Figure 1: Map of studied region in East Africa showing Sudan, South Sudan and Ethiopia, and the approximate locations of eight populations genotyped in this study.
The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape
Begońa Dobon et al.
excerpts
Abstract
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.
Population Structure We applied a principal component analysis [PCA] to investigate the population structure of the new populations genotyped in this study from the Sudanese region [Supplementary Fig. S1a]. PC1 [3.56% of the variation] follows a North-South cline and separates populations inhabiting the region between the Nile River and the Red Sea [Nubians and Arabs along the Nile, Beja and Ethiopians along the coast] from Darfurians and Nuba of South-West Sudan, and Nilotes of South Sudan. Copts are a separated group close to the North-East populations, in a more outlier position: they are the extreme of the northern genetic component. PC2 [0.7%] separates the nomadic Fulani from the other populations.
Next, we combined our new populations [140 K data set] with previously studied populations of special interest for this analysis: Qatar12, Egypt13, and three sub-Saharan populations [Luhya, Yoruba and Maasai] from 1000 Genomes Project14 to have external references both in the north and south of the Sudanese region. This new data set contains 14,343 SNPs [14 K data set]. Even if the number of SNPs in this second set is small, it is enough to differentiate components in the African genetic landscape15. Fig. 2 shows a PCA of this extended data set, where East African populations are distinct from both sub-Saharan and North African populations. PC1 [6.08%] separates between populations from North Africa/Middle East and sub-Saharan Africa [Fig. 2a]. Copts are closer to North African and Middle East populations but remain as a separate cluster when PC2 is considered. PC2 [1.46%] along with PC1 separate the two homogeneous clusters of North-East and South-West populations: Nubians, Arabs, Beja and Ethiopians on one hand, and Nuba, Darfurians and Nilotes on the other. PC2 separates all Sudanese and Ethiopian populations from the rest. PC3 [0.56%] differentiates West-African populations [Fulani and Yoruba] from Sub-Saharan East African populations [Maasai] [Fig. 2b]. Both PC analysis using data sets with different number of SNPs preserve the topology of the populations. As expected, with a low number of SNPs we observe a higher intra-population variation [Supplementary Fig. S1b].
Copts share the same main ancestral component than North African and Middle East populations [dark blue], supporting a common origin with Egypt [or other North African/Middle Eastern populations]. They are known to be the most ancient population of Egypt and at k = 4 [Fig.3], they show their own component [dark green] different from the current Egyptian population which is closer to the Arabic population of Qatar.
It is noteworthy the case of the Fulani, which feature more Sudanese ancestry [>45%] than North African [<40%] or sub–Saharan [<15%] and at k = 5 show their own component [Fig.3]. They have a high individual component variance suggesting a recent admixture event in this population.
To formally test the results of the admixture analysis, we applied the three-population test [f3 statistics]16. We used all possible pairs of populations as surrogates of the ancestral populations of each ethno-linguistic group. All populations that have a complex pattern of admixture [Fig. 3] showed statistically significant results [Z-score <−4, p-value <3.2 × 10−5]: those of the North-East cluster [Beja, Ethiopians, Arabs and Nubians] and Fulani. Populations from the North-East cluster: Beja, Ethiopians, Arabs and Nubians [Table 2] may be explained as admixture products of an ancestral North African population [similar to Copts] and an ancestral South-West population [Nuba, even if in one case Darfurians have better fit]. These four populations had an intermediate position between Copts and South-West Sudanese populations both in the PC and admixture analyses.
Nubians are the only Nilo-Saharan speaking group that does not cluster with groups of the same linguistic affiliation, but with Sudanese Afro-Asiatic speaking groups [Arabs and Beja] and Afro-Asiatic Ethiopians [Supplementary Fig. S1a]. Y-chromosome and mitochondrial DNA studies reported Nubians to be more similar to Egyptians than to other Nilo-Saharan populations1, 8: Nubians were influenced by Arabs as a direct result of the penetration of large numbers of Arabs into the Nile Valley over long periods of time following the arrival of Islam around 651 A.D20.
