There was a significant population bottleneck after the europeans reached north/south america. Nearly all native americans died, and then their population rebounded again (but not fully).

A lot of research like this makes an assumption that the genetics of modern native americans are close to pre-columbus genetics but that is almost certainly not the case.

When I was in graduate school I got a smithsonian fellowship to study the feasibility of amplifying dna from pre-columbus incan bones (they left their dead above ground on a plateau and so no contamination from tannins from the soil). I showed the dna could successfully be amplified.

I then left science and I'm not sure where the research went after that.