Advancing phylogenetic comparative methods for complex viral evolutionary histories

According to the World Health Organization, more than two million people get infected by HIV every year, and more than one million die from AIDS (Progress Report WHO/HIV/2016.24). Despite significant research progress, the characteristics of HIV disease dynamics are still imperfectly known. In order to fight and prevent it efficiently, the temporal patterns of the evolution of its virulence and spatial propagation need to be understood better. The rapid evolution of the virus represents a major challenge to effectively treating HIV infections. Any attempt at studying it should take this evolution into account. Based on the changes that accumulate in viral genomes over successive generations, we can use mathematical models to perform probabilistic reconstructions of the evolutionary relationships between the viruses we can sample. While this diagram usually looks like a "family tree", most models do not take into account the fact that viruses can sometime exchange some genetic material, through the process of recombination or reassortment. This means that a virus can formally have multiple "parents", so that the diagram does not resemble a tree anymore, but a network. The aim of this project is to study the impact those events have on the trait plasticity of the virus. We will develop new statistical methods to take these complex dynamics into account. Beyond HIV, these new tools will have the potential to be applied to a wide range of organisms and biological questions.