Interestingly, our analyses shows a unique ancestry for Sudanese Nilo-Saharan speaking groups [Darfurians and Nuba] related to Nilotes of South Sudan, but not to other Sudanese populations or sub-Saharan populations [Fig. 3]. This ancestral component is not present in places where the Bantu expansion left a strong footprint and creates a different genetic background that is not found among most African populations. Tishkoff et al.5. reported a common ancestry of Nilo-Saharan speaking populations. We also found this relationship of Nilo-Saharan Sudanese populations with other Nilo-Saharan populations from Kenya [Maasai], but not as strong, as Maasai show their own genetic component at k = 6, which is different from the Sudanese component [Supplementary Fig. S7] and do not cluster with our Nilo-Saharan speaking populations. In a previous Y-chromosome study8, most Nilo-Saharan speaking populations, except Nubians, showed little evidence of gene flow with other Sudanese populations.
The presence of the core of Nilo-Saharan languages in the confluence of the two Nile rivers suggests that the Sudanese region is the place of origin of the Nilo-Saharan linguistic family despite their fragmented distribution, as shown by the location of the Nubian language21, 22. It is interesting to note that Nuba populations constitute an homogeneous group, even if some speak Kordofanian [of the Niger-Kordofanian family] and others different languages of two branches of the Nilo-Saharan family. Their genetic composition denotes their Nilo-Saharan origin, with linguistic replacements in some groups.
Population displacement, whether it is followed with cultural or genetic exchange with local populations, would explain why not every Nilo-Saharan speaking group has this genetic component [as is the case of Nubians] and not every population that has it is mainly formed by Nilo-Saharan speakers [as is the case of Niger-Kordofanian speaking Nuba].
The North African/Middle Eastern genetic component is identified especially in Copts. The Coptic population present in Sudan is an example of a recent migration from Egypt over the past two centuries. They are close to Egyptians in the PCA, but remain a differentiated cluster, showing their own component at k = 4 [Fig. 3]. Copts lack the influence found in Egyptians from Qatar, an Arabic population. It may suggest that Copts have a genetic composition that could resemble the ancestral Egyptian population, without the present strong Arab influence.
A population that shows signals of recent admixture is the Fulani. Fulani are nomadic pastoralists who speak a Niger-Kordofanian [Niger-Congo] language and occupy a large area in Africa’s Sahel. Their origin is still controversial, as mitochondrial DNA indicates a West African and traces of North African origin23, whereas Y-chromosome studies showed shared ancestry with Afro-Asiatic and Nilo-Saharan Sudanese populations8. This shared ancestry with East African populations can be seen in Fig. 3 [k = 3], suggesting that they have admixed with local populations. This finding does not agree with studies of Fulani people in the Lake Chad Basin which reported that Fulani from West Africa’s Sahel usually have consanguineous marriages and do not seem to have admixed with local farmers24. These data together suggest differentiated genetic legacy in different Fulani populations from various geographic regions of the continent.
Maybe my man the "anti-Luyha" guy, will take a look at Fig S10 @K3. LWK. Tell me what he thinks? ;-)
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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QUOTE: Population Admixture. To infer the ancestral populations of the East African individuals, we run ADMIXTURE from k = 2 to k = 10 in the 14 populations (the analysis for the internal nine populations is presented in Supplementary Fig. S7,S10). We analysed the results from k = 2 to k = 5 as HIGHER NUMBERS OF ANCESTRAL COMPONENTS DO ***NOT*** HAVE A CLEAR ORIGIN. A complex pattern of admixture is observed in East African populations (Fig. 3). At k = 2, we already detect different ancestries in the Sudanese populations.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
Now genecist are admiting what I have been saying all along(thank “god”! Wink at Sage). High frequency does not necessarily mean “origin”. Anyone who undertstand “patterns” knows this. The cluster patterns from all these AIM/SNP studies tell the exact same story. Rosenberg made that clear back in 2002. followed by Luelza-Fox, Lazaridis and now Comas(he is the big dog on this).
