Mediterranean and its connection to WHG admixture

It seems that just as Caucasus is somehow tied to the ANE admixture across the West Asia/ Middle East-> "Mediterranean" which tends to peak in Sardinians & Northwest Africans (Imazighen/ Berbers) is the product of a WHG influence on the basic "Near Eastern"/ "ENF" (Early Neolithic Farmer-> EEFs before their WHG admixture).

I somewhat suspected this based on Sardinians who before we knew about all these ancient genomes were consistently the peak of the "Southern European"/ Mediterranean component which also peaked in NW Africans [-] [-]. Sardinians trace over 80%~ of their ancestry to the EEFs (Neolithic group in Gamba et al.) and tend to overlap with them in plots from various studies [1] [2]:

[2]

They also pretty much lack ANE as Lazaridis notes and the author of Eurogenes (Davidski/ Polako) also confirms with his test that is pretty much as good at identifying ANE as Raghavan et al. If they show ANE-> it would be trace amounts of 1-2%~. They are by all accounts ENF + WHG with the following averages at Eurogenes K8:

65%~ ENF

35%~ WHG

 Surely, they as this component's peak should be representative of the mixture it represents? However I found this preposterous and never gave it much thought because it never dawned on me that NW Africans would have WHG/EF (European Forager) admixture.

However some updates to Eurogenes K=8 shows just that:

Moroccans: 16%~

Tunisians: 14%~

Mozabites: 14%~

Here is the spreadsheet & those are the WHG/ EF levels of NW Africans. The rest of their admixture is essentially ENF + Niger-Congo + AEA (Ancestral East African/ the standard East African/ Nilo-Saharan component).

The run's ability to identify WHG seems quite accurate and it finds the generally expected and usual levels (IIRCC) in Europe as per the studies. It also finds nearly 10%~ WHG/ EF admixture in its Turkish samples which are from Cappadocia and in the past such as in Paschou et al; Cappadocians demonstrated a clear pull towards Southern Europeans. [3] 

The levels of this component in the Levant are also consistent with data like how Arabized Levantines alongside Yahudim tend to plot with Jews like Ashkenazim whom Lazaridis et al. itself notes have EEF (WHG admixed) admixture (being 19%~ WHG on average) and they tend to pull more toward Southern Europeans of the Italic-Greek variety whilst other Jews who are fairly similar to them also pull that way, Cypriots as well in basically every other PCA plot (Principal Component Analysis) one may encounter them in also show this pull but pull towards those populations less than their Judaic counterparts do and sure enough- :

Cypriot: 11%~ WHG/ EF

- they are less WHG/ EF influenced than the Yahudim groups.

If one had to explain I would go with an explanation one chap gave me and I'll just quote him:

"As for how it came to be , well Berbers/NW Africans are resultings from Ibero-Maurisian hunter -gatherers (of ultimate Paleothic Eurasian ancestry long before the Neolithic) mixed with Early Neolithic Farmers (Basal Eurasian spread) and then mixed with Afro Asiatic speaking Pastoralists from Northeast Africa (roughly 5,000 years ago with the spread of Neolithic Pastoralism in Central Sahara)."

I'll honestly do more research and try to confirm this or place it under some kind of scrutiny as I'm not at all well-versed when it comes NW African ("Maghreb") pre-history. Although prior studies on NW Africans have found that there seems to be both influences from Europe & influences from the Near East present in NW Africa. [4] And as the writer of that paragraph notes there are some general observations when it comes to NW African genetics like the following:

"NW Africans are resultings from various Eurasian migrations , and the last one was the proto Berbers (AfroAsiatic pastoralists) from Northeast Africa who were a mix of East African and SW Asian. The oldest are the Ibero-Maurisian hunter gatherers , who were 20 000 years old (see Mechta Afalou type) with ultimate Eurasian ancestry (see the Taforalt MTDNA remains) , then you had also EARLY Neolithic Farming and the whole MTDNA H (H1 H5) dominance. Pre Afro-Asiatic NW Africans were most similar to Sardinians genetically , and considering we found very old E1A lineages in Sardinia , there must have been some contacts with North Africa. On a West Eurasian-centered PCA plot , NW Africans also cluster in between Sardinians and Egyptian/Bédouins. You do know that the main MTDNA lineages in the Maghreb (H , JT , U) show a discontinuity with Egyptians , meaning much of the maternal ancestry of Berbers didn't come from the Nile Valley (unlike their main YDNA)."

I may take the time at some point to make a post on NW African pre-history and possible more detailed explanations for their WHG/ EF admixture however for now I'd advise any parties reading to just focus on the fact that the data (them having such admixture) is there and make what you will of any other data and how this admixture came to be.

All things considered though... It seems clear that the "Mediterranean" component that used to come up in runs before we just began identifying the ENF, WHG/ EF & ANE admixture across West Eurasia (counting North Africa) is in the end; ENF + WHG/ EF

An unknown Hunter-Gatherer population extremely similar to European hunter-gatherers like Loschbour seem to have contributed to the populations of the Maghreb, the rest of their ancestry is essentially AEA + Niger-Congo (20-30%~) [4] [5] + the generic Middle Eastern component called "Near Eastern" in the author of Eurogenes' run, otherwise dubbed "ENF" (Early Neolithic Farmer) as it is surely what the farmers of Europe would have been like prior to acquiring WHG admixture like Stuttgart and the rest did. 

