From what I understand, mitochondrial DNA can be used to trace lineage, but it is only passed from mother to child. So, is it possible that we have been overlooking large armies, not unlike ghengis Khan, spreading their genes because it is paternal lineage?
If a group of warriors sacked a town, would there be any lasting DNA evidence?
You should ask this over at /r/AskAnthropology, it's not a history question.
That said, mtDNA is transferred mother to child, so it does give us a one-sided picture. The best information to be had regarding DNA is nuclear DNA- XY or XX chromosomes. However, these don't preserve as well, so they are hard to analyze in ancient remains. Mitochondrial DNA is much more prevalent, and that is why there are so many studies about it. There are also studies that look at mutations in the Y chromosome, so we do have some information about paternal descent.