Aevol is an individual-centered artificial life softwate, which allows to study evolution.
Each individual is composed of a circular genome. Along this sequence, promoters and terminator sequences can be recognized and define RNAs.
In each RNAs, there can be proteins, which are delimited by START and STOP codons.
The proteins are mathematically translated to define triangles, characterized by a lateral position on the phenotype axis, their width and height.
The sum of the triangles defines the phenotype of the individuals, and the distance between it and a target function, which is the environment, represents their fitness.
Each generation is subject to selection and each clone can undergo mutational events (point mutations, duplications, deletions, translocations, inversions): this is what allows us to observe evolution.
This software is developed by the INRIA Beagle team, in Villeurbanne.
Influence of effective population size on genome architecture: a modeling and simulation study
September 2022 — August 2025 (?)
PhD thesis under the supervision of Guillaume Beslon and Nicolas Lartillot.
Genome streamlining study
September 2021 — January 2022 Publication in prep
Internship under the supervision of Guillaume Beslon.
I studied the impact of population size and mutation rate on genome size, and more precisely the conditions under which genome size decreases.
Study of a eukaryotic model
Master 2 internship in Biology
My research consisted in designing the outline of a eukaryotic evolution model, and integrating it into Aevol.
Indeed, Aevol currently simulates individuals resembling prokaryotes (1 circular chromosome, possibly plasmids, clonal reproduction).
This work consisted in the integration of diploidy, sexual reproduction and recombination into an Aevol-eukaryote prototype,
and is part of the ANR project "NeGA - Influence of effective population size (Ne) on animal genome architectures".
Study of the impact of transposable elements on genome evolution
BSc in Computer Science internship
It is common in biology to associate non-coding genome size variations to the action of various transposable elements.
However, dynamics of non-coding genome size variation can be observed in Aevol in the absence of these elements.
During my internship, I added to the Aevol code the inclusion of insertion sequences (IS), which are able to transpose in the genome, and I studied their impact on genome size variations.