Unless you’ve been asleep, you probably know by now that the Reich lab has come out with a paper that analyzes the remains of 4 individuals from western Cameroon, dating to 8,000 and 3,000 years ago (2 of each, with one of the older individuals yielding 18.5x coverage DNA!). The location and timing both matter.

This area of Cameroon is hypothesized to be the point of expansion for the Bantu migration. This expansion began about 3,000 years ago and swept east and south until the agricultural streams met back up in southern Africa.

Perhaps then the authors then “caught history in action” with a change between 8,000 and 3,000 years ago? No such luck actually. Here is the abstract, Ancient West African foragers in the context of African population history:

… One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region…However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today—as well as speakers of Bantu languages from across the continent—are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.

Basically, just like elsewhere in Africa where the Bantu expanded, you see massive discontinuity in this region of Cameroon (the modern agriculturalists in the area are Bantu-speaking). If you have ever analyzed African genetic data, the lack of high magnitude structure of the Bantu over wide areas is pretty shocking. The reason there’s little structure seems to be two-fold

1. Rapid population expansion, so not much time to accumulate distinct variants (you see this in Northern Europe too)
2. Minimal admixture with local populations, at least until you get to modern-day South Africa (then there is an admixture cline with Khoisan)

Meanwhile, you have these zones of relic hunter-gatherers here and there. These samples seem to be one of those cases. I think it’s analogous to the fact that hunter-gatherers persisted in pockets for thousands of years after the initial arrival of Neolithic farmers in Europe.

There are two types of things you can take away from a paper like this. General insights. And specific details. The plot at the top of this post illustrates a model that they generated with these data. It seems quite clear that the details are not crisp, and subject to a further specific revision. But the general insights seem robust and extend what we already knew.

First, there were several human lineages that diverged 500,000 to 1 million years ago. In Eurasia, these became Neanderthals and Denisovans. In Africa, one of the branches led to what we call “modern” humans. But a variety of lines of evidence indicate that within Africa there were also highly diverged human groups, analogous to Neanderthals and Denisovans. One could call them “African Neanderthal” analogs. But within the context of this paper, they are “ghost archaics.” But those aren’t the only “ghosts.”

Extant human populations sample only a fraction of the “modern” family tree, which seems to have diversified from one of the African human groups 300,000 years ago or so.

There is now a fair amount of circumstantial evidence that Neanderthals mixed with an African lineage that is an outgroup to most other Africans and descended-from-Africans. Because of its size and warm climate, I believe that Africa was quite a good habitat for humans, and there were a variety of them across the continent. Though I don’t discount deep-time back migration of Neanderthal/Denisovan groups into Africa, I think due to the different population sizes it is probably more the case that Africans went into western Eurasia than vice versa. Additionally, Southeast Asia seems to be a good target habit for any African species due to similarities of biome (e.g., Sundaland).

Finally, there is the fact that it seems non-African ancestry is closest to the Mota sample, dated to 4,500 years ago in Ethiopia. This makes geographic sense, though I do wonder if this is an artifact of continuous gene flow back from Eurasia, as much as the likelihood that this is near the exit path of African humans.

What about the details of this paper? Look a the supplements and notice all the admixture graphs. There are lots of potential fits to the data, and more data will come in. The paper is clear to not put too much faith in one set of weights for gene flows, and different graphs might explain the patterns in the data. Additionally, a highly dense African landscape of hominins might exhibit lots of continuous gene flow and isolation by distance. There’s a lot more to learn. Nothing is being closed in this case.