The differentiation “starts’ in the LWK. Remember Henn concluded that the LWK is ancestral to Morth Africans/Europeans while the Massai (sub-saharans) are ancestral to Egyptians. Of course all are Africans. She was looking at which had GREATER genetic influence in OOA populations.
This study confirms all of the above.
I got this!
Oh! And Henn and along with MOST geneticist agreed there was never any migration/demographic movement of INTO North Africa from Islamic Arabia. ONLY historians make that claim. Geneticist do NOT make that claim. Henn concluded in her infamous paper that “if:” there was any back-migration it was about 35,000-45,000 years ago!!! And NOT 1500years ago. The authors in this study is making a “historical” reference and no genetic input was provided.
So, to the fools who are simple-minded, here is somehting to think about. That is why I ignore the naďve fools who think Fulani and other African popualtion are admixed through recent back-migration.
Quote: Fulani, who are known to have West-African ancestry, have a NEGATIVE f3 with Copts and Yoruba as source populations (Table 2). As they have a complex history and present high levels of admixture with different populations and high individual variance, this three-population phylogeny ****SEEMS NAĎVE*** to explain their complex population history. None of the South-West populations (Darfurians, Nuba and Nilotes) appear as admixed in the three-population test. This result fits the ADMIXTURE analysis (Fig. 3 and Supplementary Fig. S10) and it confirms a specific ancestral component for these populations
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posted
"Caucasoids" have always been in Africa. Always.
I see the researchers may be reading some of my work(thank “god”). They intermittently use the term south-Saharans vs the derogatory implied “sub-saharans’ ie sub-human. Nice change in pace. Step in the right direction. I have seen a few progressive genecist strat used my label…south-Saharans.
Quote: Discussion In this study we present an extensive genome-wide data set characterizing East African human genetic diversity in populations from Sudan, South Sudan and Ethiopia. We further analyse the Nilo-Saharan ancestral component within the variation of South-Saharan Africans. This component belongs linguistically to Eastern Sudanic languages and geographically to South and West of Sudan and South Sudan, including highly diverse ethnic groups in a similar genetic background.
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This ecoregion covers a narrow band on the southern edge of the Sahara Desert, stretching from central Mauritania to the Red Sea. Annual grazing after rainfall is a key feature, in former times attracting large herds of arid-adapted migratory ungulates such as gazelles, addax, and scimitar-horned oryx. Much of the ecoregion is now overgrazed by herds of domestic livestock, and habitat degradation is widespread. Motorized hunters have decimated the wild ungulate herds, and the ecoregion's few protected areas have suffered from civil and international wars. Continued and increased external support is required to protect the ecoregion and provide alternate livelihoods and supplemental incomes for local people.
The South Saharan Steppe and Woodlands ecoregion extends in a narrow band from central Mauritania, through Mali, southwestern Algeria, Niger, Chad, and across Sudan to the Red Sea, covering the southern fringes of the Sahara Desert. Rainfall occurs mainly during the summer months of July and August, but is unreliable and varies greatly from year to year. On average, annual rainfall is between 100 and 200 millimeters (mm), declining along a gradient from south to north. However, droughts lasting several years often occur. Except near the coast of Sudan, mean annual temperature throughout the Sahelian portion of the ecoregion is between 26°C and 30°C. Pastoralism and domestic grazing are the foundations of the economy in the Sahel Region. Rainfall in this ecoregion is insufficient for rain-fed agriculture, but some irrigated agriculture is practiced near water points and along wadis (seasonally dry watercourses).
[...]
