Our group is actively developing new models to understand the evolution of genes and phenotypic traits. We recently introduced a new model that enables the identification of shifts in traits evolution while conditioning on existing fossil data, if any, to help estimate more accurately the model parameters (Silvestro et al. 2018 Syst Biol). Our new model was used to test the evolution of New World monkeys and showed that their initial body size was much smaller than previously known and that their diversification through South America showed an initial expansion towards the South before a more recent contraction towards tropical regions. The group is also actively developing new approaches to link the processes seen at the micro-evolutionary scale with our current model of macro-evolution (Rolland et al. 2018 Proc R Soc B, Duchen et al. BioRXiv).
Beside models of trait evolution, we are also developing new approaches to study the evolution of molecular sequences and in particular protein-coding genes. We have recently tackled a long standing assumption in phylogenetics that considered sites along sequences to be evolving independently from each other. This assumption drastically simplifies the reconstruction of the phylogenetic tree, but it is now to be violated in real datasets. Using reversible-jump Markov chain Monte Carlo, we recently developed an algorithm that efficiently reconstruct phylogenetic trees using a mixture of models that include both coevolution (i.e. site dependency) and standard independent site models (Meyer et al. 2019 Proc Natl Acad Sci). We showed that our new model improve the estimation of the phylogenetic relationships while providing an estimate of the coevolution occurring within a DNA or amino-acid sequence.
Finally, we have been also actively developing the first genomic resources for several non-model organisms (e.g. plants like Gesneriaceae; Serrano et al. 2017 Appl Plant Sci, ) or clownfishes (Marcionetti et al. 2018 Mol Ecol Res) and we use these resources to model and analyse the genetic basis of adaptation and speciation. We study in particular the evolution of clownfishes and we recently showed what are the genomic components that are responsible for the acquisition of the mutualism with sea anenome (Marcionetti et al. 2019 Genome Biol Evol). This provides the first clues about the genetic mechanisms that were responsible for the diversification of the clownfishes and potentially a key driver for their adaptive radiation.