Razib Khan One-stop-shopping for all of my content

July 10, 2017

The great Bantu expansion was massive

Filed under: History,Human Genetics,Punt — Razib Khan @ 12:01 am

Lots of stuff at SMBE of interest to me. I went to the Evolution meeting last year, and it was a little thin on genetics for me. And I go to ASHG pretty much every year, but there’s a lot of medical stuff that is not to my taste. SMBE was really pretty much my style.

In any case one of the more interesting talks was given by Pontus Skoglund (soon of the Crick Institute). He had several novel African genomes to talk about, in particular from Malawi hunter-gatherers (I believe dated to 3,000 years before the present), and one from a pre-Bantu pastoralist.

At one point Skoglund presented a plot showing what looked like an isolation by distance dynamic between the ancient Ethiopian Mota genome and a modern day Khoisan sample, with the Malawi population about $\frac{2}{3}$ of the way toward the Khoisan from the Ethiopian sample. Some of my friends from a non-human genetics background were at the talk and were getting quite excited at this point, because there is a general feeling that the Reich lab emphasizes the stylized pulse admixture model a bit too much. Rather than expansion of proto-Ethiopian-like populations and proto-Khoisan-like populations they interpreted this as evidence of a continuum or cline across East Africa. I’m not sure if this is the right interpretation of the plot presented, but it’s a reasonable one.

Malawi is considerably to the north of modern Khoisan populations. This is not surprising. From what I have read Khoisan archaeological remains seem to be found as far north as Zimbabwe, while others have long suggested a presence as far afield as Kenya. Perhaps more curiously: the Malawi hunter-gatherers exhibit not evidence of having contributed genes to modern Bantu residents of Malawi.

Surprising, but not really. If you look at a PCA plot of Bantu genetic variation it really starts showing evidence of local substrate (Khoisan) in South Africa. From Cameroon to Mozambique it looks like the Bantu simply overwhelmed local populations, they are clustered so tight. Though it is true that African populations harbor a lot of diversity, that diversity is not necessarily partition between the populations. The Bantu expansion is why.

Of more interest from the perspective of non-African history is the Tanzanian pastoralist. This individual is about 38% West Eurasian, and that ancestry has the strongest affinities with Levantine Neolithic farmers. Specifically, the PPN, which dates to between 8500-5500 BCE. More precisely, this individual was exclusively “western farmer” in the Lazaridis et al. formulation. Additionally, Skoglund also told me that the Cushitic (and presumably Semitic) peoples to the north and east had some “eastern farmer.” I immediately thought back to Hogdson et al. Early Back-to-Africa Migration into the Horn of Africa, which suggested multiple layers. Finally, 2012 Pagani et al. suggested that admixture in the Ethiopian plateau occurred on the order of ~3,000 years ago.

Bringing all of this together it suggests to me two things

  1. The migration back from Eurasia occurred multiple times, with an early wave arriving well before the Copper/Bronze Age east-west and west-east gene flow in the Near East (also, there was backflow to West Africa, but that’s a different post….).
  2. The migration was patchy; the Mota sample dates to 4,500 years ago, and lacks any Eurasian ancestry, despite the likelihood that the first Eurasian backflow was already occurring.

Skoglund will soon have the preprint out.

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