In terms of the phytogeographical classification of White, the ecoregion is within both the Sahara regional transition zone and the Sahel regional transition zone. It serves as a transition from the Sahara to the Sahel. Delineated by White's regs, hamadas and wadis vegetation type, the northern border of the ecoregion lies several hundred kilometers (km) north of the 100 mm rainfall isohyet, which is the northern limit of summer grassland pasture composed of the grasses Eragrostis, Aristida, and Stipagrostis spp.
[...]
This ecoregion has few endemic plants. The Mediterranean flora that are characteristic in the Northern Sahara are almost completely absent from the Southern Sahara, where tropical flora dominate. The higher massifs surrounded by this ecoregion, i.e. the Termit Massif in Niger, the Adrar des Iforas in Mali and Jebel Elba and Jebel Hadai Aweb in Sudan, which do have endemic species, have all been assigned to montane ecoregions within the Greater Sahara ecosystem.
posted
Good info lioness. See, we give credit where its due ..
^But we still gotta watch yo sneaky ways... lol
-------------------- Note: I am not an "Egyptologist" as claimed by some still bitter, defeated, trolls creating fake profiles and posts elsewhere. Hapless losers, you still fail. My output of hard data debunking racist nonsense has actually INCREASED since you began.. Posts: 5905 | From: The Hammer | Registered: Aug 2008
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posted
So the report is saying that people from Qatar are "ancestral" populations in Egypt? Really? And that Arabs are "ancestral" in Sudan?
Right.
Whatever this report is trying to say, it doesn't make sense. It keeps saying ancestral over and over again to the point where it becomes meaningless. For example, how are Copts an ancestral population when we know they are also mixed?
The point being why cant they simply go to various parts of Egypt and sample the genes of the different populations and see how they relate to each other? SOuthern Egyptian populations should be closer to Sudanese, Northern Egyptians closer to Arabia and the Bedouins somewhere in between. But they won't do that for obvious reasons. THEN they can identify which of the various Egyptian populations have more of an ANCESTRAL gene predating any later genetic signatures reflecting relatively recent foreign ancestry.
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North Africa=Levant/North Arabia Sahara=Arabian Desert South Saharan=Yemen
There is no clear demarcation, it is all fluid. The only "foreign" elements are Turks circa 1200AD. Qatari has a high frequency of south Saharan and North African component. That is why Henn chose Qatar for her infamous paper. All was discussed already. So yes. There is a genetic relationship between Qataris and modern Egytptians. Just as there is between Qatari and south saharans.
In her later work Henn made it clear that most Iraqi and Turks are NOT good repsentation of proxies for North African genetic relationships. So. Looking at the "terrorist" on TV would not help you sort this out.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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I didn't read it completely yet but this study is a step backward compared to the African Genome Variation Project published earlier this year since it doesn't use full genome. Some studies take a long time to be completed and published, so this study is almost obsolete already.
But in general, it doesn't say anything new. We know many East African populations share a common Semitic component at various degrees depending on the population. Darfurians, Nilotes, Nuba, Fulani, Maasai, Luhya and Yoruba don't have a lot of it. Those populations don't have a lot of the dark green color at K=5 in figure 3 of the main document for example. At K=2, they also don't have a lot of the non-African dark blue component. This dark green/Semitic componant is related to the migrations from Western Asia of Semitic speakers (ethio-semitic speakers) in Eastern Africa and are related for the most part to "recent" events (last 3000 years) well after the foundation of Ancient Egypt as noted in other studies (Here and Here).
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posted
Ancestral has no meaning unless you define time and place. Ancestral could mean any parent or grandparent for the current population. It does not mean ancestral as in founding population from 5,000 years ago. If ancestral means any genes from anywhere found in today's population that doesn't mean much. Those 'ancestral' genes could have arisen 100, 300, 1000, or 2000 years ago....
Again the point I am making is they aren't making anything clear. We already know modern Egypt and Sudan are mixed. So what would be the point? Like we know most modern North Americans originate from Europe.
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posted
This topic was discussed in the Facebook Nile Valley forum. I will only give my few cents.
