Lab: EGCE Team: Evolution and Genomes

Research Topic

My research focuses on the evolutionary history of insects, with a particular interest in the adaptation and evolution of chemosensory systems and their domestication. After completing a PhD at the EGCE laboratory (Evolution and Ecology Division, supervised by M. Harry and F. Mougel) on the vectors of Chagas disease of the genus Rhodnius, I continued my research at ISYEB, where I studied the evolution of the chemosensory system in aquatic beetles of the suborder Adephaga.

I use bioinformatics, evolutionary analyses, and molecular biology to study the genomic mechanisms underlying environmental adaptations. At the EGCE laboratory (Evolution and Genomes Team), I am currently working on comparative genomics of different strains of Hermetia illucens (Black Soldier Fly), an excellent model for domestication with a high potential for agro-industrial applications.

Research Experience

• Evolution of chemosensory genes related to the transition from terrestrial to aquatic environments in beetles, using a comparative transcriptomics approach at ISYEB (Sorbonne University, MNHN, EPHE, CNRS, UA), supervised by Prof. Michaël Manuel (Postdoctoral fellowship, June 2023 - Dec. 2024) Assembly of transcriptomes of Adephaga beetles and annotation of chemosensory transcripts. Reconstruction of evolutionary history through phylogenies of multigene families. Differential gene expression analysis of chemosensory genes in various organs of the great diving beetle (Cybister lateralimarginalis) in both adult and larval stages.

• Genome dynamics and molecular evolution of chemosensory receptors in Chagas disease vectors of the genus Rhodnius at EGCE (Paris-Saclay University , CNRS, IRD), Gif-sur-Yvette, supervised by Prof. Myriam HARRY and co-supervised by Assoc. Prof. Florence MOUGEL (PhD, Oct. 2019 - April 2023) Study of the evolutionary history of Rhodnius species through phylogenomic analysis, genome size estimation, assembly, and annotation of 13 genomes. Investigation of gene gain and loss dynamics related to habitat adaptation. Annotation and selection analysis of chemosensory genes according to the habitat.

Teaching and Supervision

• 2023-2024: Bioinformatics: Essential Tools (L2 LU2SV381, Sorbonne University) General introduction to the Unix/Linux operating system and data processing tools (12h).
• 2020-2022: Evolutionary Biology (L3 BiolEvol, Paris-Saclay University) Phylogenetic relationships between taxa, linking biodiversity to evolutionary mechanisms and scenarios. Bioinformatics practical sessions on phylogeny construction and multigene family history reconstruction, introduction to various tools and databases (76h).
• 2020-2022: Population Genetics (L3 GPQ, Paris-Saclay University) Tutorials on fundamental concepts of population genetics (evolutionary pressures and reproductive regimes) with applications in conservation biology, epidemiology, human genetics, and agronomy (46h).
• 2019-2020: Biological Evolution and Ecology: From Organisms to Ecosystems (L1 UESV102, Paris-Saclay University) Tutorials on ecology with case studies, calculations of allele frequencies, and computer practicals on allele frequency evolution under selection pressures. Implemented remote teaching via videoconferencing. Graded exams and assignments (60h).
• 2019-2022: Supervision of three Master’s 2 students in bioinformatics (during PhD) Annotation of chemosensory genes using multiple approaches, command-line and web server-based bioinformatics analyses.

Publications

2023

• Merle M. , 2023/04/18, Dynamique des génomes et évolution moléculaire des récepteurs chimiosensoriels des vecteurs de la maladie de Chagas du genre Rhodnius, phdthesis, Université Paris-Saclay

2022

• Filée J., Merle M. , Bastide H., Mougel F., Bérenger JM., Folly-Ramos E., Almeida CE., Harry M.. (2022) Phylogenomics for Chagas Disease Vectors of the Rhodnius Genus (Hemiptera, Triatominae): What We Learn From Mito-Nuclear Conflicts and Recommendations. Front. Ecol. Evol., (9) 750317
• Merle M. , Filée J., de Oliveira J., Almeida CE., Mougel F., Bastide H., Girondot M., da Rosa JA., Harry M.. (2022) Genome Size Variation of Chagas Disease Vectors of the Rhodniini Tribe. The American Journal of Tropical Medicine and Hygiene, 1 (107) 211-215