Using morphological information to accurately date phylogenies and understand past diversification dynamics

The fossil record provides crucial evidence to inform our study of evolution and past diversification processes. Recent methodological developments have allowed to integrate fossil species directly into the reconstruction of phylogenetic trees, providing more accurate estimates of the age of evolutionary events as well as speciation and extinction through time. However, the current methods fail to account for many of the specific characteristics of fossil samples compared to extant species. Genetic sequences are usually unavailable for fossils, so phylogenetic inferences including fossils rely on morphological characters. This morphological information interacts with other components of the analysis, such as the genetic sequence alignment, or the sorting of fossil samples into a taxonomy itself informed by morphological traits. These interactions are not accounted for by current models and could lead to strong biases in the estimates of the phylogeny, its ages and its underlying diversification process. To address these issues, the proposed project will build a new methodological framework for integrating the complex interplay between morphological evolution, diversification, and fossil sampling. We will develop new models adapted to fossil data, which will be carefully validated using realistic simulations, and then applied to several empirical datasets. Some of these datasets will serve as a comparison of our new approach to existing methods. Other datasets have never been studied under a combined phylogenetic framework with fossil evidence before, so our analyses will form a new understanding of their diversification, and build a high-quality phylogeny for future work on these groups. In conclusion, this project will pave the way for efficiently combining information on past and present species into a highly accurate and nuanced representation of the evolution of biodiversity through time.