Speciation is the process by which closely related populations of organisms differentiate following reductions in the effective rate of genetic exchange between them over time. For most speciation events, population genetic data is the only available information about how reproductive isolation has arisen. We have a poor understanding of how evolutionary forces and genomic features contribute to reproductive isolation, primarily due to the difficulty of inferring barriers to gene flow. In particular, it is unclear what role genes that are sex-biased in expression and/or sex-linked play in speciation. In my thesis, I aim to infer the locations of putative barriers to gene flow to understand to what extent different genomic features, in particular fast-evolving sex-biased genes, contribute to reproductive isolation between a sister species pair of scarce swallowtail (Iphiclides) butterflies. In my first research project, I estimate core population genetic parameters across all sister species pairs of European butterflies and fit simple models of divergence to ask how well classic phylogeographic hypotheses fit recent diversification events in this taxonomic group. In my second research project, I infer explicit models of the speciation process and model effective migration rates along the genome to locate putative barriers to gene flow. I ask whether these barriers to long-term gene flow are associated with areas of the genome that show a reduction in recent introgression across a hybrid zone. In my third and final research project, I extend the demographic modeling of speciation in the Iphiclides species pair to the Z chromosome and ask whether barrier regions are associated with sex-biased genes, as a result of their faster rate of evolution. In summary, my findings suggest that fast-evolving male-biased genes likely contribute to extensive sex-linked reproductive isolation, as well as paving the way for future research on the population genetics of European butterflies and the evolutionary genomics of speciation.