Maghrebis have no ANE though which fits with their lack of to near lack (very low levels, like with Peninsula Arabians) of Caucasus admixture. ANE also likely entered the Middle East/ West Asia via the Caucasus (where it peaks)  and it seemingly never went father than Northern West Asia (Caucasus, the Iranian Plateau, Anatolia, The Levant & Mesopotamia/ Iraq).

The Mediterranean populations ultimately look to be a mixture between WHG/ EF & ENF with an ANE influence in the Levant (Yahudim included), Anatolia & Southern Europe with this influence gone in Northwest Africa and only miniscule in Egypt. Maghrebis are ultimately also differentiated in terms of autosomal DNA via their heightened African admixture albeit Arabized Levantines have 5 to 15%~ African admixture [6] and Yahudim like Ashkenazim and the like also have a teensy negligible African influence.

And of course one must keep in mind the various distinct migrations that created these seemingly related populations which is visible i.e. in their Haplogroups (Y DNA & mtDNA markers); they're not exactly the exact same population spread out across the Mediterranean. 

In the end there looks to be just one Middle Eastern component which would be ENF (often represented by Southwest Asian/ Arabian?) which peaks in non-Levantine Bedouin, Saudis and the like who lack WHG/ EF & ANE influences. Mediterranean & Caucasus for now simply look ENF with WHG/ EF & ANE influences respectively.

The puzzle now is figuring out what ENF and its Basal Eurasian element are via ancient genomes from the Middle East & East Africa but I fear that maybe a long way off...

Reference List:

1. Ancient human genomes suggest three ancestral populations for present-day Europeans, Lazaridis et al.

2. Genome flux and stasis in a five millennium transect of European prehistory, Gamba et al.

3.  Maritime route of colonization of Europe, Paschou et al.

4.  Genomic Ancestry of North Africans Supports Back-to-Africa Migration, Henn et al.

5. Genome-Wide and Paternal Diversity Reveal a Recent Origin of Human Populations in North Africa, Fadhlaouli-Zid et al.

6. The History of African Gene Flow into Southern Europeans, Levantines, and Jews, Moorjani et al.

Notes:

We had a good discussion about ANE and its presence in the Near East along with tidbits of this post's subject matter at this thread.

Ultimately though... The only way we'll really know anything conclusive about the Middle East, the Caucasus & North Africa is by sampling ancient genomes in the area. Once we do that... Everything will be truly reliable. So I would also advise an air of skepticism whilst taking all this in.

Happy Holidays!

Lazaridis Somalis from Kenya not all representative... Some are Borana admixed?

A Somali I correspond with who has an account on 23andme whilst being tested via the site brought to my attention that the Kenyan Somalis from Lazaridis et al.'s supplemental [1] reminded him of a Gharre Somali who was half Ogadeni. The Gharre apparently clustered between him and Borana Oromos in a PCA plot (Principal Component Analysis).

I was curious to see if this would be the case for the Kenyan Somalis and approached the author of Eurogenes; asking him to throw them into a PCA plot with Pagani et al. Somalis [2] who are essentially 100% representative of ethnic Somalis, coming out no different from over 90% to almost all of the full Somalis on ancestry services like 23andme and also coming out relatively identical to their Ethiopian Somali counterparts who were also tested in Pagani et al. with the only quantifiable difference being the low levels of Omotic admixture in many of the Ethiopian Somali samples (2%~ average).

Sure enough, about 6 to 8 of the Kenyan Somali samples came out as outliers among the Somalis in an "intra-African" plot integrating other Horners:

Link to Plot

 As you can see; 6 to 8 of them break off from other Somalis and cluster as intermediates between us and Oromos who are not of the Agaw ~ Ḥabesha-like Highlander group and not of the particular group that tends to overlap with Somalis in PCA plots-> essentially the southernmost Oromos in plots/ Borana Oromos who are passed around between studies and runs & tend to break off on their own.

Here are other plots to put it into perspective.

Ultimately the one flaw with these plots is that they do not measure (as you can see) which group pulls more towards West Asians & which group pulls more towards Nilo-Saharans (Anuaks, South Sudanese et al.) and so on so I asked him to integrate these Kenyan Somalis with Pagani Somalis of both the Northern Somali & Ethiopian Somali variety:

Link to Plot

 I asked him to do so because Borana Oromos tend to come out less Middle Eastern (ME) admixed than other Horners and they break off often with Wolaytas who are known to be a little less ME admixed than Somalis. [3] They are essentially the southernmost Oromos in that PCA plot and also the Oromos who break off with Wolaytas in Hodgson et al.'s PCA plot. [4]

What this ultimately reveals is that 6 to 8 of these Kenyan Somalis look to be intermediates between representative Somalis & Borana Oromos. They do not at all overlap with the Borana samples but merely straddle between them and the Somali samples from Northern Somalia & Ethiopia who are quite representative of their ethnic group. Also, one must note that about 5 or so of these Kenyan Somalis perfectly overlap with the Ethiopian and "Somalian" Somalis from Northern Somalia so one musn't fall into the error of thinking that these 6 to 8 samples are at all representative of Kenyan Somalis at large. 

