OK, I couldn't find out what they got the fruit flies to evolve into. What was it?
Here's the gist in layman's terms; scientists have fruit fly A, a female.
They breed fruit flies B and C from that single female.
They seperate fruit flies B and C. Let's say that Fruit FLy B has a slight mutation.
The generations from fruit flies B and C eventually evolved to the point that they were unable to interbreed.
In other words, the ancestors of fruit fly B and C couldn't make babies even though they both came from fruit fly A. The generations birthed from Fruit Fly A branched off into two seperate species.
That is evolution plain and simple.