Shared ancestry

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I've read that everybody on Earth shares the same ancestor if you go back a certain amount of time (some sources claim a 100 generations (about 3000 years) while others are a bit more or less). So how is that possible, if by 1000 AD many civilizations were already set in? Like how can a person from Scandinavia be related to an Aborigine?
My father claims that history is wrong and goes rambling on about aliens, but I don't think so.
Among other he thing he talks about is the y-chromosome bottleneck
>https://www.sciencealert.com/neolithic-y-chromosome-bottleneck-warring-patrilineal-clans
and also some other bottleneck that happened in Levant about 10 000 B.C. although I can find no source on that (which he claims is somebody hiding it)
I'm pretty sure it's just genealogy and pedigree collapse, although I can't really wrap my mind around this.
So the question is:
How is it possible that we all share the same ancestor that goes back only 3000 years?