This also means they are a little less ME admixed than other Somalis. Another individual from the Horn, an Ethiopian of Oromo & Harari descent told me that at Lazaridis' K=20; these samples showed no West Asian (Caucasus) like admixture [1] which is a component Somalis often show at low levels however different studies and ADMIXTURE runs have different ways of identifying these components and I would not make too much out of such results but Borana are known to lack the more "Mediterranean" & "Caucasus" like admixed from the Middle East Somalis, Ḥabeshas & Xamir Agaws alongside other Oromos and even Wolaytas show most of the time (especially on the "Mediterranean" count) so perhaps this is the result of lowered levels of such admixture via an influence from Boranas.

This is consequently the running theory now as these Kenyan Somalis seemingly don't show Niger-Congo admixture (IIRCC as per Lazaridis' supplemental) so that is not at all what is causing the greater pull towards Nilo-Saharan & Niger-Congo speakers. Instead I would wager that they are possibly Borana admixed.

The Somalis in Kenya such as the Ajuran clan (associated with the old Ajuran Sultanate and its founders) often interact with Borana Oromos, in fact they interact to a point where many Ajuran are noted to speak Afaan Oromo as their first language and Somali as their second; they have also come to live amongst the Borana and adapt facets of their culture as is described here:

"Among the Kenyan Ajuran people, the majority speak the Borana language as their first language while others speak the Somali language as their first language especially those from Wajir North District in the areas of Wakhe and Garren. It is vital to note that since Somali is the language of wider communication in Northeastern Province, even the Ajuran who speak Borana as their first language learn the language. The link between the Garreh and Ajuran is their primary language which is Borana and not Somali."

The text comes from a missionary website [-] which utilizes sources like the CIA world factbook [-] and like to gather its info and the information is quite legitimate, it would seem. I have heard of their situation myself through a few relatives who've been to Kenya and encountered Ajuran Somalis & of course; the Borana are found in Kenya as well.

The other Somalis in Kenya tend to be Ogaden clan members however other clans are present... I ultimately assumed that these 6 to 8 peculiar Somalis might be a case of mixing between Somalis & Boranas given their intermediate clustering between us and them and in the Intra-African plot which is much more detailed than the world plot in noticing variation (consult my notes); one can see that a single one of them actually overlaps with one Borana Oromo.

Ultimately though, I would say that this plot Lazaridis et al. shared in their supplemental is perhaps not representative of Somalis:

More representative Somalis would pull closer towards EEFs like Stuttgart by some degree however it is interesting how the Lazaridis plot's Somalis look very close-knit despite their being clear "heterogeneity" present (perhaps they "treated for outliers"? I don't know). Ḥabeshas & Xamir Agaws alongside Beta Israels would cluster where the lonesome African-American (who looks to be 50%~ European based on his clustering) is sitting or perhaps just a bit closer to EEFs than he is.

On another note; the Kenyan Somalis look to be from Garissa.  All 13 of them were taken from the repertoire of a chap named George Ayodo whom Lazaridis et al. cites as the source of their samples:

[1]

The information for various samples is shared here. It would seem that four of the Kenyan Somali samples are Female while the rest are Male. It's interesting since Garissa is not exactly smack-dab where the Ajuran are known to be  (albeit these Somalis don't need to Ajurans to be Borana admixed) and I am unaware as to whether some Borana may be there or even if these Somalis are permanent residents. Either way though; this is all interesting to say the least.

Reference List:

1. Supplemental Data for Lazaridis et al.

2. Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool, Pagani et al.

3. Ancient west Eurasian ancestry in southern and eastern Africa, Pickrell et al.

4. Early Back-to-Africa Migration into the Horn of Africa, Hodgson et al.

Notes:

 1. The world plot is hampered somewhat due to utilizing low quality SNPs/ a lower number of SNPs than the creator was used to. I.e. 100,000 SNPs were used instead of 200,000 mostly because the Kenyan Somalis and the Pagani Somalis (IIRCC) were tested using a different chip set hence only 100,000 or so of their SNPs overlapped. What this ultimately does is that groups demonstrate a little less variation than they usually usually would in such a plot however the data is relatively the same.

2. Borana tend to be about 20%~ Omotic admixed (OromoB samples, run created by another ethnic Somali using Pagani et al. samples) so I wonder if we can test these Kenyan Somalis for the component and see how they come out.

Happy Holidays! A Merry Christmas to any Christians (I'm not one) reading this or anyone who celebrates the occasion (I don't)!

