Tracing the roots of genome architecture through in silico experimental evolution

Genome architecture (size, proportion of coding sequences, polycistronic mRNAsŠ) is the consequence of many interacting forces acting over very long time scales. Indeed, selection, mutation biases, drift etc. all act directly or indirectly on the different genome compartments, either triggering their increase or decrease in size or proportion depending on the life style of the organisms (e.g., environment complexity, environment variation, population sizeŠ). Understanding how the intertwining of these pressures leads to particular architecture is difficult for at least three reasons.

First, it is not clear how a given change of life-style will affect these different pressures.
Second, it is impossible to experimentally separate these forces to observe their individual action since they are all interacting one with the others at the molecular level.
Third, they act on time scales that are almost impossible to access experimentally, even with species reproducing rapidly.

We propose that in silico experimental evolution approaches, in which simulated species are let evolved in perfectly controlled (simulated) environments, can be used to study the consequences of a specific change in life-style on the genome architecture. Indeed, in silico experiments can escape most of the difficulties listed above: since the organisms and environment are simulated, they can be precisely tuned, millions of generations can ³easily² be simulated and, most importantly, it allows large parameter explorations that can help understanding the precise effect of a given environmental parameter on a given genomic structure. We illustrate the power of in silico experimental evolution using the aevol software (www.aevol.fr <http://www.aevol.fr> ).
We show how different environmental changes can lead to unexpected consequences on the genome structure due to the non-linearity of the selective/non-selective pressures. In particular, we emphasize the overlooked effect of chromosomal rearrangements on this matter.