This thesis highlights the use of museomics to study genetic diversity across time and space in two species of mayflies in Switzerland (Baetis alpinus and Serratella ignita). This work is part of the DecliNe project, which aims to trace the history of insect populations in Switzerland to understand their decline. To achieve this, historical mayfly specimens from the entomological collections of the Lausanne Zoological Museum are collected for genetic analysis. Similarly, fresh specimens are sampled from various rivers in Switzerland for the same purpose.

The DNA from these fresh and historical samples is then analyzed using new molecular biology and HyRAD genomics methods, despite the low quality and quantity of DNA in historical samples. This results in the capture of SNPs representative of mayfly populations since the early 20th century.

The analysis of these 427 historical samples and 203 fresh samples revealed significant fluctuations in population dynamics over time. Certain periods show genetic divergences and convergences, indicating population vulnerability. Overall, the results point to decreasing heterozygosity and increasing inbreeding, symptoms of species decline. Thus, museomics has proven to be an effective tool in this project, despite the challenges associated with the condition of historical samples.

These findings reinforce the global observations of insect decline seen around the world and encourage action to prevent this situation from continuing. Finally, this data can also help determine when and why the decline in entomofauna began and estimate how far it could go if environmentally harmful practices do not cease.