Tuesday, June 30, 2015

Population genomics of Bronze Age Eurasia, Allentoft et al. 2015

We have yet more ancient DNA, this time we have 101 low coverage (low number of SNPs to work with) ancient genomes from across various parts of Eurasia strewn across the map below:

We have ancient genomes from Bronze Age Armenia, the Sintasha culture, more Yamnaya genomes, results from Andronovo & Afanasievo cultures and so much more. It's all really intriguing and to a great extent like Haak et al. 2015; centers around mapping and supporting the expansion of the Indo-European languages, with the Pontic-Caspian Steppe origin hypothesis for the language family  being backed up by genetic data yet again.

Rough spread of the Indo-European languages in their homelands

"The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought."

It seems to back-up the slightly older Haak et al.'s data, this time with newer Yamnaya & Corded Ware Culture samples and proves once again that there was a massive westward migration from the Pontic-Caspian Steppe into the rest of Europe where subsequent mixing occurred between the pastoral nomadic peoples from the steppe and Early European Farmers of which modern Sardinians are the best preserved example of as a genetic isolate group in Europe that did not incur much steppe-related ancestry at all.

There seems to also be (as you can see above) a sort of resurgence of Western European Hunter-Gatherer (WHG) ancestry across Europe as most Europeans can now be modeled as a three-way mixture between Early European Farmers, Western European Hunter-Gatherers & the Yamnaya. So Haak et al. (granted, I didn't doubt their data at all) was on the money and is now backed up by another study with newer samples altogether. 

The steppe expansion into the rest of Europe is represented most strongly by the peoples of the Corded Ware culture who genomically just look like a later westward extension of the Yamnaya; looking almost identical to them on a genetic level. This new study (Allentoft et al.) backs this fact we were already aware of up via Haak et al. up as well but adds even more interesting data thanks to the sheer geographic scope of its sampling. 

It for example finds that the peoples of the Sintashta culture seem very genetically similar to Corded Ware peoples:

"Although we cannot formally test whether the Sintashta derives directly from an eastward migration of Corded Ware peoples or if they share common ancestry with an earlier steppe population, the presence of European Neolithic farmer ancestry in both the Corded Ware and the Sintashta, combined with the absence of Neolithic farmer ancestry in the earlier Yamnaya, would suggest the former being more probable."

The former seems probable to me as well, especially in that they carry Early European Farmer ancestry (referred to as "Neolithic Farmer" in this case) so it's quite likely that what the Sintashta culture's people are is an eastward migration from peninsular Europe back into the steppe belt of Eurasia. 

This study truthfully has a lot to talk about and as the first few lines of this blog post say; has 101 ancient genomes to share so there's a lot to touch upon that I may not dive into within this post but with consequent posts, however; for the time being I'd touch upon a few more interesting things they shared such as what seems to be evidence of an eastward migration from the Pontic-Caspian Steppe itself:

"The Early Bronze Age Afanasievo culture in the Altai-Sayan region is genetically indistinguishable from Yamnaya, confirming an eastward expansion across the steppe, in addition to the westward expansion into Europe. Thus, the Yamnaya migrations resulted in gene flow across vast distances, essentially connecting Altai in Siberia with Scandinavia in the Early Bronze Age."

So there was both a westward expansion (The Corded Ware Culture) from the Steppe into peninsular Europe which profusely shaped modern European demographics as I mentioned above and also an early (~3000 BCE) expansion from the steppe by peoples genetically identical to the Yamnaya who made their way into South Siberia. (The Afanasievo Culture). 

Some other information I found quite intriguing would be that the later Central Asian Andronovo culture's people seemed to have been very genetically similar to the peoples of the Sintashta culture whilst being clearly distinct from the Yamnaya and Afanasievo. The study ascertains that they represent a "temporal and geographic extension of the Sintashta gene pool". 

What's even more intriguing though is that they seem to prove that by the late Bronze Age to Iron Age; the Andronovo were essentially replaced by more "multi-ethnic" cultures owed to eventual intermixing with "East Asian" peoples.

"Towards the end of the Bronze Age in Asia, Andronovo was replaced by the Karasuk, Mezhovskaya, and Iron Age cultures which appear multi-ethnic and show gradual admixture with East Asians, corresponding with anthropological and biological research.