ANE & its connection to Caucasus admixture

For those of you who are wondering what Ancient North Eurasians (ANEs) are; they seem to be a pre-historic group who are if anything more related to Upper Paleolithic Siberians (No, don't think of East Asians or peoples like them) than any modern population, they also prove relatives of "West Eurasians", sharing an origin point with the ultimate ancestry of Loschbour and the West Eurasian side in Middle Easterners and Neolithic Near Eastern farmers (what part of them isn't WHG at least) as is demonstrated in this diagram in Lazaridis et al.'s supplemental:

[1.2]

They also found that this population apparently contributed significantly to Native Americans as they demonstrate with this other diagram from their original paper (that I often share) whilst positing that they contributed to Near Easterners as well. Another study improved upon this, finding that ANEs contributed significantly to various populations across Eurasia. I.e. to Central Asians, various predominantly "East Asian" (autosomal DNA/ admixture wise) Siberians and so on. There may even be a small ANE element in East Asians like the Han Chinese...

The study is called "Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans" ("Raghavan et al.") [2]. Some comments from it's abstract on ANE:

"Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought."

MA-1 is "Mal'ta boy"; a little boy who lived approximately 24,000 years ago whose remains were found in Siberia. His genome was eventually sequenced; he seems to be a rather unmixed example of Ancient North Eurasians. Other remains were found and their genomes were sequenced like AG-2 (Afontova Gora-2) for example...

Raghavan et al. gives us this PCA/ cluster demonstrating the general pull toward MA-1 & thus ANEs by various Eurasian populations (Native Americans counting within the "Eurasian" term here):

Ancient North Eurasians seemingly contributed significantly to Central Asians (Kazakhs, Turkmen et al.), South Asians (various ethnic groups of India, Pakistan, Bangladesh etc. etc.), Native Americans in addition to various Siberian populations. Their contribution to Native Americans is significant enough to be 15 to 40%~ essentially as Raghavan outlines:

"Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World."

As they mention &  Lazaridis et al. discovered earlier on; the rest of the admixture in Native Americans is East Asian-like. So the idea that they were basically exactly like East Asians when they crossed over to the Americas is outdated now, instead it's currently believed that they were part ANE & part pre-historic "East Asian" when they made it to the Americas. Perhaps as Raghavan et al. notes in its abstract; this is why some ancient Native American remains that have been found do not "morphologically" resemble East Asians.

The old Lazaridis et al. diagram model demonstrating the gene flow into Karitianas (used as stand-ins for Native Americans/ Amerindians):

[1]

Lazaridis et al. makes mention of there being ANE input in the populations of West Asia & interestingly a new analysis by the author of Eurogenes which seems as adequate at identifying ANE as Raghavan et al. is (can find similar to the same results) whilst utilizing different techniques indeed finds ANE in West Asia whilst unsurprisingly finding none in Northwest Africa with only trace amounts (1-2%~) in Lower Egypt (Northern Egypt). 

The pattern for West Asia seems to be that the Caucasian populations have the highest proportion of ANE admixture and they actually demonstrate this in a recent plot Davidski over at Eurogenes (the author) shared where he demonstrates that ANE is the cause for "West to East Shift" in Pan West Eurasia PCA plots:

 

Link to plot

Caucasians seem to have the most with Turks, Persians (Iranian samples), Assyrians & Levantines coming in right behind them while Peninsula Arabians (Bedouin B, Saudis) seem to lack ANE altogether though Yemenite Jews who look to be a good representation perhaps of the pre-Islamic Arabian Peninsula; have small trace amounts of 1 to 2%~ much like Lower Egyptians.

Here are the proportions in certain Caucasians simply to give an idea of their levels of ANE admixture/ ancestry:

• Abkhazians: 22%~
• Armenians: 15.5%~
• Non-Jewish & Laz Georgians: 21%~
• Azeris: 18.5%~

Link to spreadsheet for the results of West Eurasia as a whole (nearly, at least).

Abkhazians & Azeris have more than even the most ANE admixed populations of Europe who reside mostly in Eastern Europe (17-18%~ being their levels on average). This geographically makes sense to me as the Europeans most effected by ANE admixture are those in the East and if I recall correctly; the entryway of these Ancient North Eurasians into Europe would have likely been the East? So just to the south of Eastern Europe would be the Caucasian mountains where the Caucasian populations would have possibly lived even back then?

Now, this heightened ANE influence has led myself and others to believe that the component most studies either call West Asians or Caucasus/ Caucasian (independent runs do this as well) which is found all across the Middle East from Iran, to Iraq, the Levant, the Arabian Peninsula, Egypt and even one area of Northwest Africa in non-negligible levels (Libya) likely caries an ANE influence with it. As the populations who define it and it also peaks in are the Caucasians like Armenians, Abkhazians, Georgians and so on who have as you can see; a very non-negligible amount of ANE admixture.

