Look for evidence of incipient barriers to gene exchange. These may show some bimodal distribution suggestive of early steps in evolution. This depends entirely on the model of speciation that might apply to the organism under study. Laboratory populations might serve as model systems. One can establish the conditions of the specific model under question and ask if the predicted divergence is observed.
Mathematical models can address specific predictions about modes of speciation.
Knowing what's possible might spur one on to looking for it in unexpected contexts in natural populations. With the use of molecular tools the comparisons of intraspecific and interspecific genetic variation has been studied in some detail. Aim is to identify genetic changes during speciation . These data show us that genetic change is associated with speciation. We want to be able to describe the genetics of speciation and the genetics of species differences .