The original Africans are Neandertals (in part)

By Razib Khan | October 18, 2012 2:10 am

In antiquity what we term Tunisia and Tripolitania were part of “African province.” Just as “Asia” originally referred to the margins of what we now term Asia (regions of Anatolia), so “Africa” originally denoted a subset of the northwest fringe of the continent which became Africa. In biogeography this segment of the continent is actually not part of Africa (it is part of the Palearctic ecozone). And yet the vicissitudes of early modern cartography are such that continent had to be bounded by water on as many sides as possible, and today we clumsily make recourse to the term “Sub-Saharan Africa” to distinguish that region from the northern littoral, which is really part of the Mediterranean world.

This context is somewhat relevant when we evaluate a new PLoS ONE paper, North African Populations Carry the Signature of Admixture with Neandertals. This paper makes little sense unless you’ve read an earlier one, Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. In that paper authors make the case that a majority of the ancestry of modern Maghrebis seems to date back to before the Neolithic, from a late Pleistocene migration of Eurasians. Though the indigenous North African element is naturally somewhat diverged from other West Eurasian components, it nevertheless comes out of the West Eurasian milieu, on the order of 10-40,000 years before the present.


In the PLoS ONE paper the authors show that the Neandertal admixture in the modern Mahgrebis is consistent with the ancient event on the order of ~60,000 years before the present. I was curious to see that the paper was careful to observe that the balance of scholarship is still shifting toward a Eurasian admixture model, instead of ancient population structure within Africa. And these findings push it further in that direction, in particular showing that Neandertal admixture is not contingent upon European or West Asian admixture, but was found in large proportions even among predominantly North African groups.

There are some qualms I have about the number of SNPs, but I can’t say much more until I try and replicate (it may be that 50-100,000 SNPs is sufficient for their questions). What I am confused about is what they expected. After all, it is well known that the peoples of North Africa are part of greater Eurasia. What Sub-Saharan African admixture exists seems to be mostly a function of the Islamic era. As such, we’d expect to see Neandertal admixture, in particular because a previous group already argued that the indigenous substrate of North Africa derives from an Ice Age migration out of Eurasia.

More importantly the “true answer” for the question of weather the affinity to Neandertals among Eurasians is due to ancient African population structure (so that the African ancestors of Eurasians happened to be closer to Neandertals than the Africans left behind) will require Sub-Saharan data sets. With whole genome coverage and thicker sampling of the continent I’m moderately optimistic. I do know that there is some evidence of Neandertal admixture in Kenyan Masai. This is probably another clue to an ancient back migration rate, though at some point someone will try and see where African and non-African Neandertal ancestry relate to each other on a phylogenetic true (preliminary data I’ve heard about seem to indicate that it’s intrusive to the continent).

CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: Neanderthal
  • Joshua Gatera

    ” What Sub-Saharan African admixture exists seems to be mostly a function of the Islamic era.”

    There is no sufficient amount of evidence that would suggest that the bulk of African ancestry (which is in it self not a homogenous cluster) in North Africa dates back to the Islamic era. Are you implying slavery? North Africans are approximately 1/3 African, and there’s no reason not to assume that the majority of their African ancestry was autochthonous to the region prior to any Western Eurasian gene-flow into the continent. The fact that both Berbers and Egyptians speak African languages, carry African uniparental markers at moderate-predominant frequencies, and are consistently 1/3 autosomally African implies a much more ancient indigenous Tropical African presence in the Maghreb and most definitely the Nile Valley.

    As you should already know, ROLLOFF functions most effectively with populations who’ve experienced single admixture events in the past (African-Americans for example), not populations who’ve either experienced admixture at various times in history, or exchange gene-flow at a consistent pace. The aforementioned therefore perfectly explains the results of Henn et al. 2012.

    The 1,200 BP admixture date for the southern Moroccan population realistically corresponds to the most recent admixture event in which excess African admixture was assimilated into this particular Berber population. The southern Moroccan data set differs from other Maghrebi samples due to the presence of certain individuals, who are autosmally more African than the average North African. These outliers could be explained by one of two or both of the following scenerios, 1) they’re are the descendants of West African slaves or 2) they’re the descendants of indigenous Niger-Kordofanian speaking oasis dwellers who inhabited the region prior to the expansion of Berber speaking peoples in the past 2,000 years. Regardless, the initial admixture event between the African and Western Eurasian ancestors of modern Berbers likely predates the aforesaid admixture event by thousands of years.

    The relatively recent date for “Nilotic admixture” in Egypt is easily explainable. Egypt, i.e. the Lower Nile Valley, is not separated from “Sub-Sahara Africa”, so therefore gene-flow between the Delta and Tropical Africa is consistent throughout history. The aforementioned reality skews the results of programs like ROLLOFF which only work effectively in particular simplified scenarios.

    I would suggest you read the following study on mtDNA in North Africa, in particular Tunisia.

    http://www.ncbi.nlm.nih.gov/pubmed/21082907

    The inclusion of NE African samples will likely shed more light on the biological affinities of North Africans; all North Africans share a NE African signature of admixture, supporting the role of Afroasiatic speaking NE Africans in shaping the bioanthropological landscape of North Africa and SW Asia.

  • Onur

    Yes, the results of admixture dating programs (e.g., ROLLOFF) should be taken with a grain of salt. They tend to give too recent dates in the cases of multiple and/or continuous dating events between populations. Such programs are only good at dating admixtures between populations that occurred in a single and non-continuous event such as the cases of African-Americans and many Latin American groups.

    Also, according to the ADMIXTURE results of Henn et al. 2012, Tunisian Berbers are very similar to the other tested apparently litoral North Africans (thus Saharawis, southern Moroccans and a portion of Egyptians, Libyans and Algerians are excluded) in their proportion of Negroid ancestry (Tunisian Berbers certainly have Negroid ancestry; it is clear from K=2):

    http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002397?imageURI=info:doi/10.1371/journal.pgen.1002397.g001

    So, the Negroid ancestry in North Africans should be mostly pre-Islamic. It clearly follows a geographical pattern (increases from north to south) and there is no clear ethno-linguistic pattern according to the ADMIXTURE results of Henn et al. 2012.

  • https://plus.google.com/109962494182694679780/posts Razib Khan

    There is no sufficient amount of evidence that would suggest that the bulk of African ancestry (which is in it self not a homogenous cluster) in North Africa dates back to the Islamic era.

    look the chromosome deconvolution. it looks pretty obviously mostly recent admixture to me (the ‘segments’ have not broken down yet, like they have in south asians).

  • Onur

    look the chromosome deconvolution. it looks pretty obviously mostly recent admixture to me (the ‘segments’ have not broken down yet, like they have in south asians).

    The question to be answered is: how recent is it? It exists in very similar levels in Berber and Arabic speaking North Africans of similar latitudes according to the ADMIXTURE results of Henn et al. 2012, despite the fact that extant Berber populations such as Tunisian Berbers were significantly isolated from other populations during the Islamic era (clear from the weird results of Tunisian Berbers at higher Ks). So the Negroid ancestry is probably mostly pre-Islamic in North Africa.

  • https://plus.google.com/109962494182694679780/posts Razib Khan

    So the Negroid ancestry is probably mostly pre-Islamic in North Africa.

    could be roman. doubt it is as old as 4,000 years. recombination would have chopped stuff up a lot more. probably some really old stuff, “north african” component is african shifted last i checked. but not too much.

  • Joshua Gatera

    “could be roman. doubt it is as old as 4,000 years. recombination would have chopped stuff up a lot more. probably some really old stuff, “north african” component is african shifted last i checked. but not too much.”

    Roman slaves were primarily either fellow Romans or at least Italics, other Europeans, or natives from Roman SW Asia and coastal North Africa; Sub-Saharan Africans were a really small minority indeed.

    I haven’t done that much research on chromosome deconvolution, but couldn’t the larger segments in North Africans be due to either continuous gene-flow, i.e. Egyptians, or multiple episodes of admixture, Maghrebians for example. Admixture in North Africa is much more consistent and dynamic than South Asia; North Africa’s geographic location between Tropical Africa, Europe, and SW Asia has facilitated a steady flow of gene-flow, even into the historic era.

    The “North African” component is an admixed cluster, it’s typically moderately African admixed. For example, according to Treemix about 27% of the “NW African” cluster from Dodecad is derived from a population similar to modern West Africans. Interestingly, the “SW Asian” (18%) and some of the other southern Western Eurasian clusters (7%) also seem to contain traces of African-like gene-flow.

    http://dienekes.blogspot.com/2012/03/using-treemix-with-admixture-components.html

  • https://plus.google.com/109962494182694679780/posts Razib Khan

    #6, i’ll have to look at the requisite results in more detail. will get back to you later….

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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