One study that I recently ragged on noticed the West Asian/ Caucasus component (dubbing it "Eurasian") and here is its ADMIXTURE run:

[3]

For one, you can see the highest proportion of the component in that run is in Turks, Levantines (Druze included) and Persians (Iran) and likewise even Lazaridis et al. with its original PCA plot demonstrates which West Asian populations have the greatest pull toward MA-1 & AG-2:

[1]

The clime is clearly-> Turks ~ Persians> Levantines ~ Yahudim> Peninsula Arabians. Some Peninsula Arabians go more south than Stuttgart or Loschbour who are modeled as/ found to be 0% ANE though BedouinB & Saudis have about 5 to 20%~ African admixture (Niger-Congo + Ancestral East African/ Nilo-Saharan) however the current seemingly lack of ANE in them may speak to where they cluster. Nevertheless, Lazaridis et al. points out that it couldn't test the Bedouin (of the BedouinB variety) for ANE due to their African admixture. [1.2]

These are the averages for Persians and Turks who peak in Caucasus/ West Asian admixture in West Asia (while Peninsula Arabians have the least across the entire region):

• Turks: 16.5%~
• Persians: 19.6%~

Arabized Levantines like Palestinians, Jordanian, Lebanese Muslims & Christians alongside Syrians have a little less Caucasus admixture than they do and arguably display less ANE:

Syrians: 9.3%~

Palestinians: 5.4%~

Jordanians: 6.6%~

Lebanese Muslim: 9.8%~

Lebanese Christian:  7.1%~

Peninsula Arabians have the lowest of the West Asian/ Caucasus ADMIXTURE component and seem to show no ANE admixture whatsoever with only Yemenite Jews showing trace amounts at negligible levels. Northwest Africans (Imazighen/ Berbers) do not tend to show the West Asian/ Caucasus component and if they ever do-> it's a very negligible/ low amount such as the amounts they show in Hodgson et al. (the ADMIXTURE run I shared) where they have far less than even Peninsula Arabians. As a matter of fact; those isolated Tunisians [4] from Hodgson et al. do not even show a pint of West Asian/ Caucasus and an old likely somewhat less fine tuned and accurate analysis by the author of Eurogenes finds that they lack ANE [-] [-] which would be consistent with the clime of West Asian/ Caucasus admixture across West Asia itself-> the more you have of this admixture, the more ANE. Libyans show non-negligible levels of this component but they look fairly similar to Lower Egyptians who have only small trace amounts (negligible levels) like Yemenite Jews.

One could argue that African admixture is skewing the results of some of these groups however Arabized Levantiens as can be noticed in Hodgson et al.'s run are non-negligibly African admixed (5 to 15%~), other studies have launched inquiries into this in the past and found that they are something along the lines of 5 to 15%~ African admixed [5] (Niger Congo + Ancestral East African) but they still show ANE levels which I would argue are quite reliable. For one, Levantines cluster just to the right of Tuscans, Sicilians and Greeks who in Lazaridis et al. are roughly shown to be as ANE admixed as they are; the Eurogenes analysis also finds relatively the same levels in lets say Tuscans, Sicilians and also Yahudim like Ashkenazim & Maghrebim such as Moroccan Jews who in Lazaridis et al. and even the Eurogenes Pan West Eurasia plot pull toward ANE relatively as much as the Arabized Levantine populations do.

Lebanese Muslims also tend to show more African admixture than Lebanese Christians yet they show visibly higher levels (some of them having as much as 10%~ ANE admixture) of ANE admixture than their Christian counterparts so this might mean Eurogenes' analysis is not at all skewed by African admixture.

The clime in ANE admixture across West Asia or even the more large MENA region seems for now to be clearly linked to a group's proportion of Caucasus admixture with the Caucasian, Iranian (Kurds seem to always come out fairly similar to Persians) & Turkish populations being its peak. The Levantine populations (Yahudim & Cypriots included) as well as Iraqis (i.e. Arabized Iraqis & Assyrians) at large seem to follow suit and then it would be the trace amounts in Lower Egyptians and Yemenite Jews. The rest of "MENA" looks to be a dead zone of sorts for ANE admixture. 

Most of the Caucasus in Arabians is likely barely different from their Southwest Asian/ Arabian component which is visible in that Hodgson et al. run/ it's more indicative of unmixed Middle Eastern/ West Asian admixture that would theoretically (as we're learning from Lazaridis et al. & other studies) prove to be-> West Eurasian + Basal Eurasian (whatever this component may turn out to be once we have ancient genomes from the Middle East & preferably also East Africa sequenced).

I'll definitely blog about this someday if we ever have new results to counter anything I've posted.

Reference List:

1. Ancient human genomes suggest three ancestral populations for present-day Europeans, Lazaridis et al.

1.2. Supplemental Data for Lazaridis et al.

2. Upper Palaeolithic Siberian genome reveals dual ancestry of NativeAmericans, Raghavan et al.

3. Early Back-to-Africa Migration into the Horn of Africa, Hodgson et al.

4. Genomic Ancestry of North Africans Supports Back-to-Africa Migration, Henn et al.

5. The History of African Gene Flow into Southern Europeans, Levantines, and Jews, Moorjani et al.

Notes:

1. The BedouinA samples are not actual Peninsula Arabians, some Saudis may not be as well. BedouinA were cut off from other Bedouin in Lazaridis et al. and often are in many PCA plots, studies & independent runs because they seem to look more like the Arabized Levantine populations they live amongst (Syrians, Lebanese etc.) and display similar admixture levels to them alongside ANE admixture, they also of course overlap with them them in plots-> something actual Peninsula Arabians (discounting Yemenite Jews) who are distinct from Levantines and seemingly lack ANE influences simply do not do.

