The article is saying that every person bears some relation to each other, even among distant groups. No further back than 3500 years ago existed a person who was a common ancestor to every currently living human being.
Perhaps you're off by a 0 or two...?
The Americas may have been clearly separated for a while, but they have done so much interbreeding with people from other continents since 1492, that the common ancestor is more recent than that.
"Monte Carlo simulations suggest the MRCA was born surprisingly recently, perhaps even within the last 5,000 years, even for people born on different continents."