 This seems to back up the kind of data one would get if they utilized the Eurogenes K=8 model and ran contemporary Central Asians (Kazakhs et al.) through it: Central Asians prove to be a genetic mixture between West & East Eurasians; in this case Bronze Age peoples from Europe and East Asians.

However the study seems to find that Iron Age Central Asians prove more West Eurasian than contemporary Central Asians so there seems to have been an increase in East Asian ancestry since the Iron age...

On an extra note; it's not simply the Corded Ware who clearly show input from the Yamnaya during the Bronze Age but various other cultures across Europe at the time who show what looks to be a "Caucasian" component as the study notes; however this Caucasian component isn't owed to ancestry from the Southern Caucasus but from the Steppe:

"Although European Late Neolithic and Bronze Age cultures such as Corded Ware, Bell Beakers, Unetice, and the Scandinavian cultures are genetically very similar to each other, they still display a cline of genetic affinity with Yamnaya, with highest levels in Corded Ware, lowest in Hungary, and central European Bell Beakers being intermediate. Using D-statistics, we find that Corded Ware and Yamnaya individuals form a clade to the exclusion of Bronze Age Armenians showing that the genetic ‘Caucasus component’ present in Bronze Age Europe has a steppe origin rather than a southern Caucasus origin. Earlier studies have shown that southern Europeans received substantial gene flow from Neolithic farmers during the Neolithic."

The chief thing I noticed in this case is that they note this "Caucasian component" but this study simply doesn't go into some rather intriguing subjects the Haak et al. study did which would be what seems to have "formed" the Yamnaya themselves. Haak et al. touches upon two populations it called "Eastern European Hunter-Gatherers" (which it seemed to imply (if I recall correctly) were "Ancient North Eurasian (ANE) MA-1 related ancestry" + Western European Hunter-Gatherer") & what they dubbed an "Armenian-like" / "Caucasian-like" population.

It further seemed to say that these two populations (Eastern Hunter-Gatherers and the Caucasian-like population)  intermixing is what ultimately created the Yamnaya. Making the Yamnaya the mixture between ANE, ENF & WHG that they seem to be:

 The study doesn't go into this at all... It doesn't really even touch upon Eastern European Hunter-Gatherers or back up the idea that they seem to look like a mixture between ANE & WHG like the Karelian Hunter-Gatherer from Haak et al. did even via the Eurogenes K=8 model:

We don't even know if this model is correct. Is EHG a mixture between "ANE" & "WHG" or something else entirely that just shares ancestry with MA-1/ "Ancient North Eurasians"... As David (the author of Eurogenes) tells me; you could even model WHG as "EHG + something as of yet not sampled" so despite what I thought in my former post; there's still honestly some research to be done into "Eastern European Hunter-Gatherers".

There's nothing in Allentoft et al. about this Caucasian-like population that Haak et al. seemed to imply brought West Asian & Basal Eurasian carrying ancestry into the Yamnaya ("ENF") either. It would've been rather riveting if they went into all that but alas... They didn't.

Ultimately though, one thing I would keep in mind at this point is that the old "Europeans = ANE + WHG + EEF" model from Lazaridis et al. 2013-14 is clearly no longer the case. Instead; most Europeans are basically a mixture between Yamnaya descended Pontic-Caspian Steppe pastoralists (who themselves carry ANE ancestry/ share ancestry with MA-1), WHGs & EEFs.

Though of course; the Yamnaya themselves are not purely ANE but a mix between ANE/ MA-1 related ancestry, WHG & "ENF" (The EEF component with its WHG removed).

At any rate; there's obviously a lot more to say about this amazing and extensive new paper but I figured I'd stop here for now. Frankly, this is a bit of a messy post in my humble opinion especially because this study has quite a bit of for one to touch upon and I suppose I tried to ram in several different things into this one post.

The best advice I can offer for now to anyone looking to learn more about these samples would be to keep up with the Eurogenes blog where the author has some interesting things to share. Alongside that; make sure to actually read the full study as well as its supplemental.

Reference List:


1. Don't take the "East Eurasian" in the Karelian Hunter-Gatherer seriously, it's probably not real (granted, it could be as we lack confirmation of it via formal stats) in my humble opinion. Don't make much of anything in either the Yamnaya or Karelian Hunter-Gatherer that isn't ANE, WHG or ENF seriously at all, to be quite frank.

