Adaptation, integration, reticulation & evolution (AIRE)

The « Adaptation, Intégration, Réticulation et Evolution » team studies evolution, and develops new methods based on forests of trees and evolutionary networks to represent and analyze the plurality of evolutionary processes at play in prokaryotes, eukaryotes and mobile genetic elements.

We seek to address a general question by developing network methods: « how can biologists use molecular sequences to unravel more evolutionary phenomena? ». We tackle this issue from two distinct perspectives:

  • How can we improve the modeling of non-tree like evolution (of genes, genomes and organisms)?
  • How can we structure genetic diversity with less a priori in order to detect still unknown classes of objects, processes and rules produced during the evolutionary history?

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Our studies rest on a few basic hypotheses :

  • the analysis of the genetic content of chromosomes alone is not sufficient to study the evolution of all genetic diversity. A large part – possibly the majority – of genetic diversity is carried on mobile genetic elements, moving between cells;
  • DNA molecules are exchanged and transformed due to interactions between genetic partners that are not necessarily closely related but belong to a larger genetic community;
  • Because combinatory events such as lateral genetic exchanges happen in addition to vertical inheritance and replication, we expect numerous genetic chimeras in nature, at all levels of biological organisation;
  • To complement and expand traditional approaches of phylogenetics and phylogenomics, as many environmental data (from metagenomic and metatranscriptomic projects) and as many sequences from mobile genetic elements (viruses, plasmids) as possible should be included in evolutionary analyses.

Highlights

We have worked on important methodological issues, in particular to test the consistency of phylogenetic signal of molecular markers. We thus contributed to unravel the adaptive role of lateral gene transfer in prokaryotes and to start an alternative description of eukaryotic evolution, while providing new scientific and epistemological leads to overcome some of the common limits of phylogenomics.

We tackled this fundamental question both from a scientific and philosophical point of view. Therefore, we proposed alternative representations with respect to classic phylogenetics to account for lateral gene transfers. These representations include: sequence similarity networks, genome similarity networks and forests of phylogenetic tress. They played a central role in the proposal of the theory of genetic public goods with irish colleagues, and in the study of the discontinuities in the patterns of gene sharing on Earth, which typicallyresult in independent “genetic worlds”

Future directions

By enhancing the development of network methods, we try to expand the scope of the evolutionary theory in order to account for a greater number of objects (composite entities), a greater number of relationships (family resemblances) and a greater number of questions, notably by extending the classic questions of the origin of species and of the origin of adaptations to the most comprehensive questions of the origins of composite systems and of the origins of adaptations.

These ideas may lead to some conceptual developments in molecular evolution and a significant renewal of the practices used in the field of evolutionary biology.

Collaborations

  • On lateral gene transfer, symbiosis and metagenomics:

Dr. Yan Boucher (University of Alberta, Canada); Dr. Christopher Lane (University of Rhodes Island, USA); Pr. Mohamed Hijri (Montréal University, Canada), Pr. Debashish Bhatthacharya (Rutgers University, USA); Pr. Philippe Colson & Jean-Marc Rolain (U. Marseille- la Timone) ; Pr. Thorsten Stoeck (University of Kaiserslautern, Germany).

  • On phylogenomics and evolutionary networks:

Pr. François-Joseph Lapointe (Montréal University, Canada); Pr. Pierre Legendre (Montréal University, Canada) ; Pr. Bill Martin (Duesseldorf University, Germany); Dr. Tal Dagan (Duesseldorf University, Germany); Dr. James McInerney (NUI Maynooth, Ireland); Pr. Michel Habib (LIAFA, France), Pr. Laurent Viennot (LIAFA, France).

  • In philosophy of biology:

Pr. Richard Burian (Virginia Tech, USA); Pr. Frédéric Bouchard (Montréal University, Canada); Dr. Maureen O'Malley (University of Sidney, Australia); Dr. Philippe Huneman (IHPST, France), and Pr. John Dupré (Exeter, UK).