Mike Dunford has a good post on genes and their role in determining human evolution:
As you can see, different genes can have different genealogies even within a single biological genealogy. That’s why it’s not only possible but also unsurprising that the mitochondrial gene genealogy that traced back to “mitochondrial eve” and the Y-chromosome genealogy that traced back to “Y-chromosome Adam” don’t lead back to individuals who were married to each other, or even lived within 50,000 years of each other. It’s just part of the glorious complexity that you get to see when you look at the way genes get passed through populations.