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.
Highlights
Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives
The mutational events that led to genome reduction can be precisely identified [11] and the structure of the reduced sequence can be compared with the structure of real reduced bacteria to check whether the mode of reduction is similar
We present below a platform for in silico experimental evolution that belongs to the “sequence-of-nucleotides” family, where the genome encodes a variable number of genes separated by a variable amount of non-coding DNA, and where the task is the approximation of a mathematical function with a combination of elementary functions encoded by the genes
Summary
Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. The mutational events that led to genome reduction can be precisely identified [11] and the structure of the reduced sequence can be compared with the structure of real reduced bacteria to check whether the mode of reduction is similar Such a research program is almost impossible to perform. One way to perform such pure experiments and to allow practitioners to strictly change one evolutionary parameter at a time is to use synthetic experiments in which the evolving organisms are not real bacteria but rather models of bacteria. These properties make synthetic experiments a valuable - not perfect - link between phylogenetic approaches of evolution (that can study long to very long time scales but without direct access to the evolutionary process itself) and experimental evolution (that offers a close view of the evolutionary process but that rarely goes over a few thousand generations)
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