Wednesday, July 15, 2015

Horn Africans: A mixture between East Africans & West Eurasians

I recently got my 23andme results and they bolstered me to perhaps try and speed up getting to work on a post like this. 


Somalis

I've touched on many subjects about Horner / Horn African (Somali, Ḥabesha, Agaw, Oromo, Ari etc.) ancestry and of course made clear mentions of the fact that most of the Cushitic, Semitic & even Omotic speaking peoples of the Horn of Africa are substantially West Eurasian admixed but I never actually made any clear cut lone post about this admixture like I recently did for Central Asians and I figured such a post was long overdue.

You see; as has been noted in several studies on our autosomal DNA (I'm a Somali); Horners like Somalis, Amharas, Oromos, Tigrinyas, Xamir Agaws and Beta Israels / Ethiopian Jews are quite West Eurasian admixed. [1] [2] [3]

Note that the "Afar" used in these studies are not actually Afars
 The above table is from Pickrell et al. 2013; an extensive peer-reviewed genetic study on the West Eurasian input in Eastern & Southern African populations and it displays what I'm talking about quite straightforwardly.


As does the PCA / cluster (Principal Component Analysis) above from Hodgson et al. 2014 utilizing autosomal DNA which allows you to assess and display a group's ancestry. As you can see; Somalis, Tigrinyas, Oromos, Wolaytas and so on all cluster as intermediates between mostly non-Eurasian admixed African groups like the Yoruba of Nigeria or Dinkas from South Sudan (other Sub-Saharan Africa samples to the far left) & West Eurasians like Arabians.


West Eurasia
Again; clearly displaying our basal intermediacy between the two groups owed to the fact that we're seemingly the result of ancient mixing (seemingly episodic in many senses) between West Eurasians and a currently "extinct" African population. 


I say "extinct" because the East African cluster that tends to make up lets say ~60% of the ancestry in your average Somali & ~50% of the ancestry in your average Ḥabesha no longer exists in what one could call "pure form"...

It peaks in Nilo-Saharan speaking peoples sure but in the end mostly all of them have Niger-Congo admixture which Horners completely lack for the most part so they're not representative of the non-Eurasian ancestry [-] in groups like Somalis & Amharas.

What you see in this "Nilo-Saharan" component that forms much of our ancestry and theirs is seemingly just extremely ancient shared ancestry.

Honestly though I wouldn't make too much of modern ADMIXTURE components until we someday have adequate ancient DNA data from across Africa & Eurasia-> we'll understand the African and even West Eurasian ancestry in Horners much better and be conclusive about things once we have such data like we're getting nowadays with West Eurasia and some other regions.

Nevertheless, it is ultimately the case that on a basal level; we look to be a mixture between a mostly (I'd say ~98%) non-Eurasian admixed African component and West Eurasians.


Amharas


The West Eurasian ancestry itself is also pretty interesting in that Horners (whether its Somalis, Aris or Amharas) all seem to be for the time being entirely "ENF" / "West Asian" admixed. Completely lacking Ancient North Eurasian / MA-1 related ancestry as well as Western European Hunter-Gatherer or WHG-like ancestry outside of what could be making up ENF with Basal Eurasian


As you can see; Horner groups like Amharas, Somalis, Ethiopian Jews and so on all come out entirely "ENF" admixed which attests very much to the ancient nature of most if not all of the West Eurasian ancestry in these groups.

The results from David Wesolowski's K8 model above are also supported by the results of Lazaridis et al. 2013's K=20 ADMIXTURE analysis [4]:


Link to the ADMIXTURE run

Horners like Somalis & Amharas lack Ancient North Eurasian and Western European Hunter-Gatherer/ "Unknown West Eurasian Hunter-Gatherer" (WHG like ancestry) input in that analysis above as well; this time from a peer reviewed genetic study from some esteemed geneticists from Harvard Med and other institutions of great repute.

If you're wondering about "Early Neolithic Farmer" though; we don't know too much about it... For now it just seems like what you would get if you account for what shows up as Western European Gatherer ancestry in Early European Farmers like Stuttgart. It tends to peak in the following populations in the K8 model:


It carries Basal Eurasian possibly alongside something similar to WHG in my humble opinion. We will in truth need ancient genomes from West Asia and perhaps even East Africa to truly grasp this component and the Basal Eurasian component it carries.

For now, any inferences about it other than it does carry Basal Eurasian are just speculation and all you should keep in mind is that it's ultimately a West Eurasian ancestral component and the results above displayed in those two Eurogenes K=8 based charts go in line with what is already outlined in various peer-reviewed genetic studies; that Horn Africans like the ones in the first chart carry a lot of West Eurasian ancestry. 

