My primary interest is the application of phylogenetics to biological questions and the evolution of traits at various phenotypic levels. Mapping genotype to phenotype is a challenge because the mapping function is a mix of historical signal, functional signal and stochastic noise. Phylogenetics can help discriminating between these factors. How does an amino acid substitution in a protein impact that protein’s function? How does a substitution in a regulatory region effect the expression of a gene? What effect do these substitutions have in various networks or cell/tissue types? Changing selective constraints and their impact on evolutionary opportunity space are two of my main interests.
My research focuses on two complementary approaches. One is purely methodological. It is based on the fact that model misspecification is a major pitfall in phylogenetics and can lead to erroneous tree estimates. The addition of more data can, in some cases, inflate biases. This issue is particularly relevant for phylogenomics. Understanding the causes of misleading phylogenetic signal will help to select the data best suited for a given model or design more realistic models. Once one has a reliable data/model duo, one can infer a reliable tree and then use it with confidence to answer biological questions. This is the second aspect of my research. I use phylogenetics to understand the evolution of organismal traits, but I also apply phylogenetic methods and models to explore the effect of selective pressures on function at the (1) protein and (2) cis-regulatory levels.