Description of the thesis topic

Molecular-morphological discordance in phylogenetic inference.
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. In particular, genetic sequences are usually unavailable for fossils, so phylogenetic inferences including fossils rely on morphological characters. Combining molecular and morphological information into one inference in this way presents a number of challenges. This doctoral project aims to explore one particular challenge: the presence of discordance between morphological and molecular information, a situation in which the two different sources of information support different phylogenetic trees. Discordance can happen due for instance to convergent evolution, where the same phenotype develops independently in different clades which then appears to be closer evolutionarily than they actually are.
The project will be oriented around two main directions:
1) Simulating datasets with discordance. This part of the project aims at describing and exploring the underlying processes which lead to discordance, using mechanistic models of evolution. Simulated datasets will then be used to evaluate the presence of discordance in empirical datasets.
2) Evaluating the effect of discordance on phylogenetic inference. This part of the project will study the effect of discordance on current phylogenetic inference methods and demonstrate whether inferences run on discordant datasets are reliable or suffer from errors due to the discordance. The project will then explore new methodological advancements to account for discordance and correct for the observed effects.
We are looking for a PhD student with a strong interest for evolutionary processes and good computational skills. Programming experience is a prerequisite, and experience using the programming languages R or Java will be appreciated. Previous experience with phylogenetics will be an advantage but is not required. The candidate must have good communication skills (oral and written) in English, and be able to work in a team on multi-disciplinary projects.

Work Context

The successful candidate will be supervised by Joëlle Barido-Sottani and will work in Hélène Morlon's group at the Institute of Biology of the École Normale Supérieure (https://www.ibens.bio.ens.psl.eu/). The IBENS is a multidisciplinary research center in Biology with more than 300 staff members, conveniently located in the Latin Quarter in downtown Paris. The centre develops research in a wide range of disciplines, including evolutionary biology, ecology, computational biology, genetics, and comparative genomics. The PhD student will be registered in the Life Sciences doctoral school at PSL University (https://psl.eu/en/research/life-sciences-ds).

Constraints and risks

The project will include trips in France and abroad for scientific conferences and visits.