Essentially, the AI is looking for a particular emergent property, so it runs parallel simulations, each one with the same "species", but changing the parameters of the various simulation universes.
While interesting in of itself, the AI is likely doing this because it intends to seed the real universe with this species, in order to harvest whatever the effect of this emergent property actually is. For a truly awesome SFNal property, condsider "Childhood's End", by Arthur C Clarke. While the Overlords may have almost god-like powers, the Overmind wants the essence of Humanity, and dispatches the Overlords to shepherd us until such time as we have reached that level of consciousness.
Since there is no "Overlords" or Humanity, the AI must work out the possible parameters. Based on the information of the OP, the AI seems to have the ability to create both the species and set up the civilization, and create a "pocket universe" in order to run the experiment in realtime once it has the correct parameters established.
Alternatively, and more simply, the AI leaves the parameters of the Universe the same, and makes subtle changes to the simulated species until it gets the results it wants. As before, thousands or millions of runs in parallel are done to find the correct answer.