I wouldn't rack my brain over too much else like extreme details on these components themselves until we have ancient genomes to contend with. Things most likely will prove a lot more complex with these components / clusters once we have ancient genomes from West Asia and neighboring regions like North and East Africa to compare modern groups to.

On another note; this autosomal DNA data on Horners which is ultimately what's most important when assessing a population's ancestry is backed up by the Haplogroups of these same Horner ethnic groups:


As the video I linked to above with the word "Haplogroups" will tell you; Haplogroups are mostly a mark of migrations and such. A person can easily be 99% Chinese autosomally/ in terms of their actual ancestry but turn up with a typical Somali Y-DNA marker like E-V32 simply because they coincidentally have a single male Somali ancestor from about ten generations ago for example.

But ultimately the Haplogroup data in Horners is often quite in line with what you get from their autosomal DNA data (ADMIXTURE results and PCAs etc.) and that's that they're an intermingling between "East African" (a bit of a misnomer as a great many modern East Africans from Sudan to Tanzania are non-negligibly West Eurasian in ancestry) & West Eurasian ancestries.

(For further info on the Haplogroups of various Horners as well as a higher resolution look at the mtDNA data above go to Ethio-Helix's blog: [-] [-] , it's all sourced with peer-reviewed studies on population genetics)

Now, if you're a complete layman when it comes to Population genetics; you're probably wondering what each of these lineages signifies. Well, for starters the J-M267 / J1 in Amharas & Afars is basically a Eurasian marker, West Eurasian to be exact:



It also has an obvious spread among African groups with non-neligible West Eurasian ancestry

Whilst A-M118 is an "African" marker that tends to peak in populations with essentially no West Eurasian input like South Sudanese groups. The same situation can be found with Amahar & Tigrinya mtDNA markers (or Somali mtDNA markers). N & M are overtly Eurasian while L0 & L5 and such are overtly African.

Tigray-Tigrinyas

 One thing though that someone reading this should keep in mind is that not all Horn Africans / Horners are like the groups I'm touching on in this post. There are plenty of populations in the Horn who are quite genetically distinct from what you find amongst Somalis, Oromos, Ḥabeshas, Aris & Wolaytas. Such as the Anuak & Gumuz in Ethiopia or Rashaidas and Kunamas in Eritrea or Arabian & Bantu populations in Somalia.


Note


Anuaks as you can see are mostly "African" and mostly lack any Eurasian (West Eurasian) input whilst your average Rashaida probably wouldn't differ much from the numerous Saudi & Bedouin samples you see out there given that they're the descendants of recent migrants who showed up in Eritrea around 200 years ago.

The so far tested Omotic speaking group (Aris) whilst carrying non-negligibly West Eurasian ancestry are also arguably still pretty distinct from Somalis & Ḥabeshas and for example are notably less West Eurasian than those two groups, so don't fall into the trap of thinking every last group in the Horn is like the groups I'm touching upon; the majority seemingly are though.



Horn of Africa

 Finally, one more point I would like to place absolute importance in understanding is that West Eurasian ancestry in Horners is simply not owed to recent input. By recent I mean where many ethnic Somalis think we're somehow a mixture between Arabians & "native peoples", a mixture that may have occurred around ~1400 years ago or so.

Or where some Ethiopians I've encountered ignorantly think they're the result of the same kind of mixing that occurred between South Arabians & "native peoples" 2-3 thousand years ago. These myths are owed to a plethora of misunderstandings such as the Somali peoples' fabled but fraudulent Arabian genealogies & perhaps also the fact that groups like Amharas speak South Semitic languages



I want you to tenaciously observe the ADMIXTURE analysis above from Hodgson et al. 2014. Now, Hodgson et al. had a lot of flaws in some of its assertions but its results are often quite useful (it did also make good points I touch upon about the unreliable dating in studies like Pagani et al. which I note in that old post of mine about the study).

For one; it discovered an ancestral cluster it dubs "Ethio-Somali" that forms at the higher Ks amongst Somalis, Oromos, Wolaytas, Ari Cultivators, Tigrinyas & Amharas:



Now, what this ultimately shows as I tend to explain in this detailed post about the more recent shared ancestry between these groups is that it refutes the idea that any of these groups actually got most of their West Eurasian ancestry from the events their members misguidedly tend to think they did. [note]

To put it simply. That component also shows up in both Somalis & Ḥabeshas like Amharas & Tigrinyas who haven't shared a gene pool arguably in about +3,000 years  and not just that but the component also shows up in the Maasai who are South Cushitic admixed.

