This is tautological, sub-saharan genetic markers are found predominantly in sub-saharan populations by definition.
Given how humanity has evolved, "european" markers are a subset of the diversity found in subsaharan populations that are overrepresented from founder effects, with very few exceptions. 40,000 years ago sounds like a long time, but it really isn't.
You need an amazingly small amount of migration (about one person per generation) to keep a population in sync with each other genetically.