Without going through a whole page of buys and sells, I think that Liberty acquired them from Ted Turner.
That's possible too, they're still likely seperate entities. The Braves, I guess, could have a seperate system set up, but I know most of them are independently owned. That's why you can have as much movement from city to city. The teams still keep the same names and such, but their affiliation changes. I know the Royals are set up so the minor league affiliates are owned seperately. When the Cubs sale went through it was for the Cubs, not their AAA team and on down. So, even though Liberty Media owns both Atlanta and Gwinnett, they are still seperate entities, in all likelyhood.