The population genetic structure of Northeast Africa

The major frontier in the understanding of human population genetic structure in the next five years is going to be Africa. There are several reasons for this.

The ‘standard model’ of late has been that a group of humans left eastern Africa ~50,000 years ago, and swept across the world in one go. Though Africa itself was often an afterthought in that discussion, it now seems that there was a lot of demographic history that occurred after the “Out of Africa” event within Africa. Second, the whole picture outside of Africa and within Africa has been greatly complexified over the last decade.

The idea that modern humans, defined as the descendants of anatomically modern populations present in Africa ~100,000 years, only ventured out of the continent a bit before 50,000 years ago, is now rather shaky. There are several fossils from eastern Asia which seem older. But just as interestingly, there are Neanderthal genomic results from Altai populations which indicate an early admixture with an anatomically modern human population basal or almost basal to all extant groups. This means that this lineage is an outgroup to modern Africans and non-Africans, or, it was part of the original diversification of African lineages (one of which was the primary ancestor for non-Africans) ~200,000 years ago, give or take.

And that is the second major issue of complexification. Population structure within Africa, of both archaic and modern lineages, is going to be a major topic of interest. Just as non-Africans have admixture from highly diverged ‘archaic’ lineages (Neanderthals and Denisovans), some scholars have been arguing for years that Sub-Saharan Africans, especially those from “hunter-gatherer” lineages, have similar admixture. The most recent work seems to support the contention of very deep structure within Africa.

But much of this structure has been elided by the reality of the Bantu expansion. Starting 3,000 years ago a wave of agriculturalists from the environs of modern Cameroon pushed eastward and southward. Today the Bantu languages are dominant from the Gulf of Guinea to South Africa. This is a major problem in trying to understand the genetic variation which served as the context for the origin of modern humans, because the older structure has been overlain or replaced across much of its geographic extent. Though it is correct that modern Africans have the most genetic diversity one the whole, the between group diversity for Bantus is quite low, because they descend from a common population in the recent past.

But there are peoples within Africa who may preserve some of the ancestry of groups before the arrival of the Bantus. A new paper in PLOS GENETICS uses a very dense marker set to analyze Sudanese populations in particular. These groups are of interest because they seem reasonably distant from West Africans, but some of them do not have much Eurasian ancestry either. Like Mbuti Pygmies, or Kalahari Bushmen, they may therefore be one of the descendent groups from those which flourished within Africa when the ancestors of non-Africans left.

It’s called Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. It’s an uncorrected proof. Kind of like a preprint. So it may change. But here is the abstract:

…We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400–200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.

The Eurasian admixture is well known. So not a big surprise. But I do think that this paper, like most, is somewhat biased toward detection of the most recent admixture event.

There are several Coptic samples in this data set. These individuals are descendants of recent migrants to the Sudan from Egypt. Because they are Christian, and resident in northern Sudan (I believe sampled in Khartoum), they are by necessity endogamous (marriage to a Muslim would have resulted in the result being raised as Muslim). It is no surprise that they are genetically similar to the Egyptian Muslim sample. But interestingly like the Egyptian Muslims they have a substantial minority of Nilotic Sub-Saharan African ancestry.

In much of the paper the admixture between Eurasian and Sudanic peoples is dated to after the rise of Islam. This is reasonable. For various reasons I am not totally clear on the emergence of Islam resulted in a far greater interconnectedness between Sub-Saharan Africa and North Africa & West Asia. But as non-Muslims Egyptian Christians, Copts, would not be part of the genetic admixture which slavery produced across the Middle East. Non-Muslim minorities tend to be rather less cosmopolitan than their Muslim neighbors. Perhaps the situation was different in Egypt, with Copts being a majority up until 1000 A.D. But, another factor may be that there were older pulses of admixture dating back to antiquity which the LD decay methods are missing (notice that Egyptians have West African ancestry which Copts lack).

