Modeling genomes and the origin of species

Different lineages of the tree of life have very different species diversity, from 400'000 known beetles to species which form a group on the own, such as the Ginkgo biloba. There are many cases of species-rich groups closely related to species-poor groups. There has been a recent regain of interest in these patterns, from two directions. First, progress in mathematical modeling of speciation and extinction rates allows quantitative studies; this is closely linked to progress in phylogenetics. Second, the recent accumulation of genomic data has generated hypotheses about the possible relation between major events in genome evolution, such as whole genome duplications or the apparition of new gene types, and species diversity. In this project, we propose to improve mathematical models of speciation and extinction, with a specific aim of testing hypotheses of the impact of genome evolution on species diversity. The main missing feature is a measure of uncertainty around the timing of changes in speciation or extinction rates, to allow for rigorous testing of a priori hypotheses such as whole genome duplication. This project will help us understand the relation between genomes and biodiversity, and contribute new bioinformatics tools, which might be useful in fields such as conservation biology.