Nilo-Saharan component

Scientific Reports 5, Article number: 9996 doi:10.1038/srep09996

The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape

Begoña Dobon et al.

East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations.

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Out-of-Asia and Into-Africa (?)

The publication of version 2 of the Pickrell et al. paper on South Africa is as good an opportunity as any to discuss something anew something that I've been hinting at for some time now.

First things first: Pickrell et al. find West Eurasian admixture in the Hadza and Sandawe:

Both of these are consistent with west Eurasian (either European or, more likely, Arabian), gene  ow into these populations. To further examine this, we turned to ROLLOFF. We used Dinka and French as representatives of the mixing populations (since date estimates are robust to improperly speci ed reference populations). The results are shown in Supplementary Figure S22. Both populations show a detectable curve, though the signal is much stronger in the Sandawe than in the Hadza. The implied dates are 89 generations ( 2500 years) ago for the Hadza and 66 generations ( 2000 years) ago for the Sandawe. These are qualitatively similar signals to those seen by Pagani et al. [65] in Ethiopian populations.

The presence of West Eurasian ancestry in the Hadza and Sandawe was anticipated in my world9 calculator, where both these populations were shown to possess Caucasoid admixture entirely of the "Southern" component. This component peaks in Arabia, and is unaccompanied by any other type of Caucasoid element really only there. So, it is very likely that there was indeed such a migration into East Africa. What Pickrell et al. have added to our knowledge is that this migration is fairly recent.

Razib repeats one of his favorite analogies about events taking place in Africa after the pyramids were rising in Egypt. I will use a Greek epic analogy, by pointing out that at the time that Memnon the Ethiopian led his contingent to the aid of Troy, these events had not yet taken place.

Depictions of Memnon changed during classical antiquity, from a Caucasoid norm, as in the red-figure kylix on the left, to a more stereotypically African form by Roman times. This is sometimes taken as simply a consequence of the fact that the ancient Greeks were unfamiliar with African phenotypes, and changed their portraiture of Ethiopians as they became more familiar with them during Hellenistic and Roman times.

But, the very name of Aithiopes first attested in Homer (8th c. BC) attests to the fact that the Greeks were aware of what Ethiopians looked like, at least in terms of their dark pigmentation. And, there are depictions of Africans in classical art, as well as a famous quote in Herodotus which makes abundantly clear that he was aware of the physical characteristics of what we would call "Sub-Saharan Africans".

We don't only need to look at Ethiopia for evidence of the strange events that were taking place in Africa during classical antiquity. A great punch-in-the-face reminder of these events comes from the much later Greek author Pausanias who records that a statue of Athena he observed in Attica had blue eyes which he ascribed to the Libyan origin of her myth. How strange it seems to us that one would look to Africa for an explanation for the blue-eyed goddess.

Libya was of course, the ancient name for Africa, and especially Africa west of Egypt, what we might call Berber-land. Egypt was often reckoned by the ancient as part of Asia. In any case, Pausanias' strange assertion finds support in the Egyptian monuments that really do depict the ancient Libyans (=Berbers) as Caucasoid, and often lighter than Middle Eastern people. This would also accord with Coon's famous discovery of "Irish-like" Berbers among the Riffians; I often dismissed such assertions, but in a landscape of human prehistory that is getting stranger by the month, it is worth digging for gold nuggets in old texts.

A recent study claimed that there was back-to-Africa gene flow into Eurasia more than 12,000 years ago. On the other hand, both HAPMIX and StepPCO estimate the admixture in Mozabite Berbers as taking place ~120 generations ago, or, about 3.5kya assuming a generation length of 29 years as Patterson et al. (2012) do. I have observed that rolloff produces generally lower dates than these two methods, so I would not be surprised if that is the case here as well.

It seems that as recently as a few thousand years ago, West Eurasian populations were moving into Africa from both north and east. As Pickrell et al. have discovered, their eastern branch also contributed to South Africans, tagging along the dispersal of pastoralists from East-to-South Africa.

The big question is: did West and Central Africa escape this population movement?

I seriously suspect that it did not. I base that assertion on several arguments, of varying strength:

1. Why would they? If they inundated East and North Africa, why would they not venture further?
2. Living Sub-Saharan African farmers are not symmetrically related to West and East Eurasians: they are closer to the former. West Eurasian back-migration would explain this phenomenon.
3. The Great Event in Sub-Saharan Africa was doubtlessly the Bantu explosion, and it is a curious coincidence that this took place precisely close to the time of these events
4. The Iwo Eleru crania from Nigeria are of late Pleistocene age, archaic in character, and unlike modern West Africans. Something did happen in West Africa over the course of, say, the last 10,000 years

And, I always try to remind myself of the Kiffians and Tenerians. I have not seen any follow-up work on them, but if anyone has an ancient DNA lab, I'd think they would be prime candidates for a study.