2. Some highly interesting notes from a linguist friend of mine: [-]

3. Now, there's a lot of interesting new ancient Haplogroup data available via this study (some notes from my linguist compatriot & an image from the Allentoft et al. itself just to share a few) and while I myself am not known to touch upon Haplogroups much (my knowledge of them is not as keen as my knowledge of autosomal DNA); I highly recommend looking into this study if you're interested in Haplogroups.

Saturday, June 20, 2015

Peer-reviewed study shows that Kennewick-Man was Native American

I'd heard news on these results long ago [2] and was hoping to actually see them and get a glimpse at what some researchers were yammering on about. It seems we finally have uniparental (haplogroups) & autosomal DNA data on the infamous Kennewick-Man of North America & proves that he was ultimately most similar to Native Americans and of a genetic continuity with them. [1]

Kennewick-Man Skull

"Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon-dated to 8,340–9,200 calibrated years before present (bp). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. In order to resolve Kennewick Man’s ancestry and affiliations, we have sequenced his genome to ~1× coverage and compared it to worldwide genomic data including the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genomic-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia."

There's actually been a good degree of drama surrounding this chap's possible origins despite the age of his remains (8th millennium BCE), believe or not. From odd original claims that he had a "Caucasoid" morphology [3] to later more reliable anthropological teams finding that he looked rather similar to Ainus and Polynesians. [4]   

This clay facial reconstruction of Kennewick Man, who died about 8,500 years ago in what's now southeast Washington, was based on forensic scientists' study of the morphological features of his skull. [6]

Those suggestions were probably ridiculous from the start as to my knowledge there's no evidence of pre-colonial or pre-Norse peoples other than what are taken to be the ancient predecessors of Native Americans  having crossed over to the Americas. 

A PCA/ cluster, ADMIXTURE run and a heat map of f3-outgroup statistics; warmer colours indicate higher allele sharing

If I had to say I found anything about this rather interesting; it's that 1) that we have some more ancient genomic data from the Americas 2) Despite seeming very genetically similar to contemporary Native Americans and likely being of the same basal mixture as them (MA-1 related/ Ancient North Eurasian ancestry + ancient East Asian ancestry [5]) he seems to look notably distinct (phenotype wise) from many contemporary Native American populations & has more of a phenotypic affinity for groups like Ainus for example.

Otherwise, I don't think there's much else I in particular can say here as Native Americans aren't my forte. Enjoy the study... Christmas really came early this year with all of these new papers from the Sudan study to the Bronze Age Eurasia study (101 ancient genomes)  & now even this.

Reference List:


1. I'm not entirely sure but I think that first image I shared of the skull is basically a plastic casting or replica of some sort? It was even shared by the LA times and other sources and I wasn't sure if it was the real skull as it seems to clean/ white but it is an image of relatively the same skull (same damage on them and so on). I added it as it just looked visually appealing, to be fully honest.

2. Information from the study on his Haplogroups: The mitochondrial genome was sequenced to ~71× coverage and is placed at the root of haplogroup X2a , and the Y-chromosome haplogroup is Q-M3; both uniparental lineages are found almost exclusively among contemporary Native Americans.

Recommended read:

The genome of a Late Pleistocene human from a Clovis burial site in western Montana, Rasmussen et al. 2014

Thursday, June 18, 2015

The Azanians: A Cushitic speaking people

I normally don't make these kinds of quick "Copy & Paste" types of posts but in this case I think the material I'm trying to touch upon is pretty self-explanatory & doesn't require me to hunch over and scrounge through various forms of data or information to share and research for your reading pleasure so consider this a mere recommend/ interesting share that I recently encountered.

"The Azanians of the 1st to 4th century A.D.were no doubt Cushitic speakers, and their descendants and related immigrants from the north brought with them their traditions and funerary customs,some of which were passed on to the peoples living in Kenya at the time."

If you're at all interested in learning more about the Azanians you can consult documents like the Periplus of the Erytraean Sea [2] among others of the time (I'm honestly no expert on the Azanians and only have a face-value knowledge of them); authors from antiquity who referred to Azania and Azanians are referred to rather accurately in the Azania Wikipedia page. They seem to have been Southeast Africans (Kenya down to Tanzania).

