Recombination and adaptation to a new host are keys factors of pathogen emergence. While studying host-parasite interactions in the European house mouse hybrid zone, we recently demonstrated parasites with an intimate host relationship have genetic structure mirroring the host zone and produce hybrid parasites at its centre. We have also evidence, for a DNA virus, that genes which subvert the mouse host immune system introgress preferentially. The first goal of this project is a comparative genomic approach to test the universality of this pattern of preferential introgression using two additional parasite models belonging to two other kingdoms, a yeast-like fungus Pneumocystis murina and a nematode Syphacia obvelata. The second goal is to test the adaptive nature of implicated genes via a common garden experiment. By incorporating the use of state-of-the-art sequencing, analytical and computational methods this project will elucidate major processes in parasite recombination and evolution fundamental to the field of emerging diseases.