While the evolutionary mechanisms responsible for decreasing gene flow and creating genetic subdivisions are generally well understood, the potential role of interspecific hybridization and introgression in facilitat- ing colonization of new habitats and ecological specia- tion remains a very contentious issue in speciation research (Mallet 2007). This problem is particularly dif- ficult to track in the aquatic environment, where hybrid zones are less stable (Petrusek et al. 2008), hybrids are distributed along large ecological gradients (Pantel et al.
2011) and have an assortment of mating systems. One challenge in studying speciation involves pinpointing the reproductive barriers that initiate speciation, and understanding the succession of these barriers through time, leading to the completion of speciation (Coyne & Orr 2004). The speciation process becomes even more complicated when gradual divergence is punctuated by reticulate evolution. Species-rich complexes that involve relatively young lineages with various degrees of repro- ductive isolation, sharp genetic subdivision between populations and potential for hybridization and intro- gression provide very good models for studying the evolutionary forces that drive speciation. Such complex systems offer the opportunity to examine a broad range of genetic divergences from the population to the sister species level. By studying the genomic landscape of genetic differentiation across various geographical scales and ecological settings we can make important