What do we do?
At the Computational Phylogenetics Group we develop software to better understand the evolutionary history between organisms and to test macroevolutionary hypotheses. We are looking at the ecological, genomic and morphological factors that limit and constrain speciation and adaptation. We focus on phylogenetic reconstruction methods, clownfish and plant genomics, the estimation of positive selection on genes, modelling the evolution of DNA sequences and phenotypes, the mode and tempo of species evolution and the spatially explicit evolution of diversity. Our aim is to develop better models to analyse sequence data and quantitative models to estimate macroevolutionary patterns and processes.
The group is developing new ways to estimate the rate of species evolution by using complex Bayesian approaches. These developments are important to understand the factors that influence the emergence and extinction of species over time. The method was implemented into a python software called pyRate. The models implemented in pyRate were extended by developing a novel Bayesian approach that can estimate the standard heterogeneous birth-death process on fossil data. The advantage of such an approach is that the birth-death process can be directly compared with estimates done on phylogenetic trees, and can provide information on the divergence times of the nodes in a phylogenetic tree estimated by molecular data. Such an approach is very flexible and the group incorporated several models to fully account for the heterogeneity in the tempo of species evolution. This allows for shifts of speciation and extinction rates during species evolution, but also the association with external factors such as climate variation, or competition with other clades.
The models fully complement existing approaches and are currently used to estimate the evolution of large groups of mammals such as canids, or the origins of flowering plants.
Main publications 2015
- Dib L et al. Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree. BMC Bioinformatics 2015;16:394.
- Laurent S et al. Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions. BMC Evol Biol 2015;15:157.
- Silvestro D et al. Measurement errors should always be incorporated in phylogenetic comparative analysis. Methods in Ecology and Evolution 2015;6(3):340-346.