First, Doug is correct that the paper may seem somewhat confusing as to their use of the term "ancestry" especially in regards to ethnic or cultural groups. Again a common mistake is to identify genetic population with cultural group. "Nilo-Saharan" is a linguistic group that covers a broad expanse of ethnicities and peoples who obviously have diverse genetics. These genetic lineages predate the cultural or linguistic groupings by far.
Nubians are the only Nilo-Saharan speaking group that does not cluster with groups of the same linguistic affiliation, but with Sudanese Afro-Asiatic speaking groups [Arabs and Beja] and Afro-Asiatic Ethiopians [Supplementary Fig. S1a]. Y-chromosome and mitochondrial DNA studies reported Nubians to be more similar to Egyptians than to other Nilo-Saharan populations1, 8: Nubians were influenced by Arabs as a direct result of the penetration of large numbers of Arabs into the Nile Valley over long periods of time following the arrival of Islam around 651 A.D20.
Duh! Every egyptsearch member here knew this for how many years and could have told the authors that before they received their findings! Unfortunately I couldn't help feeling that the authors may use "Afro-asiatic" as a euphemism for 'Eurasian'. Suffice to say the majority of "Arab" Sudanese are actually Nubians who have been linguistically and culturally "Arabized".
Posts: 26238 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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posted
^ Just to be fair, the 'Nile Valley' is not exactly an original name you made up. But it would be interesting to know what other names Swenet or others could use for their blogs or fora.
posted
What is interesting is his claim that a number of "replica" tombs are to be created. Under these replicas, the original African images can be modified, altered and whitewashed away. There are a number of these sites and some are faux. One guy on "Reloaded" wanted to create a "sub" web to "host" info on "Africa-centered" Kemet. I think the idea is to suck contributors away from ES on to another forum where their efforts can be better controlled. Then there are the bogus Wikipeda moles hoping to lure people there too to be exhausted and tied up with "stealth" edit tactics. Also on Facebook a number of other groups have sprung up.
I just wonder how credible this charge of "replicas" is.
-------------------- Note: I am not an "Egyptologist" as claimed by some still bitter, defeated, trolls creating fake profiles and posts elsewhere. Hapless losers, you still fail. My output of hard data debunking racist nonsense has actually INCREASED since you began.. Posts: 5905 | From: The Hammer | Registered: Aug 2008
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quote:Originally posted by Djehuti: ^ Just to be fair, the 'Nile Valley' is not exactly an original name you made up. But it would be interesting to know what other names Swenet or others could use for their blogs or fora.
quote:I see the researchers may be reading some of my work(thank “god”). They intermittently use the term south-Saharans vs the derogatory implied “sub-saharans’ ie sub-human. Nice change in pace. Step in the right direction. I have seen a few progressive genecist strat used my label…south-Saharans.
"South Saharans" is still a problematic term. What exactly is the human commonality between a Wolof person from Senegal and a Xhosa from South Africa? When was the MRCA?
And "South Sahara" covers such enormous distances both culturally and linguistically. Why not just specify the restricted area?
The same for "Afro-Asiatic" which is specifically a nonsense term given that the area referred to is less than 2% of the Asian landmass.
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posted
I haven't given up on this forum either. I actually have plans to post some info I have been doing some research on but a new job (with more hours) and what little social life I have is postponing that. In the mean time I will be able to make comment on certain topics every now and then. =-=-=-=-=-
Viva el DJ!
=-=-=-=-
wHOOPS
WAS SUPPOSED TO BE REPLY NOT EDITING OF YR ORIG POST
PLEASE REPOST IT THX
[ 16. June 2015, 09:11 PM: Message edited by: ausar ]
Posts: 26238 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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The history of these languages is intimately connected to the history of one of the greatest rivers that no longer exists, the Yellow Nile, which once rivaled the two main sources of the modern Nile River, the White Nile (which flows more or less due North from Lake Victoria), and the Blue Nile (which flows through Ethiopia to the confluence with White Nile). As the Yellow Nile (now called Wadi Howar) dried up in the wake of the 4.2 kiloyear climate event and was dealt the final death blow in the climate event that led to the Bronze Age Collapse, the language family spoken up and down the Yellow Nile fragmented into many daughter languages as their civilization collapsed and they were exiled to wander Africa with their herds chasing new sources of water.
