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Research

I am interested in deciphering the molecular mechanisms that are responsible for the emergence, maintenance and loss of genetic and phenotypic diversity across various taxonomic ranks, from the individual level to populations and broad taxonomic clades. Overall, my research focuses on reconstructing the history of present and past taxa to assess how much their evolutionary trajectories have been shaped by their environment. 

Equid ancient genomics

My PhD and first postdoctoral research focused on deciphering the origins of horse domestication, using ancient genomics and next-generation high-throughput sequencing technologies. Suprisingly, we discovered that the first horses ever managed were not the ancestors of modern domesticated horses, and we pinpointed the origins of modern domesticated horses in the Western Eurasian Steppes, some 4,500 years ago, while several now extinct populations existed by the time humans started managing horses. Our work also showed that the development of modern breeding in the last 2 to 4 centuries impacted genetic diversity more dramatically than the previous millennia of human management. Finally, as part of the sampling effort, we sequenced the genomes of ancient donkeys and mules, which informed us about diverse breeding practises of past societies, thus bridging genomics to archaeological science and history. 

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Vertebrate dietary adaptations

This is a SNF Sinergia funded project, investigating the molecular and ontogenic underpinnings of adaptations of vertebrates to diet, at the level of the two main organs of the digestive system: the intestine and the liver. As part of this project, we use as a study system the chlid fishes from Lake Tanganyika, which have radiated into 240+ species in the last 10 million years, and have adapted to a wide variety of diets, from algae to invertebrates, fish and even scales from other fish. I generated single-cell RNA sequencing data (scRNAseq) from the digestive system of 25 species representing all major clades and diet categories. I uncovered substantial cell type diversity in both epithelial and immune cells, and am now leveraging both scRNA and bulk RNA sequencing data to investigate dietary adaptations and plasticity at unprecedented resolution using phylogenetic comparative methods, to detect potential ecological adaptations at the level of the intestinal and liver cell types.

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Evolution of the visual system of cichlid fishes

This is a new project, in which I propose to to assess the extent of hard-wired adaptation and ontogenic plasticity in the visual system - including both the retina and the main visual brain structure of teleost fishes, the optic tectum (OT)- of the Lake Tanganyika cichlid fishes. These fishes occupy a wide range of visual environments, trophic niches and habitats, and are thus a perfect system to test the adaptive nature of the visual system. The aim here is to go beyond the well-studied photoreceptors (PR) in the retina, and investigate the phototransduction cascade in the retina, how visual cues are then transmitted first to retina ganglion cells (RGCs) and then to the OT. A combination of state-of-the-art single-cell functional genomics, spatial transcriptomics, imaging and X-ray microtomography will be used to reveal the fine-scale spatial cellular organisation of the visual system, and its diversity across species and development.

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