If I had any extra comments; I wonder why these Azanians were named distinctly from the pastoralist Barbaroi tribes to their north. From Northeastern Sudan down to Northeastern Somalia; the inhabitants were conflated together often under the label of "Barbaroi" by the Greco-Romans and even in some cases the Aksumites

As fellow Cushitic speakers one could expect these Azanians to perhaps have been culturally similar enough to their north lying neighbors to maybe be conflated with them yet the Greco-Romans, South Arabians and such they traded with saw fit to give them a distinct label. It's interesting, that's all I can say.

If anyone would like to share any extra information on the Azanians; go ahead in the comment section. Anyway, this was in all candor meant to simply be a quick share sort of post, so enjoy the information.

Reference List:


I actually upload lengthy recordings of various Cushitic languages onto Youtube, those of you interested in hearing what various Cushitic languages sound like can go ahead and listen to them.

Sunday, June 14, 2015

Copts: an example of Pre-Islamic and Arab conquest Egypt?

What you see above in the middle & in red are the Nagada Copts (residents of Khartoum, Sudan) from the recent autosomal DNA study on Sudan (Dobon et al.). That's them in a Global PCA (Principal Component Analysis) made by the author of Eurogenes upon my request. [1]

They interestingly look to be more Eurasian / West Eurasian / West Asian than their Muslim Egyptian counterparts ("Egyptian" samples). As you can see in the Global PCA, they pull more north toward West Asians and straddle between Muslim Egyptians and Palestinians. Palestinians are about ~5 to 10% African admixed (I'm speaking of components like the East African cluster and perhaps "Niger-Congo" here) while Muslim Egyptians are about ~20 to 25% on average, much like Northwest Africans whom they cluster close & who are known to be at that level. [2]

You can see in the new study's own PCA above that the data is more or less the same, the Copt samples pull more to the right on the X axis like Qataris while Egyptians pull more to the left; they once again clearly prove more West Eurasian / West Asian than their Muslim counterparts.

Muslim Egyptians often show small trace levels of Ancient North Eurasian ancestry (ANE), if I recall correctly though; their region is mostly a near dead zone for this kind of ancestry especially when you go south to the Horn and now seemingly even North Sudan where there is more or less no ANE ancestry about. The situation is the same to their west where Maghrebis / Northwest Africans seem to lack ANE input altogether

Northwest Africa / The Maghreb

Though Maghrebis have Western European Hunter-Gatherer (WHG) ancestry as has been noticed via Eurogenes K=8 and even Lazaridis et al.'s old ADMIXTURE analysis from 2013. [3]

Muslim Egyptians and Copts both show trace or low levels of WHG ancestry however there's really no way of knowing if this is real WHG ancestry or perhaps something very ancient that could have come out of West Asia similar to WHG (many I know tend to refer to this as "UHG/Unknown Hunter-Gatherer") so this WHG might not entirely be real though some of it could be.

At any rate it seems to me as though these Nagada Copts, the descendants of migrants who came from Egypt within the last 2 centuries as Dobon et al. notes, might honestly be representative of Copts as a whole. I say this because I have seen a random Egyptian Copt from Upper Egypt's results and she came out quite similar to them. No ANE, low WHG levels, ~15% East African / Sub-Saharan African and clearly more West Eurasian than Egyptians, in fact from what I've heard of her results and seen, she seems quite identical to these samples.

Her results from Eurogenes K=7:

ANE: 0.38%
WHG-UHG: 7.70%
ASE: 0.0%
East Eurasian: 1.54%
West African: 0.0%
 East African: 11.87%
ENF: 78.52%


She's "LifeisDandy"and the users to the far right are Europeans (rich in WHG. "Jusarius" is a Finn) and some ("Stellacritic" is Northwest African) to her south like the Assyrian and Iraqi (IQ) Mandaean samples are about 10-15% ANE

The results above are based on Eurogenes K=7 which was somewhat less fine tuned than
K=8 especially at times with its WHG estimates. It would give Northwest Africans something along the lines of 20-30% WHG ancestry which is ridiculous, those are in fact Italic & Greek levels of WHG ancestry. So her "WHG" score in those above results is most likely quite inflated.