Speaking of ancient DNA, this unexpected archaeogenetic study from the University of Khartoum, hints at important changes in Africa:

The area known today as Sudan may have been the scene of pivotal human evolutionary events, both as a corridor for ancient and modern migrations, as well as the venue of crucial past cultural evolution. Several questions pertaining to the pattern of succession of the different groups in early Sudan have been raised. To shed light on these aspects, ancient DNA (aDNA) and present DNA collection were made and studied using Y-chromosome markers for aDNA, and Y-chromosome and mtDNA markers for present DNA. Bone samples from different skeletal elements of burial sites from Neolithic, Meroitic, Post-Meroitic and Christian periods in Sudan were collected from Sudan National Museum. aDNA extraction was successful in 35 out of 76 samples, PCR was performed for sex determination using Amelogenin marker. Fourteen samples were females and 19 were males. To generate Y-chromosome specific haplogroups A-M13, B-M60, F-M89 and Y Alu Polymorphism (YAP) markers, which define the deep ancestral haplotypes in the phylogenetic tree of Y-chromosome were used. Haplogroups A-M13 was found at high frequencies among Neolithic samples. Haplogroup F-M89 and YAP appeared to be more frequent among Meroitic, Post-Meroitic and Christian periods. Haplogroup B-M60 was not observed in the sample analyzed.

I was reminded of it recently when this curious abstract came up, which I still believe is missing a zero somewhere, but these days you never know.

Evidence that Sub-Saharan Africans too have experienced gene flow from West Eurasians occasionally comes up, but formal tests of admixture, e.g., f3(Yoruba; San, French) usually do not achieve significance. But, we must be cautious: South Africans do appear admixed between San and East Africans, but this is a consequence of the fact that admixture is recent, leaving a trail of populations of varying East African ancestry, and the San still exist and can serve as one pole in a comparison of admixture.

David Reich has hinted at dual origins for West Africans. I am looking forward to learning what he means by it, but I would not be surprised if it involves admixture between a Eurasian-like population with a Palaeoafrican population of indigenous West African hunter-gatherers.

In any case, ex Africa semper aliquid novi even today. But, interdum, aliquid novum in Africam.

UPDATE: Pickrell and co-authors discuss their paper here.

Clusters Galore analysis of East Africans

I have included the new data from Pagani et al. (2012) together with various other East African datasets available to me, including various East African Dodecad Project participants.

The first four PCA dimensions can be seen below:

Project participants can find their co-ordinates in the first four dimensions below:

I have also run MCLUST over the first 4 dimensions, which resulted in 12 clusters inferred:

All Project participants fall in the expected clusters, so there is no need to report any individual clustering results.

Assessing East Africans of Pagani et al. (2012) using 'weac2'

Thanks to the publication of new data from Pagani et al. (2012), we now have 235 more individuals from East Africa, mainly Ethiopians, but also Somalis and South Sudanese with dense genotype data.

Naturally, I wanted to make sure that everything was in order, so I applied the 'weac2' calculator on the new data. Here are the normalized median admixture proportions:

I have also created population portraits for the 12 different populations, which appear to show rather homogeneous samples.

Here are the descriptions of the data from the original paper:

The populations sampled (numbers) were the Semitic-speaking Amhara (26) and Tigray (21); the Cushitic-speaking Oromo (21), Ethiopian Somali (17), and Afar (12); the Omotic-speaking Ari Cultivators (24), Ari Blacksmiths (17), and Wolayta (8); and the Nilotic-speaking Gumuz (19) and Anuak (23). In addition to these groups, we also generated South Sudanese data from mixed populations (24) and Somali data from Somali populations (23).

Newer versions of the Dodecad tools will of course take into account the new samples, which ought to  help better define the "East_African" component that often arises at higher levels of detail.

And, of course kudos to all researchers who make their data publicly available and hence provide genome bloggers such as myself with much appreciated "fuel" for their inquiries.

Cranial nonmetric traits of Garamantes

Am J Phys Anthropol DOI: 10.1002/ajpa.21645


Sahara: Barrier or corridor? Nonmetric cranial traits and biological affinities of North African late holocene populations

Efthymia Nikita et al.

The Garamantes flourished in southwestern Libya, in the core of the Sahara Desert ∼3,000 years ago and largely controlled trans-Saharan trade. Their biological affinities to other North African populations, including the Egyptian, Algerian, Tunisian and Sudanese, roughly contemporary to them, are examined by means of cranial nonmetric traits using the Mean Measure of Divergence and Mahalanobis D2 distance. The aim is to shed light on the extent to which the Sahara Desert inhibited extensive population movements and gene flow. Our results show that the Garamantes possess distant affinities to their neighbors. This relationship may be due to the Central Sahara forming a barrier among groups, despite the archaeological evidence for extended networks of contact. The role of the Sahara as a barrier is further corroborated by the significant correlation between the Mahalanobis D2 distance and geographic distance between the Garamantes and the other populations under study. In contrast, no clear pattern was observed when all North African populations were examined, indicating that there was no uniform gene flow in the region.

Link

Y chromosomes of Sudanese

American Journal of Physical Anthropology

Y-chromosome variation among Sudanese: Restricted gene flow, concordance with language, geography, and history

Hisham Y. Hassan et al.

Abstract

We study the major levels of Y-chromosome haplogroup variation in 15 Sudanese populations by typing major Y-haplogroups in 445 unrelated males representing the three linguistic families in Sudan. Our analysis shows Sudanese populations fall into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 7.9, 34.4, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur mainly in Nilo-Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel tests reveal a strong correlation between genetic and linguistic structures (r = 0.31, P = 0.007), and a similar correlation between genetic and geographic distances (r = 0.29, P = 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. The bulk of genetic diversity appears to be a consequence of recent migrations and demographic events mainly from Asia and Europe, evident in a higher migration rate for speakers of Afro-Asiatic as compared with the Nilo-Saharan family of languages, and a generally higher effective population size for the former. The data provide insights not only into the history of the Nile Valley, but also in part to the history of Africa and the area of the Sahel.

Link