“South-Central Hunter-Gatherers” suggestive of remnant West African Pygmy DNA?

I have created a new page featuring the AncestryDNA results for West Africans from the following countries: Liberia, Ivory Coast, Burkina Faso, Ghana, Togo & Benin. I will create a new section for the remaining part of West Africa (Upper Guinea) shortly. The number of results I have collected so far might be minimal but already my survey findings turn out to be quite insightful. I also provide some statistical data, analysis and relevant context. Follow this link to view the page:

• West African results (part 1)

In addition I also discuss the implications these findings might have for Afro-Diasporans in an attempt to improve proper interpretation of their West African regional scores, in particular for “Ivory Coast/Ghana” and “Benin/Togo” as well as “South-Central Hunter-Gatherers”. One of these implications I will also discuss in greater detail in this blog post:

 “SC Hunter-Gathers” can also be predictive of West African ancestors

• In particular Liberian, Ivorian and Sierra Leonean ancestors might have passed on socalled “Africa South-Central Hunter-Gatherers” DNA markers, which are also present in their own genome. The “Africa South-Central” labeling by AncestryDNA is therefore not to be taken too literally. Despite usually appearing as “low confidence” trace region this still represents a very distinctive type of DNA.

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Map 1 (click to enlarge)

Source: ancestry.com. (text in red added by myself)

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Chart 1 (click to enlarge)

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My West African survey has produced several insightful findings which can be used to improve interpretation of the AncestryDNA results for Afro-Diasporans. Furthermore it  may possibly lead to a better understanding of West African genetics and its (ancient) population migrations. A somewhat conjectural finding but still very intriguing are the so-called “South-Central Hunter-Gatherers” (SCHG) scores I have observed for mainly my Sierra Leonean, Liberian and Ivorian survey participants (on average between 2%-4%, see chart 1). The highest individual scores (2x 6%) were obtained for Liberians. For other West African countries featured in my survey the SCHG group averages so far are below 1% as for most of these countries these SCHG scores were usually absent. However for a few individual Nigerians I did also observe similar SCHG scores in the 2%-4% range. Interestingly especially from southeast Nigeria: Ijaw & Efik persons (see this overview). Despite that these SCHG scores are usually being reported as trace amounts this finding could still have significant meaning.

As can be read in the regional description above (map 1), this SCHG category on AncestryDNA measures a genetical similarity to Pygmy (Mbuti & Baka) samples from Central Africa as well as Khoi-San samples from Southern Africa. Hence why I have labeled this region “Pygmy/San” in my survey. These hunter-gathering groups are very marginalized and small in numbers. But in more ancient times they may have been far more widespread than nowadays. They have been extensively studied. Among other things they are noted for their distinctive genetics. Many important studies have been published on the genetics of these so-called “Hunter-Gatherers” (to be frank I personally do not agree with the choice of this labeling, but soit..). See end of the page for some references to these studies.

Given this genetic distinctiveness it makes it all the more remarkable that a minor but still consistent (so far) genetic similarity to their DNA is to be found among certain groups of West Africans! Obviously my ongoing African Ancestry DNA survey has a quite minimal sample size. It should be obvious therefore that a greater degree of genetic diversity and individual variation might be expected. On the other hand my survey already includes most West African countries and also elsewhere its coverage it already quite extensive. Enabling an evenhanded comparison with for example Central or Southern Africans. Reviewing chart 1 we can verify that “South-Central Hunter-Gatherers” indeed peaks for South Africans as well as Equatorial Guineans. Based no doubt on genuine Khoi-San admixture for the former and genuine Pygmy admixture for the latter. It should be noted that my South African survey participants are mostly Coloureds which explains the extra pronounced degree of these SCHG scores. For Bantu speaking South Africans it is also still very much detectable but on a decreased level (6%-15% instead of 41% for Coloureds, see this overview).

However otherwise it seems practically equal SCHG scores are appearing for Congolese as for Sierra Leoneans, Liberians and Ivorians! While the preliminary group average for Cameroon is even less (see chart 1)! Again my survey sample size is very minimal at this stage. Also it might be that the actual Pygmy admixture for Central Africans is systematically being underestimated by AncestryDNA either because of the samples being used or its algorithm. But still at first sight this finding look quite striking and unexpected. Especially given the “Africa South-Central” labeling by AncestryDNA. See also:

• Central & Southern African AncestryDNA results

It is very tempting to link these (preliminary!) findings to widespread local traditions about the original inhabitants of West Africa (rainforest zone) being dwarfs, in other words Pygmy-like! These nowadays extinct and mythical people are known under various names (Jinna in Liberia; Mandébélé (Senoufo) or Kakatika (Baule) in Ivory Coast; Mmoatia in Ghana). It may not be a coincidence that the highest degree of these SCHG scores seems to occur for Sierra Leone, Liberia and Ivory Coast. While in other West African countries so far this region is either absent or only appearing with a minuscule group average (<0.5%, see chart 1). After all the so-called Guinean rainforest zone is supposedly still at its most densest and pristine in Liberia and surrounding countries.

