Reconstruction of what a Neanderthal may have looked like in the Museum für Naturkunde, Berlin, Germany

The Widespread Appearance of Neanderthal DNA: Africans Have It Too

It has long been argued that Neanderthal derived DNA is found in all non-Africans. As a result, it has been assumed that Africans fail to carry Neanderthal ancestry… even though Neanderthal skeletons have been found in North Africa at Jebel Ighoud and Haua Fteah.

The Percentage of Neanderthal Ancestry in Africans

The idea that Africans fail to carry Neanderthal DNA has recently been proven as wrong. Marc Haber, a British geneticist from the Wellcome Trust Sanger Institute in Hinxton, has found that the Touboo in Chad and the Amhara in Ethiopia carry Neanderthal genes. Whereas Eurasians carry ~2% Neanderthal ancestry, Ethiopians carry ~1% Neanderthal ancestry, and Central Africans carried ~0.5% Neanderthal ancestry.

Haber maintains that Africans who carry Neanderthal DNA show gene flow from Eurasians. The detectable Neanderthal DNA in Africans is found among Africans that carry the R1b haplogroup.

Male and female Homo neanderthalensis in the Neanderthal Museum, Mettmann, Germany.

Male and female Homo neanderthalensis in the Neanderthal Museum, Mettmann, Germany. (UNiesert/Frank Vincentz/ CC BY SA 3.0 )

Haber believes that the R1b haplogroup penetrated Central Africa via two migrations. The first migration he believes took place 6000 years ago (6kya), and the second migration around 3kya. The major problem with this theory is that there is no archaeological evidence of a back migration from Eurasia to Africa.

The discovery of Eurasian "admixture" among Africans is not a recent discovery. Pickrell et al estimated Eurasian ancestry among Africans from East and South Africa ranged from 2.2-50% and that the Mande people carry 2% Eurasian admixture. This supports the original claim of the authors of the Mota article – i.e. the claim that as much as 6–7% of the ancestry of West and Central African groups was "Eurasian" was not an error.

There are numerous populations in East, South, and West Africa that carry Eurasian admixture. The highest frequency of R1 is found in Western Eurasia. Cruciani et al claim that the pristine form of R1*M173 was found in Africa. The frequency of Y-chromosome R1*-M173 in Africa ranges between 7-95% and Coia et al said that R1-M173 averages 39.5% in Africa. R haplogroups are characterized by R1-M207/M173 genetic background. The Eurasian R haplogroups in Africa include: R1-M269, R-V88, R-L754 (R1b1a) and RL278 (R1b1).

Autosomal researches for the genetic admixture in Eurasian continent (Dodecad project).

Autosomal researches for the genetic admixture in Eurasian continent (Dodecad project). (CC BY SA 4.0)

Y-chromosome V88 (R1b1a) has its highest frequency among Chadic speakers, while the carriers of V88 among Niger-Congo speakers (predominately Bantu people) range between 2-66% (Cruciani et al, 2010; Bernielle-Lee et al, 2009). Haplogroup V88 includes the mutations M18, V35, and V7. Cruciani et al (2010) revealed that R-V88 is also carried by Eurasians - including the distinctive mutations M18, V35, and V7.

Haplogroup R1b1* is found in Africa at various frequencies. Berniell-Lee et al (2009) found in their study that 5.2% carried Rb1* (RL278). The frequency of R1b1* among the Bantu ranged from 2-20%. The bearers of R1b1* among the Pygmy populations ranged from 1-25% (Berniell-Lee et al, 2009). The frequency of RL278 among Guinea-Bissau populations was 12%. The Toubou, Laal, and Sara have frequencies between 20%-34% of RL754 (R1b1a).

Bantu farmers near Kismaayo in November 1993. (Public Domain)

Neanderthal Tools

Neanderthals used Mousterian tools. These tools were also being used in Africa as early as 130kya. This places Neanderthals in North Africa.

The Neanderthal tools found at Jebel Ighoud and Haua Fteah resemble contemporaneous European Neanderthal tools. The presence of Mousterian tools suggest that Neanderthals mixed with Africans because we know that anatomically modern humans were living in the area at the time.

The North African Neanderthal people used the common Levoiso-Mousterian tool kit originally discovered in Europe. Ki-Zerbo said the Neanderthal skeletons came from Djebel Irhoud and El Guettar in Morocco. Later Neanderthal people used the Aterian tool kit. It was probably in Morocco that Neanderthal and Khoisan interacted.

Mousterian tools made by Neanderthals.

Mousterian tools made by Neanderthals. (Didier Descouens/CC BY SA 4.0)

Carleton S. Coon, in The Living Races of Man (1965), Anthropology A to Z (1963), and The Races of Europe (1939), claimed that the Khoisan had formerly lived in North Africa from the Atlas Mountains down into the Fezzan and Sahel. Coon also said that the “The Duwwud also look like Hottentots. Other partly Bushman and partly Negroid people are also to be found in the Sahara.” Coon maintains that the Haritan also include ancient South African Khoisan (SAK) population elements.

