Understanding the genetic and genomic processes behind adaptive phenotypes remains a holy grail in biology. Fungi are poorly studied regarding these processes, despite their great tractability as model eukaryote organisms and their medical, industrial, and ecological importance. This project therefore aims to investigate the major evolutionary forces in the adaptive divergence of fungi —as model eukaryotes with small genomes— by the integration of high-throughput sequencing and innovative approaches. Two groups of fungi will be used to investigate different time scales and footprints of adaptation. The first model group are Penicillium fungal species. Some species being used for cheese and antibiotic production, they are excellent models for understanding adaptive processes under strong and recent selection. The second model is Microbotryum violaceum, a complex of sibling species, causing anther smut disease on different Caryophyllaceae plant species. This model is ideal to address the question of long term pathogen-host adaptation. We will integrate high-throughput sequencing and state-of-the-art inference methods to identify the evolutionary processes involved in adaptive divergence and the genomic consequences of domestication. Different experimental and sequencing approaches will then help to validate the flagged genes and genomic regions. The proposed research should yield unprecedented insights into the genomics of adaptive divergence, i.e. on the kinds of traits, the genetic architecture of these traits, the genomic regions and processes involved, and the importance of neutral processes. There are also applied implications for understanding emerging fungal diseases in plants and processes of domestication in micro-organisms, and more generally adaptation to global changes.