I think future techniques will be able to extract DNA from things up to 1 million years old. Sure, DNA breaks down in the environment, but when you start with 60,000,000,000,000 copies of a genome in a human, I think there is a very high chance that enough fragments of that will remain to reconstruct one copy - the only hurdle is coming up with a method to do it practically.
In a hypothetical world where we could have infinite compute power and a map of the exact location of every atom in a skull, I don't think there would be any issue getting a DNA sequence.
Then we can draw the full family tree and know for sure.