West Eurasian ancestry extremely similar for the most part to the ancestry you'd find in Somalis for example also shows up in various Khoi-Kwadi speaking groups who are, like the Maasai; South Cushitic admixed:


"Putative Eastern African ancestry" = basically South Cushitic admixture

This ultimately speaks strongly to the ancient nature of this West Eurasian ancestry.

And not just that but components like "Ethio-Somali" & the "Lowland East Cushitic" component from Shriner et al. 2014[5]- :


Cyan colored component peaking in Somalis

-ultimately tend form in genetically isolated and often somewhat inbred ethnic groups who haven't endured outside admixture in a long while. For Somalis it's quite evident that all of the West Eurasian ancestry in us is basically extremely ancient (pretty much entirely within these components) and most likely goes back far enough to a time when the ancestors of Somalis & the ancestors of lets say Beta Israels / Ethiopian Jews or South Cushites shared a gene pool or at the very least clearly and grossly predates the medieval Islamization of Somalis.

 
(the model above is explained here)


In conjunction with this autosomal DNA data; the Haplogroups you find in modern day substantially West Eurasian admixed Horners as a friend once noted- :


"Y-DNA J1 is more diverse in Ethiopia than Arabia, indicating an ancient presence in the former and some sort of bottleneck in the latter. There is even J*, so neither J1 nor J2, in the Maale Omotics from southwestern Ethiopia. Many Eurasian mtDNA lineages in the Horn like M1, U6, R0a, N1a etc. are often substantially differentiated from lineages found in Arabia. M1 is even almost nonexistent in Yemenis from various parts of the country according to Cerny et al., and autosomally, modern Arabians are significantly more affiliated with more northerly West Asian populations than the Middle Eastern component found in the Horn and the Maghreb

-are not really compatible with a massive recent influence from places like the Arabian Peninsula.

Truthfully; we will need ancient genomes from across East Africa, North Africa and West Asia to truly grasp the history of both the East African cluster based and West Eurasian ancestry in modern Horn Africans but for now it's quite clear much of this admixture is quite ancient.

I would place the earliest influence in some of these groups at circa. 800 to 1000 BCE when the Central Cushitic speaking ancestors of modern Ḥabeshas linguistically shifted to South Semitic [7], this could explain the extra amount of "New West Asian" ancestry Ḥabeshas have over Agaws like the Xamir and recently Ethio-Semitized Agaws like Ethiopian Jews but that's mostly speculation on my part.


Oromos


I suppose I'll see someday if I'm still alive when they start sampling ancient remains across the Horn and various other parts of Africa and West Asia  but for the time being; that along with a lot of what I outline in many of my older posts about the Horn is what we tend to know about Horner ancestry.

In the end though Horn Africans / Horners like the groups I've touched upon and ones seemingly closely related to them (Afars, Sidamas, Gurage, Sahos etc.) are all ultimately on a fundamental level a mixture between West Eurasian & non-Eurasian / African ancestry that tends to peak in groups like the Dinka.

I strongly advise reading all of the posts I'm going to be recommending below and also the peer-reviewed papers I tend to cite.


Reference List:









Recommended reads:

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

2. The Oromo people: Heterogeneous

3. The Jewishness of Ethiopian Jews

4. The Omotic Cluster: A Horn Specific Cluster

Notes:

1. I would note that much of the West Eurasian ancestry in Horners while ultimately West Eurasian is probably African mediated / owed for example to populations that were probably by majority West Eurasian in ancestry but geographically resided in Africa itself; North Africa in particular. They may have had East African cluster like ancestry themselves but honestly; we'll know when we have sufficient ancient genomes from across Africa and Eurasia.

2. If you're anyone from an as of yet generally un-sampled (in terms of autosomal DNA) Horner ethnic group (Afar, Saho, Sidama, Gedeo, Kambaata, Gurage, Benadiri, non-Ari or Wolayta Omotic speaker, Somali Bantu etc.); do order a 23andme kit and if you wish: email me your raw data as well as your Haplogroup data once you have your results.

It would really be extremely enlightening to see some hint of your group's genomic data via you and perhaps some of your acquaintances and relatives. It won't be like a peer-reviewed population genetics study or anything extensive (small number of samples to work with) but it'd be extremely intriguing nevertheless. My email: Awaleking@gmail.com

3. I advise you to keep reading this blog (looking at newer posts) because newer and newer studies keep coming out and I might have to tack extra details onto what's in this blog post (i.e. some of the new stuff we know about some of West Eurasian that might be in some Horn Africans).

