A problem with DNA research, that isn’t backed up by physical evidence, is that there are the rare beneficial mutations that can change genes in a species without contact with other groups. And there isn’t likely to be physical evidence remaining of crude humanoids from so long ago.
I guess when there is enough knowledge that will be addressed. Seems, for now, everyone just assume the changes come from contact with ‘new’ groups.
The problem with using DNA is to try to determine ultimate geographical origin based on where this or that DNA bit survives today. The technology has been improving remarkably, such that DNA sequences can be extracted from very, very old remains, much moreso than might have been suspected even ten years ago.