Sons of the farmers, the origins of Africans

Most readers at this point are aware that I am very curious as to the origin of Europeans at the interface of hunter-gatherer populations and Neolithic farmers. What we thought we knew around the year 2000 does not seem to align very well with the conflicting results coming out of recent analyses. There is no ascendant consensus at this point. All possibilities are still in the field of play. Part of the issue of course is that the spread of farming in Europe was a prehistoric affair, very far back in time. There have been several cultural, and possibly demographic, revolutions in Europe since the arrival of the first farmers. Pulling apart the manifold layers of the palimpsest is a task of great difficulty, and the confident results utilizing the tools of the past should make us cautious of the inferences of the present. This is why I believe focusing on case-studies such as Japan are essential. From a range of specific cases we may infer general patterns, which will then allow us to have firmer ground when making conjectures about times and places where the empirical results can not resolve conflicts of opinion. Japan is an island which made the transition to agriculture relatively late, so the fog is a bit less daunting than is the case with prehistoric Europe. Africa is perhaps even a better case: the Bantu expansion is very recent, having reached its stable frontier only within the last ~1000 years. If it is true that Phoenicians circumnavigated Africa in the ~600 BC, then they would have encountered many non-Bantu groups south of Kenya at that time. Linguists have long noted the similarities of the Bantu languages from north to south, but the genetic similarities also exist. Here's a figure from the Bushmen paper in Nature: