Etienne Patin has another paper out on the genomics of Central Africa, and the relationship of the Pygmies to their agriculturalist neighbors, The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists. It is to a great extent expanding upon earlier work with denser marker sets, larger sample sizes, and of course ~2014 statistical genomic techniques (e.g., ALDER). As background you have to remember what Patin established before: the western and eastern Pygmy populations of the Congo rainforest seem to have diverged tens of thousands of years ago, tens of thousands of years after their divergence from the ancestors of their agriculturalist neighbors. By and large these neighbors speak Bantu languages, which have swept out of the eastern fringe of what is today Nigeria only within the last 3,000 years. The numbers alluded to the paper are separations on the order of ~20,000 years before the present for the Pygmy groups (west vs east), and then ~50,000 years for the ancestors of the agriculturalists vs. the proto-Pygmies. Think about this: diversification within Africa occurred at about the same time that the most distant of the non-African groups were starting to become isolated from each other. The Pygmies are not just interesting from an ethnological perspective, along with the Khoisan they preserve to a high degree an ancient and diverged group of populations which have largely been marginalized due to the demographic expansions of peoples speaking Niger-Congo and Nilo-Saharan languages (the Pygmy speak the languages of their agricultural neighbors, but this seems a recent development).
An interesting twist revealed in this paper is that admixtures seem to be relatively recent (on the order of 1,000 years), and, those levels are quite high indeed in many Pygmy populations. This is not the case with agriculturalists. In other words, the genes of agriculturalists seeped into the Pygmies, but far less moved in the reverse direction. As analogy, consider that the average Native American is far more European than the average European American is Native. But, as with the case of the Pygmies and their neighbors it may be that there is more Pygmy ancestry in the aggregate in their numerous neighbors, than among the relatively rare Pygmies!
Finally, I think we need to now broach the topic of genomic value for posterity. It is well known that in the Congo region today Pygmies have been the target of conscious genocide, as well as suffering from the consequences of the great wars of the past few decades (I recommend Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa to anyone with a modicum of interest in this topic). But the results in this paper indicate that the Pygmies are under clear threat of being demographically absorbed by their neighbors before the passing of this century. In particular this paper reinforces what has been clear in other results: the Mbuti of the eastern regions of Congo in particular harbor unadmixed genetic variation. While the Khoisan of southern Africa reside in a quiescent zone of the continent, the Mbuti are not so fortunate. I hope that we get at least hundreds of whole-genome sequences from this population within the next decade, for the sake of all of humanity. Ancient DNA seems unlikely from most of Africa, so massive surveys of the contemporary genomic landscape of this continent is going to be essential to understanding our species’ collective past.