2. Ultimately though... The only way we'll really know anything conclusive about the Middle East, the Caucasus & North Africa is by sampling ancient genomes in the area. Once we do that... Everything will be truly reliable. So I would also advise an air of skepticism whilst taking all this in.

Finally:

Thanks must go to Davidski/ Polako for all his great work over at Eurogenes.

I'd also like to thank a member of Forum Biodiversity whose username I won't add here until I get his permission. He is in the end responsible for bringing this ANE influence in Caucasus to my attention. So... Thanks, man.

Happy Holidays!

"Ethio-Somali" is a farce...

I recently encountered a member on a Forum I frequent and he made mention of Hodgson et al.'s following statements in its abstract which is called back to on wikipedia when discussing Somali autosomal DNA:

"The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka."

Along with its following claim that this supposed component is related to the "Maghrebi" component:

"A single prehistoric migration of both the Maghrebi and the Ethio-Somali back into Africa is the most parsimonious hypothesis. That is, a common ancestral population migrated into northeast Africa through the Sinai and then split into two, with one branch continuing west across North Africa and the other heading south into the HOA. For the Ethio-Somali, the lowest F_ST value from the ADMIXTURE estimated ancestral allele frequencies is with the Maghrebi (Text S1), which is consistent with a common origin hypothesis."

[1] 

I often wonder though how some of these studies make it onto journals or how they were made by professionals. Ultimately, "Ethio-Somali" is not a real ancestral component, nor is it truly related to another "not real" component they dub "Maghrebi" (it is but not in the way they perhaps posit). The study does good work in some respects such as showing us the flaws in dating systems for admixture such as ALDER & ROLLOFF. Horners used to and sometimes still do have their admixture dated to about 2 to 3 thousand years ago using dating methods and of course those dating points make no sense and are generally not possible. They also in my own opinion do a good job in dating some of the admixture in the Horn as being newer than some of the rest; ultimately identifying the newer Middle Eastern input into Agaws ("Afar" samples are in fact Xamtanga speaking Agaws) & Ḥabeshas (i.e those who have been tested so far such as Tigrinyas & Amharas)  over Somalis but otherwise...

It's results are honestly based on finding some mixed component at K=12 via the ADMIXTURE software and by some insane leap; it assumes that the component is not mixed/ "Near Eastern/ Middle Eastern + East African/ "Nilo-Saharan" " as it really is if you simply observe their own run:

[1]

Like in most ADMIXTURE based runs using African & Eurasian (Out of Africa) populations; the run at K=2 starts out with every population being utilized coming out as either "Eurasian" or "African" (in this case these two macro-components are represented by "European" & "Niger-Congo") and observe the Horn of Africa populations. We all look like a clear mix of the two with Somalis looking almost half-half but visibly more "African" shifted than "Eurasian" shifted yet Ethio-Somali makes up a whooping 57%~ of the ancestry in them and it is supposedly 100% Non-African? 

Want further proof? I believe some old posts I made on that Forum I frequent will be adequate:

" Ethio-Somali is similar to the Maghrebi component in that it is slightly "mixed". It has an ancient East African influence however that influence is minor, I suppose and it is predominantly a West Eurasian component that is most probably a very ancient variant of Southwest Asian/ "Arabian". You can observe it's clear "Arabian" like affinities at the lower Ks in the Hodgson study.

Observe K=6 in that image where all the ancestry in the Horn is seen entirely as "Arabian" (dark brown) and "Nilo-Saharan" (light blue). There is some "Ethiopic"/ Omotic ancestry hidden for all Horners in that Nilo-Saharan but then I want you to look at K=12 in that image where all of a sudden Horners seem to be pred "Ethio-Somali" especially in the case of Somalis yet there's less Ethiopic (purple) + Nilo-Saharan than there was "Nilo-Saharan" at K=6. I have other ways to show you it's influences so just ask."

"Maghrebi" which is another "component" the study finds is also not really real... Now, any respectable geneticist who's studied the populations of the Maghreb/ Northwest Africans (Imazighen/ Berbers) is aware that they are "African" admixed at a rate of about 20 to 30%~.  In fact the very study Hodgson et al. gets its Horner samples from notes the African admixture in Maghrebis as do various other inquiries into Maghrebi ancestry such as a study from 2012 titled "Genomic Ancestry of North Africans Supports Back-to-Africa Migration" [2] [3].  

