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.
>You need an amazingly small amount of migration (about one person per generation) to keep a population in sync with each other genetically.
Well it depends on the size of the population, but even then I don't see how this can be the case. One individual only contributes half their genes to each child, so assuming 2 surviving children that's a 25% lost immediately in the next generation. In just a few generations about half the incomer's genes will be lost in this way. The remainder will likely persist, but equally the number of their descendants that have none or very few of their genes will rise to predominate. In a stable population of 1,000 people, one single individual is unlikely to contribute much more than 1/2,000th of the genes in circulation.
https://en.wikipedia.org/wiki/Early_human_migrations#Homo_sa...
Europeans have pretty low levels of sub-saharan genetic markers, with some remnant markets in southern Europe dating to the late Roman era, diminishing substantially as you move north.
https://en.wikipedia.org/wiki/African_admixture_in_Europe