It may be the 20% mentioned below.
"About 8,000 years ago, said Underhill, a more advanced people, the Neolithic, migrated to Europe from the Middle East, bringing with them a new Y chromosome pattern and a new way of life: agriculture. About 20 percent of Europeans now have the Y chromosome pattern from this migration, he said.
Generally speaking when a more advanced society moves in and takes over the guys that are already there are reduced in number and the females become the property of the migrating males.
It is possible that this was one of those occasions where that didn't happen. Or that there weren't enough people in the second migration to genetically overwhelm the natives.
Still if the Indo-Europeans took over so completely that Basque was no longer used except in a small region I would think that this could not have been the case.
Otherwise the languages would have combined and (IIRC) they did not.
Of course if Basque was not the commonly used language then my speculation falls flat and bloodies its nose.