She seems just like the new Nagada Sudanese Copts David Wesolowski ran through K=8: ~15% Sub-Saharan (in this case it seems to be entirely East African), ~80-90% ENF/ the West Asian
component that carries Basal Eurasian, and finally; small trace levels of WHG that probably
isn't entirely real WHG.

Like LifeisDandy in Eurogenes K=7, their "Sub-Saharan African" ancestry seems to be solely East African and not at all Niger-Congo (sometimes referred to as "West-Central African") based. You can see this in Dobon et al.'s own ADMIXTURE analyses like with the following run at K=3 where Copts show none of the light blue Yoruba (YRI) component but the Egyptian samples do:

Now, the reason this is all actually interesting is because. as I've stated in the past, Christian and non-Western (Ashkenazim + Sephardim) or Northwest African (Maghrebim) Jews from West Asia's Arabized regions often come off as distinct from their Muslim counterparts to some degree and seem to have avoided waves of more recent admixture that's affected their Muslim counterparts or at least absorbed much less of it.

The Spread of the initial Caliphates

This admixture can vary from being Niger-Congo ancestry to Peninsula Arabian ancestry
that is higher in some Muslim populations and either lower in their Christians (or Jews) or in the case of Niger-Congo ancestry completely absent.

One can only for now imagine that this new Niger-Congo input that isn't present in the Christian and Jewish groups who at times look like isolates in their home regions or display some substructure when compared to their Muslim kinsman [4] might just be a legacy from The Arab Slave Trade?

At any rate, a good example of these newer waves of admixture especially in terms of newer African ancestry absorbed likely through the Slave Trade would be Yemenite Muslims and Yemenite Jews.

Most Yemenite Muslims I've encountered either in studies or outside of them tend to come out with North African levels of African admixture, at a level of ~15-25% as you can see with how they plot at the same level as Mozabites, Moroccans, Egyptians and so on with only one of those samples just ending up at the very south of the Nagada Copts. 

Some Yemenite Muslims can indeed be about ~15% African in my experience, that isn't necessarily abnormal. But as a whole they're clearly more admixed than Saudis, Qataris and so on (fellow Arabians of the Peninsula). [5]

The Arabian Peninsula

Yemenite Jews in contrast are at African admixture levels comparable to those of Levantines who are more along the lines of ~5-15% African admixed. [6] Yemenite Jews' African admixture is also likely much more ancient as they only show East African cluster based African ancestry and none of the seemingly newer Niger-Congo input in Yemenite Muslims. 

I'd go on and on but it's generally obvious that they avoided various forms of outside admixture (not just Niger-Congo admixture) that Yemenites of a Muslim extraction simply did not.

Notice how Yemenite Muslims ("Yemen") show the Yoruba / Niger-Congo component whilst Yemenite Jews only show the pink Dinka / East African cluster component [3]

This perhaps seems to be the case with our new Copt samples as well. I personally wouldn't be too surprised if these Copts are a reliable genetic example of Christian and Late Period EgyptIranians, Anatolians and Caucasians are very rich in Ancient North Eurasian ancestry and from glancing at this recent incredulous Bronze Age Ancient Genomes study on Eurasia; it seems the Caucasus was rich in ANE as far back as the Bronze Age, Anatolia and the Iranian Plateau likely were too in my humble opinion. 

The point is, from what David says about the WHG and ANE levels in these Copts & even the levels LifeisDandy shows; it's clear that they really don't have Persian or Greek admixture. Persian or Iranian admixture would've likely brought with it notable ANE ancestry and Greek admixture would've brought with it much more notable and solid WHG ancestry (not negligible trace levels that might even be actual WHG admixture).

The Achaemenid Empire, the first great Persian empire
Although Bedouin admixture can't entirely be ruled out as one friend has noted. Many or most Arabian Bedouin do not show ANE or WHG ancestry in K=8, they're much like these Copts and mostly just look like a cross between East African/ Sub-Saharan ancestry (~5-15%) and ENF ancestry (the West Asian component that carriers Basal Eurasian with it) though some can show some Niger-Congo input.

