Saturday, February 18, 2012

Were there Neanderthals in Africa?

“Neanderthal” admixture seems to be higher in West Africans than in East Africans. How come? (Source)

When modern humans began their expansion from a small core somewhere in East Africa, the continent probably had several different archaic populations.

It now seems that one of them was related to the Neanderthals in Europe. In an ongoing study of Neanderthal admixture in present-day humans, John Hawks has found an apparently higher level of admixture in the Yoruba of Nigeria than in the Luhya of Kenya (see chart above).

This is counter-intuitive, as Hawks himself notes. The closest source of admixture would have been Neanderthals in what is now Israel (and probably elsewhere in the Middle East). Genes from that source should have first introgressed into northeastern Africans.

Perhaps this “Neanderthal” admixture actually came from a related archaic population that was already established in Africa. As modern humans spread west from East Africa after c. 60,000 BP, they would have partially intermixed with these archaic hominins before finally replacing them. There would thus be an east-to-west cline of increasing archaic admixture.

This would be consistent with the finding that dental traits are more “ancestral” in West Africa than in East Africa. When Irish (2011) compared dentitions from west, central, east, and south Africa, ranging in age from the late Pleistocene to the mid-1950s, the early Holocene Kenyans and Tanzanians were the ones that had the fewest ancestral traits of the Sub-Saharan African Dental Complex.

This may also explain why the level of Neanderthal admixture is almost the same throughout Eurasia (although John Hawks has found slightly higher levels among Europeans than among Asians). Perhaps this “Neanderthal” admixture was simply admixture with a Neanderthal-like population within Africa itself. Modern humans would have picked it up on their way out of the continent.

But this raises another question. Why is “Neanderthal” admixture lower in present-day sub-Saharan Africans than in present-day Eurasians? Perhaps there was another archaic population, very different from the Neanderthals, that modern humans encountered only in Africa. This might be the quasi Homo erectus represented by the Broken Hill (Kabwe) skull. It might also be the population that accounts for about 2% of the present-day African gene pool and that seems to have split away from the ancestors of modern humans some 700,000 years ago (Hammer et al., 2011). This secondary archaic source may have proportionately reduced the admixture from these “African Neanderthals.”


Hawks, J. (2012). Which population in the 1000 Genomes Project samples has the most Neandertal similarity? John Hawks Weblog, February 8

Hammer, M.F., A.E. Woerner, F.L. Mendez, J.C. Watkins, and J.D. Wall. (2011). Genetic evidence for archaic admixture in Africa, Proceedings of the National Academy of Science (USA), 108, 15123-15128,

Irish, J.D. (2011). Afridonty: the “Sub-Saharan African Dental Complex” revisited, American Journal of Physical Anthropology, 144(supp. 52), 174


Insightful said...

In 2010, Svante Paabo told us of the Neanderthal admixture in Eurasians. He also did tests on Yoruba and Khoisan (san bushmen) in Africa and determined they had none. Now, we hear that the Yoruba have more neanderthal admixture than an East African population called the Luhya. My question is what was done in 2012 to now yield Yoruban neanderthal admixture that escaped Svante in 2010?

Peter Frost said...


Paabo simply assumed that sub-Saharan Africans had no Neanderthal admixture. He used their genome as a benchmark for zero archaic admixture.

A theoretical model is only as good as the assumptions built into it.

Kiwiguy said...

OT. Peter, I thought you'd find this discussion thread on GNXP of interest.

It started with Razib asking that social scientists stop citing Lewontin's Fallacy, and later an anthropologist blogger Jason Antrosio asked readers to consider the 2009 issue of the American Journal of Physical Anthropology titled “Race Reconciled: How Biological Anthropologists View Human Variation. Razib has subsequently provided a link to view the papers referred to.

Ben10 said...

R. Dawkins and others apparently believe that Chimps are basically some old Autralopithecus forms that choose to go back in the trees. So it would be interesting to compare the genome of the two, i am curious to know if the chimps 'lost' some australopithecus genes in the process.

By analogy, is it possible that all homo sapiens had originally the same amount of archaic DNA (from different archaics), but those who stayed in Africa selectively lost some archaic DNA while those who migrated lost other archaic DNA?

Peter Frost said...


Lewontin's study is more popular among social anthropologists than among physical anthropologists. Even Cavalli-Sforza didn't begin to cite it until the 1990s (apparently in response to pressure from his academic milieu).


No, not if by "selectively" you mean "through natural selection." We see this archaic admixture at gene loci that are close to selective neutrality, i.e., they seem to sit on the chromosome and do nothing.

On theoretical grounds, I would expect to see more archaic admixture in sub-Saharan Africans than in other humans. There are two reasons:

1. Archaics were physically and behaviorally more similar to modern humans in Africa, so there should have been fewer barriers to intermixture.

2. Contact between modern humans and archaics went on for a longer time in Africa than elsewhere. In Europe, the transition lasted about 15,000 years. In Africa, it was more like 40,000 years.

Kiwiguy said...

***Even Cavalli-Sforza didn't begin to cite it until the 1990s (apparently in response to pressure from his academic milieu).***

Yes, I recall your excellent series of posts discussing the "evolution of Cavalli-Sforza" :)

Anonymous said...

J. Lyon Layden said...

I think there are two possibilities far more likely than a "Neanderthal-like African."
The first- there was more neanderthal in the first back-migration into Africa, which brought y hap ED and the oldest forms of y hap E. Later populations who brought J and I diminished the neanderthal content, but Nigeria escaped that influx.
The second- Ibero-Maurusians were definitely highly neanderthal. They came from the last neanderthals on Gibralter across the straight, and were later assimilated or pushed down into Nigeria by the Capsians.