Even independent ADMIXTURE runs created by various individuals who are not even geneticists with degrees under their belt can obviously notice as much [-] , heck; a meager & intensely flawed profit orientated ancestry pinpointing service like FTDNA managed to notice the African admixture in a random Tunisian.[-]  In terms of having African admixture; the same can be said for Peninsula Arabians, Egyptians and the like, the former of which having their admixture confirmed by not only Hodgson et al. but various other runs such as the recent revolutionary study focused on ancient genomes by Losif Lazaridis. [1] [4]

To be fair it does note the African admixture in most Maghrebis outside of the "Maghrebi component" however it finds that "Tunisians" (this is more of a genetically isolated Tunisian population (supposedly practicing endogamy) that may not entirely be representative of all Tunisians [3]) are more or less entirely made up of this supposed ancestral component which they claim diverged from Ethio-Somali (according to them-> a 100% Non-African component) but obviously from looking at these Tunisians at K=2 in their own analysis one can see the African influence in the component also & at the higher Ks before it's introduction-> various influences such as "Arabian", "European" (more representative of the more "Northern" admixture of the Middle East. I.e. a component often dubbed "Mediterranean" in this case).  

In a PCA (Principal Component Analysis), these Tunisians don't even cluster different from other Maghrebis with only likely perhaps the most African admixed such as some Southern Moroccans and a few outliers here and there breaking off noticeably:

[1]

Yet these Tunisians are supposed to have a supposedly fully "Eurasian" ("Non-African") ancestral component that makes up pretty much all of their ancestry but they cluster relatively no differently from Moroccans, Sahrawis, Algerians, Libyans and Mozabites who have very visible post-formation of this Magrebi component Niger-Congo & "Nilo-Saharan" (what I often call AEA/ Ancestral East African) admixture. These Tunisians have been tested in various ADMIXTURE runs like those independent ones and have been found to be about 10 to 20%~ African admixed. If you don't trust them (I don't know why... Some of them clearly know more than this study does in terms of ADMIXTURE components) then really just know that the same study that identified those Tunisians' isolated-ness on a genetic level, also pretty much finds them to be like other North Africans to be African admixed. [3] 

For good measure, here is another study that finds similar admixture in them whilst also using those Tunisians who are supposedly according to Hodgson et al. (a study that lets its own ADMIXTURE runs and what they show at the lower Ks as well as its PCA plots go way over its own head) 100% Non-African/ composed of a component related to a supposed 100% Non-African component ("Ethio-Somali"):

"Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans."

[5]

They're basically saying what even complete layman should know about Maghrebis/ Berbers/ Imazighen and those Tunisians-> they're a predominantly ancient/ pre-historic Near Eastern population with non-negligible African admixture.

The suggestion that this Maghrebi component is a fully Eurasian/ Out-of-Africa (OoA) component component is utterly laughable and it hence is shocking that this study headed by actual geneticists with degrees claims it is and is pretty much related to an even more African admixed component (30%~ or so based on more accurate estimates of the admixture in Somalis that I will share later in this post from other studies including a more recent one) like Ethio-Somali.What's even more puzzling is that they're aware of and acknowledge what other papers say about "Maghrebi":

"Like the Ethio-Somali, the Maghrebi IAC in North African populations derives from a early back-to-Africa migration. Studies of North African populations reveal a complex layered history of admixture in North Africa, with an inferred pre-Last Glacial Maximum settlement of North Africa by a non-African population followed by gene flow from European, Middle Eastern, and sub-Saharan African populations dating from the end of the LGM to the recent past."

[1]

However they still claim it diverged from a component they believe to be Non-African entirely...

The admixture in the Horn ultimately though does show a strong affinity for the admixture in Peninsula Arabians (Saudis, Yemenis, Qatari Arabs, Omanis et al.) which is demonstrable enough at the lower Ks where the component looks more like "Arabian" in Hodgson et al.'s ADMIXTURE run that anything else in the MENA region (Middle East & North Africa):

[1]

This fact has been noticeable to other sources like those independent types I shared who also identify the exact same "Arabian" component that Hodgson et al. does however they dub it "Southwest Asian" as I often do, they find far less of the "Mediterranean" (the majority of the ME admixture in Maghrebis) & "Caucasus"("Eurasian" in Hodgson et al. analysis) component in Horners at large. However, interestingly; in terms of uniparental markers (Y DNA + mtDNA markers), Horners do not entirely fit well with Peninsula Arabians however modern Peninsula Arabians are by no means to be mistaken for the pre-historic peoples who mixed with AEA rich East Africans episodically to create us. I say episodically because both in terms of uniparentals and autosomal DNA data like that found through ADMIXTURE-> the admixture interactions that created Horners seem to have been episodic in nature/ we didn't become the way we are in one fell swoop.

To its credit; Hodgson et al. notes the episodic nature of our admixture and of course manages to notice the newer ADMIXTURE in Agaws & Ḥabeshas and many Oromos which I applaud it for doing as this is somewhat useful. Otherwise it's a crap study in that it makes too much of several mixed components it finds at the higher Ks/ it's ADMIXTURE software spits out for it. There have been "Cushitic components" (it's a pseudo-Cushitic component) in the past and even after Hodgson et al. One in Tishkoff et al. in 2009 and one just recently during this month by a study with some really ridiculous and incorrect notions that are heavily disproved by ancient DNA/ genomes like those used in Lazaridis et al. , Fu et al. , Gamba et al.  & Raghavan et al. which are really making amazing strides in re-defining Modern Human population genetics. [6] [7]

Just to entertain you, I'll go into that more recent study's findings on Horners... They essentially claim that a component dominating the ancestry in Somalis is a component called "Lowland East Cushitic" and that it is of a "Macro-related-group" with components it dubs "Indian", "European", "Levantine-Caucasian" & "Arabian" and it claims (this is the punch line now) that this component diverged from them 61,000 years ago. 

