Darwin suggested that natural selection not only leads to adaptation but also promotes the origin of species. Ecological speciation acts through divergent natural selection and one of the most informative circumstances in which one can investigate how adaptive traits and how species evolve – and what the genetic basis of species differences and adaptations are - are repeated adaptive radiations that are based on parallel adaptations that evolved more than once. In only a few species has the genetic basis of adaptations been identified so far. It is not generally known what portion of the genome, what kind of genes and what kind of genetic changes cause adaptations. The investigation of the genetics of species formation and adaptations requires the comparative investigation of genetic divergence in the entire genome. This is now possible by applying recent methods in next-generation sequencing technology to a tractable group of closely related species that vary in how far speciation and adaptive divergence has proceeded. In the crater lakes of Nicaragua a natural experiment is taken place where several adaptive radiations of cichlid fish formed independently from two large source lakes within only a few thousand years. These extremely young adaptive radiations consist of species that arose in sympatry and evolved parallel adaptations repeatedly in their new habitats. We will investigate the mechanisms of natural selection and identify the genetic basis of species differences and parallel adaptations - they could be standing genetic variation or repeated de novo mutations - through comparative genomic analyses that will include the establishing of a reference genome, genome resequencing, QTL analyses, population genomics, and linkage and association maps. Then we could test the causal relationship between identified candidate genes and the phenotypic differences and parallel adaptations through functional analyses.