The study of eco-evolutionary dynamics is important for understanding natural systems and offers valuable knowledge to protect biodiversity, as these systems host unique species. The study of biodiversity has recently experienced a revolution through phylogenemics. In this context, this research will study eco-evolutionary processes that shaped biodiversity on the isolated and species-rich island of Cyprus, through a Next Generation sequencing approach. Innovative methods will reveal the genetic structure of populations and evolutionary processes, in a parallel approach of many classes, mainly local endemics, from different taxonomic groups. Valuable knowledge is expected for efforts to predict the consequences of climate change on biodiversity, given that Cyprus is vulnerable to it. The project will highlight Cyprus as a global model for eco-evolutionary research and will be implemented by a team of internationally recognised research organisations, with significant and complementary know-how in such research. It will thus provide added value for the Cypriot research community, as it will help local researchers expand their knowledge towards methods at the cutting edge of the scientific spear. The Coordinator (Projects) Ecology & Biodiversity, University of Cyprus) will work with the project. Molecular Ecology of the same Department, Work. Molecular Systemics (Department of Biology/MFIC, University of Crete) and Work. Exelixis (Heidelberg Institute of Theoretical Studies; Computational Molecular Evolution Group). In addition to the ddRADseq protocol, Sanger sequencing will provide data on branch dating and the results will also be analysed from the point of view of population genetics in order to identify demographic trends. The results will be presented in scientific conferences and publications in journals, and to the general public through websites, articles in the press and a workshop that will be presented to the public.