Used to considering fruit flies as a household and office pest (my office being adjacent to biological labs), I was surprised to read this story in the New York Times about a non-native species causing problems in the western U.S. (NYT requires a user name and password). It turns out that there are many native species of fruit flies whose populations have been in decline since the arrival of Drosophila subobscura, a European native. Unfortunately native Drosophila suffer from a lack of attention due mostly to the fact that they're, well, flies. If you don't want to deal with logging in to the NYT, you can read a similar article from 2000 from the Seattle Post Intellingencer. For more detailed information, check out this book, though it might be in German.