Honestly, I think it's entirely possible that some of these ethno-religious isolates of West Asia do have influences likely owed to the Arab Conquest. Christians in the Levant do in fact show Arabian admixture at a non-negligible level in some independent ADMIXTURE runs or studies. [6]

Nevertheless, these populations did seemingly avoid admixture their Muslim counterparts have endured (though sometimes not at all entirely) whether it be Peninsula Arabian admixture or African admixture most likely owed to the Slave Trade or some other events.
These Copts who are honestly just descended from Egyptian migrants who arrived to Sudan within the last 2 centuries (as this new Sudan autosomal DNA based study notes) & Egyptian Copts like "LifeisDandy" among others seem to keep to this pattern. They seem more West Eurasian than their Muslim counterparts, lack some outside input in them such as Niger-Congo admixture & are most likely a better representation of what Egypt was like genetically before its Islamization and Arabization.

But this is merely an assumption on my part based on how they're keeping to an already well-known pattern among the Christians & non-Western or Northwest African Jews of "The Middle East" (Assyrians, Lebanese Christians, Yemenite Jews etc.) who often to some degree even to geneticists seem to perhaps be a better representation of their region's pre-Islamic & pre-Arab conquest population. [7]

The way they lack Niger-Congo input exactly like Lebanese Christians & Yemenite Jews do whilst their Muslim counterparts (Lebanese Muslims, Yemenite Muslims and Egyptian Muslims) actually have such admixture is especially compelling.

That alone to me establishes that they've at least avoided some admixture from the outside but the question as to whether or not these Copts lack Peninsula Arabian influences is still up in the air from what I can tell. Frankly, I'm not an expert on Egyptian autosomal DNA data and don't know if Egyptians Muslims themselves lack Arabian input or have any.

Granted, from looking at the ADMIXTURE results from Dobon et al. above; one is left to wonder given that Egyptians at K=10 and several other Ks seem more similar to Qataris than Copts. But that can be a bit skewed in that these new Copt samples are forming their own mixed component (similar to how some Mozabites or Tunisian Berbers form a "Maghrebi" component or Somalis form components like "Ethio-Somali") from K=5 and onward, but you'd expect the Egyptian samples to show more of this component than they are in my humble opinion.

Reference List:


1. For the record, it has been known for a while now that Yemenite Jews are pretty much mostly native to the Arabian Peninsula, it's pretty clear that they aren't a Levantine migrant group that came to Arabia and mixed with the locals too as they don't share IBD segments with other Jews like Iraqi or Sephardi Jews while these Jews do share IBD segments with one another. [-]

2. To touch upon that Lazaridis et al. ADMIXTURE run I linked you to; you can see that Northwest Africans like Mozabites and Tunisians have WHG admixture by observing K=16 in that run for example where Northwest Africans show the blue WHG/ Loschbour based component alongside EEF (pink).

3. I referenced Hodgson et al. ("[5]") when I mentioned that Yemenite Muslims are more African admixed than Saudis and Qataris because you can view that data in that study's ADMIXTURE analysis. (names of the components)

4. My old post on ANE's spread that I linked to in this post needs to be updated a bit/ followed up perhaps with a newer post giving everyone a clearer image of what seems to for now be Ancient North Eurasian ancestry's spread across the world. Also, populations like Negevite Bedouins and Copts likely do have some negligible ANE-related ancestry owed to Caucasus Hunter-Gatherer-related admixture (which they show).

5. Link to note

6. Keep in mind that Coptic is a dead language (only used for liturgy) and that Copts are indeed simply Christian Egyptian Arabic speakers just like Maronites in Lebanon don't really speak Aramaic anymore.

Extra share:

A new variant of the Pan-Northeast Africa PCA where Tunisians, Moroccans, Mozabites and Morccan Jews have been added. A mapping of the group clusters in it I made.

Special thanks to:

David Wesolowski, the author of Eurogenes.