A conference paper from 2009 by Dr. Claude Rilly makes the connection.
[W]hen did Proto-NES split into different groups? The earliest attested daughter-language is by far Meroitic. Early scholars thought it appeared in the Nile Valley at the time of the first rulers of Napata, around 850 BCE. However, I have presented elsewhere (Rilly 2007b) evidence that traces of Proto-Meroitic personal names could be found in Egyptian texts dated to the end of the Kingdom of Kerma (ca. 1600 BCE).
In addition, strong elements in favour of the presence of names fitting with the Proto-Meroitic phonology can be found in the Egyptian lists of bewitched enemies from Kerma as early as the 12th Dynasty (ca. 2000 BCE). Therefore a chronological span around the second half of the third millenium BCE for the splitting of the NES-group is by no means exaggerated. The question is now to find what event caused this splitting.
The University of Cologne have conducted in the last decades an ambitious archaeological project (BOS, later ACACIA, cf. Kuper & Kröpelin 2006, Jesse 2004) in the region of the Wadi Howar. This wadi – also called the "Yellow Nile" – is a former tributary of the Nile running from Ennedi range, in Chad, through Darfur and Kordofan and joining the Nile at el-Debba, north of the great bend of the Nile, 100 km south of Kerma, where the first Kushite state was founded around 2500 BCE. As Eastern Sahara underwent desertification, between 5000 and 3500 BCE, the Wadi Howar attracted a numerous population, especially from the North, until its course became disrupted and finally just temporary around the middle of the 2nd millenium BCE. Nowadays, only the Upper Wadi Howar, in Darfur, retains some water at the time of the seasonal rains. The Wadi Howar was densely populated during three millenia, as can be deduced from the 1700 archaeological sites of various size spotted by the Cologne team. The banks of the wadi are surrounded by additional archaeological sites such as Gebel Tageru in the south, Erg Ennedi in the north and Ennedi range in the west.
Three phases of settlement have been determined in the Wadi Howar. From 5000 to 4000 (phase 1), the river is continuously full and its bank harbour settlements of hunter-gatherers, that live also on fish and molluscs. From 4000 to 2200 (phase 2), the Lower Wadi Howar, close to the Nile, gets dry. New settlers, coming from the neighbouring regions where desertification is gaining ground, are now living mainly on cattle. Goats and sheep are introduced at the end of this period. Contacts with the Nile valley are indicated by imported ceramics of the "herringbone" type. From 2200 to 1100 BCE (phase 3), the whole wadi is dry most of the time, with some humid places during the rainy season in the Upper and Middle Wadi Howar. Settlements are still numerous, but more scattered. The main diet is now made of sheep and goats, as cattle is too exacting for an increasingly arid environment. Donkeys, introduced to Sudan from at least 2500 BCE, play a major role in the nomadic way of life of the last settlers. After 1100 BCE, the region becomes hardly hospitable, excepted in the Upper Wadi Howar.
What can be deduced from the history of Proto-NES fits perfectly with these archaeological and palaeoclimatic data. The crystallisation of the proto-language possibly occurred when cattle-tenders settled together along the Wadi Howar around 4000 BCE, whereas the splitting into different linguistic groups would result from the progressive dessication of the river.
The death of the Yellow Nile coincides closely in time with the death of another famous river, the Saravasti River, which is mentioned frequently in the Hindu epic the Rig Veda, and which archaeological evidence indicates was a lifeline for many of the major cities in the Harappan civilization until it went dry.
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