AIRE

The AIRE team seeks to consolidate and to generalize evolutionary explanations beyond their traditional approaches and objects studies.

Specifically, the AIRE team works to enhance the evolutionary theory i) by expanding its scope by targeting additional objects of studies (such as novel units of selection and novel still unknown taxonomical groups from the microbial dark matter, and mobile elements) and ii) by expanding evolutionary studies towards more general models, able to in particular account for chimerism and interactions between biological elements, from molecules to ecosystems.

To this end, the AIRE team investigates the foundations and blind spots of major current evolutionary theories and develops new methods that better account for biological diversity and complexity. We particularly focus our studies on two universal aspects of the biological world: i) the ubiquity of interactions in biology and ii) the ubiquity of microbes. Owing to their remarkable distribution, making novel findings about interactions or microbes could have broad scientific, applied and epistemic consequences, lifting some of the current limits in our knowledge on the history of Life on Earth.

 Our former works were 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.

 Consequently, in the past ten years, the AIRE Team developed sequence similarity networks, a powerful inclusive scalable network-based approach to structure and analyse the evolution of genetic diversity, at multiple levels of biological organization, in particular, in the context of an ERC grant (the EVOLUNET project).

These original methodological developments allowed us to develop a second 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.

Now, based on this expertise, our lab tracks the evolution of interactions upon which past and extant biodiversity and biological processes rely along four major research avenues, united by their common goal and methodology. Namely:

- we develop novel methods of phylosystemics, e.g., comparisons of evolutionary labeled newtorks, required to understand how biological processes emerged from the functional integration of molecular materials from multiple phylogenetic origins;

- we analyze the evolution of molecular chimerism (induced by gene remodelling, lateral gene transfer and symbioses) within prokaryotes and eukaryotes;

- we mine unknown environmental entities and interactions using networks to decipher their evolution;

- we develop network-based approaches to analyze some of the systemic and evolutionary causes of aging, to enhance the evolutionary theories of aging with consequences on the general theory of evolution.

 Finally, to enhance the scope of evolutionary explanations, The AIRE team also actively supports interdisciplinary researches, which are fruitful to share and to confront concepts and methods from many fields, and thus can help to discover common trends in knowledge and practices, and generalize evolutionary explanations…beyond their field of origin.