One of the most common (if not universal) traits of human societies are incest taboos. What exactly constitutes incest is variable, but some prohibition exists. We can fairly safely assume that this is true of most human societies in the past as well.

As for hunter-gatherers, one suggestion for how they exchanged genetic material is at "trade fairs" on an annual or semi-annual basis. Basically, agreed upon points on the landscape were groups could meet at an agreed upon time of year in order to exchange materials potentially, but also mates. There is also this possibility purely from random or structured encounters between a smaller number of groups during the year.