In this project I investigate the molecular underpinnings for the evolution and reinforcement of reproductive barriers upon seconday contact between species of birds. In particular I am using a vast genomic dataset of 300 individuals from wheatear species to investigate the role of structural variants and transposable elements as molecular mechanisms that can facilitate the reinforcement of reproductive barriers upon hybridisation and therefore contributing to the speciation process. The wheatear species complex I focus on is formed by 4 species that hybridisa in multiple zones and in slightly different combinations. While hybridisation can create new biodiversity by mixing existing traits, it can also cause the origin of genomic problems in the parental species. One of these problems are genetic conflicts, namely, a mix of genetic variants (e.g., genes) that do not work well together and cause a reduction of fitness in the species (something similar to the health of a species). In the last few decades, one class of genetic elements has been linked to the origin of several genetic conflicts: transposable elements. Transposable elements are selfish elements that can jump and copy themselves throughout genomes and cause small and large mutations. The level of conflict caused by transposable elements can be estimated by studying how regions containing transposable elements get effectively exchanged by the parental species through the hybrids (gene flow). If transposable elements are involved in conflicts, we expect that regions dense in transposable elements to be resilient to gene flow. I am going to use a species complex of birds that hybridise in nature to understand how much genetic conflicts are introduced in the genomes of the parental species. Ultimately, the project will give us more insights on what molecular mechanisms contribute to the formation of species. This aspect of hybridisation and species diversification is important to understand, for example, for conservation biology to make the correct decision when dealing with hybridising endangered species. For this project to be carried out would need the use and help of a NAISS compute project.