The second major issue in this paper is that some groups, such as the Nuer, show no evidence of Eurasian admixture. This is not true of all Nilotic peoples. The Masai of Kenya for example have clear Eurasian admixture. But if indisputably Nilotic groups in southern Sudan lack it, it suggests that this occurred in East Africa due to mixing with Cushitic groups, some of whom, such as the Somalis, are also pastoralists.

Remember that Khoisan in southern Africa have Eurasian ancestry through the migration of Nilotic pastoralists. And yet somehow the Nilotic peoples of the Sudan, who have lived near to Cushitic and Semitic peoples with copious Eurasian admixture, lack that element. Similarly, the Bantus swept from Cameroon to the highlands of South African in 1,300 years, but were totally ineffectual at penetrating the Sudd. What this illustrates is that when it comes to human gene flow simple considerations of distance “as the crow flies” is not so important in many cases. Rather, cultures occupy territory in a geographically patchy manner, constrained by ecology and local human geography.

This reiterates the likely importance of ancient DNA in understanding African prehistory, and therefore, the prehistory of humankind as a whole.

Citation: Hollfelder N, Schlebusch CM, Günther T, Babiker H, Hassan HY, Jakobsson M (2017) Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. PLoS Genet 13(8): e1006976. https://doi.org/10.1371/journal.pgen.1006976

 

6 thoughts on “The population genetic structure of Northeast Africa

  1. “But interestingly like the Egyptian Muslims they have a substantial minority of Nilotic Sub-Saharan African ancestry.”

    “notice that Egyptians have West African ancestry which Copts lack”

    There are Coptic Christians in Ethiopia to this day. A pre-Islamic Coptic Christian community in Sudan would explain this pattern.

  2. Before Islam the Nubians up the Nile had followed the Copts to Christianity. There survives, in manuscript, Christian literature translated into the Nubian language using the Graeco-Coptic alphabet. There were a few Nubian kingdoms up to the seventh century; after the dislocations of the Umayyad takeover of Egypt (‘Amr bin al-‘As, ‘Abd al-‘Aziz bin Marwan) the Makuria kingdom seems to have emerged on top.

    I expect the Christian population in Sudan to be mixed Coptic and Nubian, with negligible West-African.

  3. There are Coptic Christians in Ethiopia to this day. A pre-Islamic Coptic Christian community in Sudan would explain this pattern.

    this community migrated in the last 200 years.

    also, just because xtians are miasophyte they aren’t coptic. copts just means egyptian christians (who are miasophyte by and large).

  4. Razib, I only brought in Ethiopian Christians to show that it is plausible that there were some local Christians in Sudan 200 years ago, that mixed with Copts when they migrated from Egypt.

  5. Late to comment on this, but was thinking about this aspect:

    Razib: Though it is correct that modern Africans have the most genetic diversity one the whole, the between group diversity for Bantus is quite low, because they descend from a common population in the recent past.

    How does this square with Busby’s finding of high levels of TVD (haplotype copying) structure among Niger-Congo speaking populations – https://elifesciences.org/articles/15266#fig2?

    If you take as an extreme case, the Mandenka group from West Africa and Kenyan Bantu groups, the TVD value is around ~760, or taking Yoruba from Kenyan Bantu groups ~600. Comparing Bantu from West Central Africa to Kenyan Bantu groups ~550.

    This is actually quite high when we compare it to comparable values within Eurasia, with TVD separation CEU-GBR ~50, CEU-IBS ~107, TSI-IBS ~87, CEU-FIN ~340, CEU-GIH ~463, CEU-JPT ~711, CHB-JPT ~193.

    In the old school mode, my model of African differentiation was that Fst was low as populations just hadn’t been through many bottlenecks that increase Fst. Assuming a recent expansion makes sense as another explanation for low Fst… but how does this fit with what looks like extensive haplotype structure, seemingly more so than extant between Eurasian populations with what looks like older and deeper language divergence?

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