The project goal is to infer the role of intragenomic conflict in the origin and/or breakdown of species barriers. Genetic traces of admixture between modern humans and Neanderthals have provoked strong interest in fine scale patterns of introgression within genomes. Recently we have constructed a survey of precisely these fine scale patterns in the only mammalian admixture system with equivalent genome resolution: the European House mouse hybrid zone (HMHZ). Our high resolution analysis allows ancestral and introgression polymorphism to be clearly distinguished – a fundamental problem in understanding the history of species. This project capitalises on this unique genomic resource. We will use our extensive sample databank and prior understanding of the HMHZ supplemented by targeted sampling of new material. The history and action of candidate genes will be verified using focal genetic surveys (hybrid enrichment technology), combined with lab crosses and phylogeographic analyses of house mouse colonisation history.