AIRE

The team "Adaptation, Integration, Reticulation and Evolution" studies evolution, and develops new methods of tree forests and evolutionary networks construction and comparison to represent, characterize and analyze evolutionary processes in prokaryotes, eukaryotes and mobile elements. Our works are inspired by some simple ideas:

• The study of the single genetic content of microbial chromosomes is not sufficient to study all of the natural genetic diversity. Much, if not most, of genetic diversity is carried by mobile genetic elements, in permanent transit between cells;
• DNA molecules are exchanged and transformed through interactions between partners that are not necessarily related but belong to a larger genetic community;
• Genetic chimeras are particularly numerous in nature because of lateral exchanges that add to the process of vertical inheritance and replication.
• The inclusion of as much environmental data (metagenomic) and mobile element sequences (phage, plasmids) as possible in evolutionary analyzes is essential to complement traditional phylogenetic and phylogenetic approaches, and to delve deeper into some of them.

In the past ten years, the AIRE Team has developed sequence similarity networks (SSN), a powerful inclusive scalable network-based approach to structure and analyse the evolution of genetic diversity, at multiple levels of biological organisation.

These original methodological developments now allow us to propose and implement a new research approach: the coupling of phylogenomics, interaction networks and Sequence Similarity Networks to develop a new type of evolutionary analyses, that we call phylosystemics or evosystemics. Phylosystemics uses evolutionary labeled interaction networks to model the evolution of biological organisations and of biological processes, and to better explain the evolution of biological complexity and diversity by retracing interactions between phylogenetically related or unrelated components.

Currently, the AIRE Team uses phylosystemics to describe (micro)biological evolution from an increasingly systemic perspective