Up until M. Gallego Llorente’s Mota man article and the Haber article, researchers claimed that Africans had no relationship to the Neanderthals. But Prufer et al found that the Khoisan share more alleles with Altaic Neanderthal than Denisova.

Earlier depiction of a Neanderthal.

Earlier depiction of a Neanderthal. (paleolithicpersonhood)

Haber has noted that derived DNA in all non-Africans is more closely related to Neanderthals from the Caucasus: Alraic Neanderthal(s).

In the Supplemental section of Prufer et al’s work, there is considerable discussion of the relationship between Neanderthal and Khoisan. In relation to the Altaic Neanderthal, non-Africans have a lower divergence rate than Africans - between 10-20%. Prufer et al (2013) note little statistical difference between non-African and African divergence.

An interesting finding made by Prufer et al (2013) was that Altaic Neanderthal and Denisova are estimated to have similar split times. However, the divergence estimates for African Khoisan-Mandekan and Altaic is younger than the split between Africans and Denisova archaic individuals and modern African individuals. The split times between the Khoisan and Mandekan may be explained by the presence of AF-24 haplotype in West Africa.

Khoisan engaged in roasting grasshoppers on grills. 1805. Aquatint by Samuel Daniell.

Khoisan engaged in roasting grasshoppers on grills. 1805. Aquatint by Samuel Daniell. (Public Domain)

Prufer et al (2013) detected a relationship between Neanderthals and the Mandekan. This is not surprising now that we know the Mandekan have 2% Eurasian ancestry, according to Pickerell et al.

In summary, diverse African populations carry Eurasian ancestry. As a result, researchers will probably find more Africans that carry Neanderthal ancestry in the future.

Top Image: Reconstruction of what a Neanderthal may have looked like in the Museum für Naturkunde, Berlin, Germany. Source: כ.אלון/ CC BY SA 3.0

By Clyde Winters


CoiaV, G Destro-Bisol, F Verginelli, C Battaggia, I Boschi, F Cruciani, G Spedini, D Comas and F Calafell, 2005. Brief communication: mtDNA variation in North Cameroon: lack of Asian lineages and implications for back migration from Asia to sub-Saharan Africa, American Journal Physical Anthropology.

Ki-Zerbo,J. (1981). Unesco General History of Africa Vol. 1: Methodology and African Prehistory (1981), pg.572.

Joseph K. Pickrell, Nick Patterson, Po-Ru Loh, Mark Lipson, Bonnie Berger, Mark Stoneking, Brigitte Pakendorf, and David Reich. (2014). Ancient west Eurasian ancestry in southern and eastern Africa. PNAS 2014 111 (7) 2632-2637.

M. Gallego Llorente, E. R. Jones, A. Eriksson, V. Siska, K. W. Arthur, J. W. Arthur, M. C. Curtis, J. T. Stock, M. Coltorti, P. Pieruccini, S. Stretton, F. Brock, T. Higham, Y. Park, M. Hofreiter, D. G. Bradley, J. Bhak, R. Pinhasi, A. Manica.Erratum for the Report "Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa" (previously titled "Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent") by Science. 2016 Feb 19;351(6275). pii: aaf3945. doi: 10.1126/science. aaf3945.

Kay Pruler, Racimo, F., Patterson,N et al. (2014). The complete genome sequences of Neanderthal from the Altai, Mountains. Nature, 505/7481: 43-9. doi .10.1038/ Nature 12881.Epub.2013. Dec.18.

Scozzari, R, Massaia,A, Trombatta,B. et al.(2014). An unbiased resource of novel SNP markers provides a new chronology for human Y-chromosome and reveals a deep phylogenetic structure in Africa. Genome Research, January 6,2014, doi: 10.1101/gr./60785.113.


No one in the know has ever stated there was no Neanderthal genetics on African populations. To quote Neanderthal expert John Hawks on Neanderthals in Africa: "We don't know if it's zero but it's much less" [than non Africans].
Of course, he is talking about Sub Saharan Africans and not those Africans living north of the Sahara who have about the same distribution of Neanderthal genes as the rest of us.

It is good however to see you finally joining the rest of the Anthropological community though. It wasn't too long ago that you flat out denied that humans and Neanderthals ever interbred at all.

Clyde Winters's picture

Granted Hawks may have felt the Neanderthals mixed with AMH, but the Max Plank Institute popularized the idea that only non-Africans carried Neanderthal genes.

The Max Plank Institute noted on its website that: “We knew from Neanderthal DNA found in the genomes of humans outside Africa that Neanderthals and humans have interbred. This interbreeding is estimated to have happened less than 65,000 years ago, around the time that modern human populations spread across Eurasia from Africa. We now find evidence for a modern human contribution to the Neanderthal genome. This is likely the result of much earlier interbreeding”, says Sergi Castellano from the Max Planck Institute for Evolutionary Anthropology

I suspect that races flowed back and forth mating along the way as ice ages, droughts and the like came and went. Not really a surprise that Neanderthals would be part of the mix.

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