A similar process might have taken place in that heavily forested area as when Bantu-speaking people started populating Central Africa a few thousand years ago. Causing the Pygmy people to be gradually displaced to the Congolese rain-forest zone. However instead of going completely extinct it seems the DNA of these hunter-gathering populations was partially absorbed by later waves of migrating agricultural peoples in both Central and West Africa. And in that sense these supposedly mythical people still live on and the local traditions about them would in fact be based on historical reality! See also:

• Forest Peoples: Sierra Leone, Liberia and Cote d’Ivoire (Ivory Coast): History of to 1800 (Fanthorpe, 2013)
• House of Stones: Memorial Art of Fifteenth-Century Sierra Leone.
• The People Groups of Liberia (H. Vogel, 2012)
• Existait-il des peuples en Cote d’ Ivoire avant le XVIIIème siècle?
• Mmoatia: Ghanaian Tricksters of the Forest

Again the basis for these findings is quite shakey. Aside from AncestryDNA’s analysis having its inherent flaws, we should for example also take into consideration that during the 1800’s both Sierra Leone and Liberia took in socalled Recaptives, a.k.a. liberated captives from Central Africa. In Liberia therefore the colloquial name for Americo-Liberians is apparently still “Congo’s”. Even when as a group they actually have much more diverse origins (incl. African American & West Indian!). In Sierra Leone it seems people of genuine Congolese origin managed to maintain a separate identity. But otherwise they might also have intermingled with other Recaptives or “native” Sierra Leoneans. I intend to blog about this very fascinating part of the Afro-Diaspora in the near future.

I am just mentioning this circumstance to cover all grounds. After all hypothetically speaking some of these “SCHG” scores could also have been inherited from Liberian/Sierra Leonean “Congo’s”. During my research I have always attempted to verify to the best of my capabilities the exact background of each of my survey participants. And precisely because of these potential complications in regards to the highly diverse origins of Krio and Americo-Liberians I was especially keen on questioning my Liberian and Sierra Leonean survey participants. I have not come across any strong indication that any of my West African survey participants was fully Krio or Americo-Liberian. However several persons (incl. 3 Ivorians and 3 Liberians) did mention distant Krio/Americo-Liberian lineage. Given the generational dilution involved and the lack of additional indications of substantial Central African DNA (judging by minimal group averages for “Cameroon/Congo” & “Southeastern Bantu”) I am inclined to think this “Congo” scenario might not be the primary cause for the increased SCHG scores I have observed among a subset of my West African samples. Still I cannot rule it out either. See also:

• Country versus Congo: A Liberian Cultural Metaphor (Liberianpatriot, 2006)
• Talking Points: For Liberia a New Leader, and a Ray of Hope (NY Times, 2006)
• Sierra Leone Congo Town Association (SLCTA, 2007)

Obviously more research is needed to get to the bottom of this issue. Either way it will be a remarkable finding if found to be legitimate. Whether these SCHG scores are to be traced back to Congolese Recaptives or to the very first inhabitants of West Africa’s rainforest zone! Personally I am not aware of similar research findings having been published yet. At least not in direct relation to an increased incidence of Hunter-Gatherer DNA to be found specifically among Sierra Leoneans, Liberians and Ivorians. However several studies have already remarked upon the minor presence of Hunter-Gather DNA across Africa, and also within West Africa. Most recently a very fascinating and relevant study came out in 2017. Basing itself on the ancient DNA remains (genome wide) of 16 Africans it stated that:

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“the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions“. (Skoglund et al., 2017)

But also that:

“present-day western Africans harbor ancestry from a basal African lineage that contributed more to the Mende than it did to the Yoruba“. (Skoglund et al., 2017)

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The ancient DNA was however only available for Africans from East & Southern Africa. Ideally ancient West African DNA is needed to gain more insight. Rain-forested areas are of course far from perfect for preserving ancient DNA remains. But who knows in the near future we will learn more about the earliest inhabitants of West Africa! And my survey findings might prove to have been tantalizing previews 😉

Further reading:

• Reconstructing Prehistoric African Population Structure (Skoglund et al., 2017)
• Admixture into and within sub-Saharan Africa (Busby et al., 2016)
• The African Genome Variation Project shapes medical genetics in Africa. (Gurdasani et al., 2015)
• Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection (Hsieh et al., 2015)
• Sociocultural Behavior, Sex-Biased Admixture, and Effective Population Sizes in Central African Pygmies and Non-Pygmies (Verdu et al, 2013)
• The genetic prehistory of southern Africa (Pickrell et al., 2012)
• Complete Khoi-San and Bantu genomes from southern Africa (Schuster et al., 2010)
• Anthropological Implications of Sickle Cell Gene (Livingston, 1958)