Conceptualized stages of species differentiation at the genic level – illustrated are chromosomes of diverging populations, which come into contact at the specified stage and experience net gene flow in parts of their genomes. Only loci directly contributing to differential adaptation are shown and alleles at such loci are assumed to be differently fixed (A, B, C, etc. in population 1 and a, b, c, etc. in population 2). As the populations diverge, there will be more loci involved in differentiation. Between these differentiation loci, there are certainly many more sites of neutral divergence, which can be shared between populations. Double‐headed arrow represents net gene flow (with migration overwhelming local selection) and is shown to decrease in magnitude as speciation progresses. Shaded block indicates the prevention of gene flow by local selection at and near the loci of differential adaptation. The fate of diverging populations (fusion or not) at a given stage can be inferred if there are sufficient data on the extent of divergence; see text for details.