Speciation, or the evolutionary process by which new species arise, is among the most controversial topics in evolutionary biology. The presence or absence of gene flow between incipient species occupies a central role in this discussion. The conventional view states that there is no gene flow during speciation and that genomes are cohesive units. The recently proposed Genic View of Speciation (GVS) theory challenges this paradigm and states that genomes are porous and that gene flow during speciation is possible. Under this scenario, the genes influenced by disruptive selection should start diverging first, whereas neutral genes should flow freely between emerging species, generating a heterogeneity of genetic divergences among different regions of the genome. Thus, the GVS predicts that speciation with gene flow (sympatric) leaves a distinct genomic signature different from that of speciation in isolation (allopatric).Our project consists of the first comprehensive test of the GVS using coral reef fishes, a very diverse group with high dispersal ability, which defies the traditionally accepted pre-requisite of complete isolation for formation of species. We will test for heterogeneous divergences among thousands of loci using a novel high throughput DNA sequencing method (RAD-sequencing) to test predictions of the GVS in both allopatric and sympatric species pairs and identify genomic signatures of speciation modes.The questions that will be addressed are of fundamental importance to studies in evolutionary biology and include: Do different speciation modes leave distinct genomic signatures? Are there genes that flow freely across incipient species boundaries? Is introgressive hybridization common in fishes and how does it affect molecular clock calibrations? Outcomes from this project will further our understanding not only on the diversification of reef fishes, but also on general patterns of molecular evolution and the origin of marine biodiversity.