Self-funded PhD - The genomic basis of major evolutionary transitions

Life on Earth has undergone major evolutionary transitions that reshaped its biology, including the emergence of multicellularity, adaptation to terrestrial environments, and parasitism. The genomic mechanisms driving these changes remain poorly understood. This project will analyze large-scale genomic datasets using methods such as comparative genomics and phylogenetic reconstruction to uncover the genetic basis of these evolutionary leaps.

The student will investigate genetic innovations associated with key adaptations, including the origin of new genes, loss of redundant genes, and horizontal gene transfer. This work will involve comparing millions of genes across more than a hundred species, leveraging custom computational tools to identify functional roles of genes implicated in these transitions.

The student will apply an evolutionary genomics pipeline developed in the host lab, which we have used in recent publications in Nature, Nature Ecology and Evolution, Nature Communications, New Phytologist, or Current Biology. The biological function of genes of interest (e.g., gained during terrestrialization) will be interrogated via Gene Ontology and protein domain analysis. For molecular dating, the gene family members will be aligned with MAFFT, ambiguous regions will be trimmed with TrimAl, and trees will be inferred with software like IQTree and Phylobayes. The student will contribute to the execution of these analyses and the overall design of the project and expand them by bringing in their own ideas and informing the research direction.