16 comments:

  1. Did you make the Eurogenes K8 ancestry proportions yourself?

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    1. "Did you make the Eurogenes K8 ancestry proportions yourself? "

      I simply took the Eurogenes K8 spreadsheet- :

      https://docs.google.com/spreadsheets/d/1x8pm8sVcHqceiNFJMO082kxaBF5ePr4__bAK05VQRFw/edit#gid=1138248510

      -got the averages for each population via google sheets, rounded them (some would for example be 41.32% or some such) and then made the charts you see.

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    2. But I should add that for example I added "Unknown Eurasian" or "Unassigned".

      Unknown Eurasian: in K8 Horners, Arabians, Jews, Northwest Africans and some such keep showing "East Eurasian". David who made K8 notes that this isn't "real East Eurasian" but some sort of odd Eurasian element that won't fit well into any other clusters. Truthfully; I would advise not making much of it. But he noted to me via email once for example that in his fateful triangle (http://eurogenes.blogspot.com.au/2014/12/the-fateful-triangle.html); this odd affinity is what pulls Arabians a bit "eastward".


      Unassigned: just an amalgamation of nonsensical decimal point noise values various samples probably showed. Like one Tigrinya showing 0.05 "Oceanian" and 0.05 something else nonsensical.

      Unknown Eurasian 2: Anuaks and such turn up with "ANE" in K8 but as the chap who made it noted to me-> this is obviously not "real ANE" but some sort of archaic Eurasian element in his opinion (something to what's going on with the other "Unknown Eurasian"). Wouldn't make too much of it.

      Otherwise-> the components and percentages (once rounded) are as you'd find them in the original K8 table.

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    3. Btw, this is stalker from ABF :P

      Nice blog post, are you doing a world regions series, because you've done central asia and east africa so far?

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    4. "Btw, this is stalker from ABF :P"

      Heh, welcome, then. :)

      "Nice blog post, are you doing a world regions series, because you've done central asia and east africa so far?"

      Well, East Africa and further the Horn is where I'm from so I'm not necessarily going "international" with this post. But yes, I do like to and possibly will touch upon various world regions from time to time. There's going to be some interesting stuff from South Asia soon (they're going to be sampling remains from the Harappa civilization, apparently) and I plan to touch upon that to some extent for example.

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    5. Harappa is going to be very interesting. I think they'll come out very Iranian-like, but with significant native south asian admixture, but we'll see. Do you have a link to the pre-print for the south asian paper?

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    6. No pre-print but here's some news on the subject:

      http://timesofindia.indiatimes.com/india/Ancient-Harappan-era-skeletons-found-in-Haryana/articleshow/46930943.cms

      http://www.dawn.com/news/1180023

      http://www.bbc.com/news/world-asia-india-32313702

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  2. How old is the Ethio-somali part admixed with the basal HOA people?? IMO the idea of total rejection of recent Eurasian admix is not acceptable as we know Y DNA haplotypes like E-M34 and J158 are yound and recent comers from the middle east. The myth of Habeshas linked with the middle east around 980 B.C has got several other evidences.

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    1. "The myth of Habeshas linked with the middle east around 980 B.C has got several other evidences."

      It's hardly a myth and does have genetic evidence behind it as even I have noted but there's no evidence of further notable West Eurasian gene flow into Habeshas after that linguistic shift event from Central-Cushitic to South-Semitic about 3,000 years ago. And this is still ancient admixture that doesn't make up the majority of their ancestry (most of the ancestry in Habeshas still seems to mostly be shared with their Cushitic speaking neighbors whether Central-Cushitic (Xamir/Xamtan) or East-Cushitic (Somalis)). I noted much of this here:

      http://anthromadness.blogspot.ae/2015/02/cushitic-admixture-levels-somalis-as.html

      Somalis and Agaws like the Xamir/Xamtan were seemingly left untouched by this ancient South Arabian influence too.

      "How old is the Ethio-somali part admixed with the basal HOA people??"

      Exact dates are difficult to ascertain and honestly; I wouldn't make too much of the actual component itself and it's representation of a possibly "real ancient people" but rather that it signifies shared ancestry between groups such as Somalis, Habeshas; groups that haven't shared gene pools meaningfully in seemingly over 3,000 years which speaks if anything to the pre-historic nature of most of the West Eurasian ancestry present in these populations.

