The way it works for molecular phylogeny is that you try to find things that are conserved. E.g. if you find a small village in Europe where people haven't moved around much and you find a rare mutation that is also present in one other part of the US, then you might be able to put some numbers on the likelihood that this mutation/gene came from a the original place. Find a second gene, find some artefacts from the right place/time and you have an emerging picture.