because of the many phenomena that are intertwined during their evolution e.g. changes of population size, environment structure and dynamics, selection strength, mutation rates



Here we propose a methodology based on synthetic experiments to test the individual effect of these phenomena on a population of simulated organisms. We developed an evolutionary model - aevol - in which evolutionary conditions can be changed one at a time to test their effects on genome size and organization e.g. coding ratio. To illustrate the proposed approach, we used aevol to test the effects of a strong reduction in the selection strength on a population of simulated bacteria. Our results show that this reduction of selection strength leads to a genome reduction of ~35% with a slight loss of coding sequences ~15% of the genes are lost - mainly those for which the contribution to fitness is the lowest. More surprisingly, under a low selection strength, genomes undergo a strong reduction of the noncoding compartment ~55% of the noncoding sequences being lost. These results are consistent with what is observed in reduced Prochlorococcus strains marine cyanobacteria when compared to close relatives.





Author: Bérénice Batut - David P. Parsons - Stephan Fischer - Guillaume Beslon - Carole Knibbe -

Source: https://hal.archives-ouvertes.fr/



DOWNLOAD PDF




Related documents