Then you know what they were before they mutated into fruit flies ...
Speciation can occur by divergence within a population leading to isolation - sympatric speciation
Best example is divergence in insects - can happen in less than an eye blink of geologic time, even in a few generations of insects. There is a genus of fruit flies, one species of which, prior to 1864, only lived on hawthorns, a native type of fruiting tree, in North America. In 1864, the species invaded domesticated apple trees in the Hudson River Valley. The colonizing flies only breed while host fruit is available so those breeding on apple trees would be immediately reproductively isolated from those breeding on hawthorns since apples mature first. A second group colonized cherries in 1960 in Wisconsin. Cherries mature before apples. So in 100 years, one species has become three.