Wednesday, June 10, 2015

Sudanese Arabs, Beni-Amer Beja and Nubians: Autosomal DNA data

An amazing new study came out recently with several Sudanese samples of Sudanese Arab, Beni-Amer Beja, Nubian, Darfurian, Copt, Nilote, Fulani and various other Sudanese origins.  [1]


The data is quite exciting as we can finally compare the populations of Sudan to other Mainland East Africans such as Horners and Southeast Africans. I contacted David Wesolowski (the author of the Eurogenes genome blog) and asked him to run the new samples into a Global PCA/ cluster as well as another PCA (Principal Component Analysis) which he made into a sort of Pan Northeast Africa PCA with Arabians, Levantines, Maasais and Fulanis thrown in:


The results seem quite interesting. There's intriguing information on several of these population sets but my main interest in this particular blog post are the Sudanese Arab, Nubian and Beja samples. The Beja seem mostly more West Asian/ West Eurasian than Ḥabeshas (Amhara-Tigrinya), Somalis, Ethiopian Jews, Wolaytas & Oromos and seemingly within a ~50-60% West Asian range of admixture. However in the Northeast African PCA they form a cluster with Horners like Somalis, Ḥabeshas, Oromos and Wolaytas while Sudanese Arabs and Nubians form their own cluster:

  In conjunction with this, they also come out extremely similar to this paper's Ethiopian samples (who are mostly a composite of Amharas and Tigrinyas accompanied by 2 Oromos) when put through the study's ADMIXTURE runs:

It seems to me that whilst they are actually often more West Eurasian/ West Asian than Horners like Ḥabeshas, Oromos and Somalis; these Cushitic speaking Beja still seem to share a gross amount of ancestry with Horners based on how they plot in the Pan Northeast Africa PCA and their greater similarity to Ḥabeshas/ these Ethiopian samples than to Nubians and Sudanese Arabs in this study's ADMIXTURE runs.

Information (including locations) on the various sampled populations:


Overall, these Beja seem quite homogeneous. All clustering very close in the Global PCA, demonstrating a generally close/ uniform distance from non-Eurasian admixed Africans (f.e. Yorubas and South Sudanese) and West Eurasians. However one must wonder if this is because virtually all of the samples were gathered from one location/ town and are of the same Beja subgroup/ tribe (the Beni-Amer).

In contrast, the Sudanese Arab and Nubian samples were gathered from a variety of locations. 
Sudanese Arab locations:



However, from what a friend tells me, Hadendoas were sampled a long time ago in Tishkoff et al. [2] alongside Beni-Amers and both groups seemed to look extremely similar so it's entirely possible that these Beni-Amer are representative of virtually all to most Bejas but we'll see in due time, I suppose.

Sudanese Arabs and  Nubians in terms of admixture levels are a different story from Beni-Amer Bejas however and are notably quite diverse in terms of admixture levels:

The more left a sample/ person pulls-> the more West Asian/ West Eurasian they are. That's what I mean by "Admixture Levels"; how much a population splits between West Asian ancestry and the kind of mostly non-Eurasian admixed African ancestry you'd find in a Dinka for example. 

Sudanese Arabs and Nubians seem very heterogeneous in this regard. Some few Sudanese Arabs and Nubians actually seem to be at a Somali level of West Asian ancestry (~40% or so), others sit between Somalis and Ḥabeshas (~40-50%) whilst many seem practically identical to Ḥabeshas & Ethiopian Jews in terms of admixture levels (~50%), on the other hand; a great number of them (more Sudanese Arabs than Nubians) seem well-over Ḥabesha levels of admixture (>50%).

As you can see Beni-Amer Bejas-:

-who form a cluster with non-Ari Horners are much more homogeneous and often more West Asian than Ḥabeshas (>50%) though a good number of them are more or less at a Ḥabesha level of West Asian ancestry. 

Sudanese Arabs & Nubians seem to be more similar to each other (forming a cluster with one another) than they are to non-Ari Horners like Ḥabeshas, Wolaytas, Somalis, Ethiopian Jews & Oromos (forming their own sort of cluster) while Beni-Amer Bejas seem more similar to these same Horners but sit at a sort of intermediate position between them and North Sudanese like Sudanese Arabs and Nubians.