      Also, I wouldn't call our non-West Eurasian side "basal HOA"; most evidence I've seen (from genetic to linguistic) tends to suggest that Horn Africans of types I've been talking about in this blog post come from further up north in Northeast Africa; with their ancestors having migrated from areas like Sudan down into the Horn very early on in pre-history; this is most likely why we share so much ancestry with modern Sudanese populations like the South Sudanese.

      An old post of mine on Ethio-Somali:

      http://anthromadness.blogspot.ae/2014/12/ethio-somali-is-farce.html

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    2. Awale Abdi your blog is a God send, gosh do you know how many people are still calling you and other Horners Black Caucasians? This is fascinating that the non Eurasian component is closely related to the Southern Sudanese. How did you get into this stuff? I need to learn, I need crash course in genetics etc.

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    3. I replied to you via google+, by the way. :-) So that should answer your questions about how you can learn stuff like this. Also, thanks for the compliments and yeah; I'm aware of the pseudoscience a lot of people still believe in like the "Hamitic" and "Ethiopid" "races".

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  3. When exactly did these West Eurasians begin migrating back-to-Africa during neolithic times? When are the specific dates that these migrations first begin back to the HOA?

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    1. Honestly... I can't say with any exact certainty. These back-migrations were probably Neolithic but we're really going to need ancient DNA from around Egypt & Sudan over the last ~15,000 years to have exact dates.

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  4. Seems like Horn Africans SSA ancestry is some sort of ancient East African ancestry. Do we have any idea regarding the haplogroups of this ancient EA ancestry? Not only that but how much West Eurasian autosomal DNA do Sudanese people from North Sudan (specifically the "Sudanese Arabs") have overall? Are they largely a product of back-to-Africa migrations from West Asia during neolithic times and Ancient East African ancestry like Horn Africans? The table from Pickret et al. didn't include Sudanese but a lot of other Northeast African ethnic groups.

    Overall it's interesting to see Maasai are 20% West Eurasian admixed mostly as a result of Cushitic migrations and intermarriage with Cushitc peoples as they were the vector for this West Asian DNA -- would've hoped Tutsi would've been included in the table to see if they had any autosomal West Eurasian DNA. I know they're y-DNA is like 20% E1b1b.

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    1. "Do we have any idea regarding the haplogroups of this ancient EA ancestry?"

      We have a good idea based on the mtDNA diversity of populations like Somalis (http://anthromadness.blogspot.com/2015/08/somali-mtdna-frequencies.html). And in terms of Y-DNA, they were probably carriers of E-M215 subclades (particularly subclades of E-M35) and A-M13, at least in my humble opinion. You can see a low-res representation of the Y-DNA lineages among various Cushitic and Ethiopian Semitic Horn Africans here:

      http://anthromadness.blogspot.ae/2016/06/the-african-west-eurasian-elements-in.html

      "would've hoped Tutsi would've been included in the table to see if they had any autosomal West Eurasian DNA. I know they're y-DNA is like 20% E1b1b."

      I've seen some commercially genotyped Tutsis (23andme etc.) and they tend to be like 60-70% Somali-like from an autosomal perspective which means they're even more Cushitic speaker admixed than Maasais overall. ~65% or so Somali-like would mean something like ~25% West Asian/West Eurasian, I guess. Studies like Tishkoff et al. have done tests on them too but I don't recall exact values being espoused and that study's data is somewhat outdated (it even used an old method like STRUCTURE instead of ADMIXTURE):

      http://anthromadness.blogspot.ae/2015/05/south-cushitic-admixture-in-southeast.html-

      "Not only that but how much West Eurasian autosomal DNA do Sudanese people from North Sudan (specifically the "Sudanese Arabs") have overall? Are they largely a product of back-to-Africa migrations from West Asia during neolithic times and Ancient East African ancestry like Horn Africans? The table from Pickret et al. didn't include Sudanese but a lot of other Northeast African ethnic groups."

      I've done some posts on the Northern Sudanese:

      http://anthromadness.blogspot.ae/2015/06/sudanese-arabs-beni-ameri-beja-and.html
      http://anthromadness.blogspot.ae/2015/10/inferences-that-can-be-made-from.html

      I'm actually planning on doing another post soon as I've managed to find a new study with some new and seemingly viable Sudanese Arab and Nubian samples so stay tuned.

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  5. Very interesting reading! Thanks for sharing your knowledge. Did a 23andme test a few years back. I'm Somali like you.

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