There are two other PCAs that David Wesolowski made upon a request from a friend (user Lol_Race):


In these PCAs, that friend requested that Hadzas be added because it was curious how Somalis alongside Oromos, Wolaytas, Ḥabeshas & Ethiopian Jews were seemingly pulling up toward Aris who are the current best representation we have of the Omotic component

He hoped the Hadza being added would maybe introduce something similar enough to Ari Blacksmiths and Ari Cultivators & the ancestry in Somalis that might be similar to Omotic speakers like Aris. This, in turn, could perhaps separate Somalis from Ḥabeshas a little bit in a PCA since, due to some older analyses that I've touched on in the past, Somalis seemingly don't have Omotic admixture despite what studies like Hodgson et al. and Shriner et al. seem to posit. However, the separation he was hoping to see simply did not occur:

Somalis, Beni-Amer Bejas, Wolaytas, Ḥabeshas, Ethiopian Jews & Oromos all consistently formed a cluster together in both new PCAs where Hadzas were included. Leading both him and me to wonder whether or not Somalis do actually have at least a tiny amount of Omotic admixture? Though I personally suggested that this could be something else binding the populations of the Horn (including Aris) together. No truly strong inkling as to what it might be however.

I also do wonder if these Beni-Amer Bejas have any Omotic admixture because if they lack it; it would make a good case for linguists who pose the rather plausible idea that Cushitic speakers (the pre-historic peoples who likely make up a large chunk of the ancestry in most Cushitic and Ethiopian Semitic speaking peoples) originally came from further up north in Northeast Africa/ essentially down from areas like Egypt and Sudan and into the Horn.

Northeast Africa

That leads me to talking about a possible ADMIXTURE analysis. David over at Eurogenes put together a small dataset from these various populations that one could run through an ADMIXTURE calculator:

If anyone is interested in running them through any number of ADMIXTURE calculators then go on ahead. If you download all of the samples by yourself then you may sadly encounter very poor labeling of the samples but I emailed some of the authors and managed to get a spreadsheet that properly labels every sample with its ethnic designation:

The original data was really just ID numbers for each sample and it was pretty much impossible to know which sample belonged to which population. If anyone with a good calculator for helping spot Omotic admixture like the kind in an old fellow Somali's following spreadsheet- :

-is out there then it would be quite appreciated if you could run these samples through such an ADMIXTURE analysis and email me the results: Awaleking@gmail.com. Or really just post it here in the comment section. I'm going to try fiddling with them myself in the meantime and see what I can share.

 This is certainly not the last post I'm going to be making on this subject. This is honestly more of a rushed post where I'm ecstatically trying to get some of this new and incredibly interesting information out, I'll probably do several follow ups on this paper, especially once I have enough interesting data via ADMIXTURE. I'll even touch upon populations other than the ones focused on in this post. Stay tuned...

Reference List:


1. David over at Eurogenes did attempt to run some of the samples through Eurogenes K=8 and while I haven't seen the data directly myself-> it seems to be that Sudanese Arabs, Nubians and Beni-Amer Beja (most likely all Beja as well) lack Ancient North Eurasian and Western European Hunter-Gatherer input much like the substantially West Asian admixed populations of the Horn such as Somalis, Habeshas, Ethiopians Jew & so on.

2. David did note that the chip used in this paper didn't overlap well with the chips usually used in other studies so a much lower number of markers than usual were used for these PCAs (15,000 SNPs when most other PCAs he's made tend to use more than 150,000 SNPs), there could be some differences in clustering noticeable with more markers, nothing radical but some groups could show slightly more variation from each other.

3. The Ethiopian samples from this new paper also seem to basically be diaspora folk as they reside in Khartoum, Sudan. The Ethiopians David used in his PCAs however are basically from Pagani et al. / the ones you usually see in papers like Hodgson et al. , Shriner et al. and so on.

4. Beni-Amers in Eritrea are thought to mix with Tigres (Ethiopian Semitic speaking pastoralists, linguistically very closely related to Tigrinyas). I wonder if the case is similar at all for these Sudanese ones or if meaningful mixing (enough to show in terms of  the Beni-Amer's general autosomal DNA) between these two groups even in Eritrea truly occurs. Though Tigres have yet to be sampled in any study, to my knowledge.  

5. If you're wondering why Ethiopian Semitic speakers and Cushitic speakers would likely share in some decent amount of ancient/ pre-historic ancestry: [-]

Very Special Thanks to:

All the authors involved in this study and David Wesolowski (the author of Eurogenes).

Recommended reads:

Population Genomics of Bronze Age Eurasia, Allentoft et al.  , it's unrelated to this but is extremely exciting and something I simply had to share. I'll make posts on this in due time as well.