Don't take my word for it:

"Lowland East Cushitic ancestry diverged from the Caucasian/European/Middle Eastern/south Asian cluster 2,041 generations or ~61,000 years ago"
[8]

They ultimately find something very much like "Ethio-Somali which they also say makes up not all but a great part of the ancestry in ethnic Somalis"- :

[8.2]

-then they make the humorous claim that it's essentially 100% Non-African by claiming it diverged from "Indian" for example but there is not at all one Indian component, in fact one of the people involved in Lazaridis et al. found 5 years ago what many already know now; that South Asians are predominantly a mixture of a sort of "North Indian" component that is seemingly at least predominantly West Eurasian alongside another component often called "South Indian" which is a component that is clearly differentiated from West Eurasian ones and also seemingly East Eurasian ones as well. [9]

European as well have for a long time been divided into "North" & "Southern" European (autosomal DNA wise) but of course anyone who has been keeping up with European genetics knows how mixed Europeans are based on the findings of Lazaridis et al. , Gamba et al. and hell even the sequencing of Ust-Ishim's genome. These studies are 100% more reliable than this farce and essentially use ancient remains from as far back as 45,000 years ago in Fu et al.'s case for Ust-Ishim and as far back as 24,000 years in the case of MA-1 & Lazaridis' use of his genome for example. They are essentially what is largely accepted in genetic circles now and are truly redefining population genetics.

This study essentially like this dendrogram for the divergence of components demonstrates claims that "Lowland East Cushitic" diverged from those components I mentioned (Oh, look, there's a Berber/ Magrebi component too and look where they claim it sits):

[-]

.

Apparently it makes absolutely nothing of its own dendrogram for fst distance between the ancestral components it identifies:

[-]

Funny how in terms of fst distance (i.e. distance between these components in a sense): "Lowland East Cushitic" is closer to Nilo-Saharan, Niger-Congo and Omotic than it is to those components it supposedly diverged from 61,000 years ago (a completely laughable and fictutious time frame btw).

.

Oh, Hodgson et al. showed similar fst distance results too btw but chocked it up to the component's supposed 23,000 year divergence from other Non-African components like MENA ones such as Maghrebi being obviously a very long time ago:

[1]

Once again it's a supposed Non-African component that's visibly much closer to the African components than any other Non-African component is...

I'm a bigger fan (sarcasm here) of this newer study's ("Shriner et al.") explanation for its pull toward the African components and the well-known pull West Eurasians who lack any known African admixture such as Europeans display toward the African groups in comparison to how East Eurasians (Han Chinese, Onge etc.) pull toward them which is visibly always much farther away.

It's according to Shriner et al. that there were two Out of Africa migrations... The second marking an occasion where the Indian, Kalash, European, Levantine-Caucasian, Berber & Arabian components left Africa after theoretically diverging from Lowland East Cushitic. 

This is incredulous fiction and if they'd read a single paper on the latest finds in the genetic field pertaining to what we're learning from ancient genomes finally being sequenced (a thousand times more reliable than studying modern populations to explain pre-historic genetic history)-> they'd know that the reason West Eurasians like Europeans pull towards Africa more is due to Basal Eurasian (whatever the component might ultimately prove to be once we get ancient DNA from the Middle East and hopefully also East Africa sequenced) as Lazaridis et al. and other studies lately have noticed. Fu et al. also proves that the reason modern Europeans are not as close to Ust-Ishim whose genome sits between pre-historic non-Near Eastern admixed (and thus non-Basal Eurasian admixed) West Eurasians like the Western European Hunter-Gatherer dubbed Loschbour & East Eurasians is very likely explainable by something with the affinities Basal Eurasian possesses:

[9]

But ultimately, the study (Shriner et al.) is crippled heavily by what the author of Eurogenes describes below:

"The authors are under the illusion that running enough samples with the ADMIXTURE software can reveal pure ancestral components from thousands of years ago, and thus uncover the story of the peopling of the world in all of its glory. That's an incredibly naive view, to put it mildly."

 Well said... Incredibly naive, indeed. They have no regard for ancient genomes and just think they can describe Human pre-history via the ADMIXTURE software and whatever it craps out for them. ADMIXTURE software pushes out mixed components like this often, just like it did with Maghrebi for Hodgson et al. and that's really all Ethio-Somali is (beyond perhaps being useful for marking migrations and gene flow from Cushitic or Cushitic-like groups into other groups); a mixed component the software just shat out for Hodgson et al. and they just ate it up. 

More accurate results for the admixture in the Horn of Africa is shared for example by Pickrell et al. :

[11]

 .

The study went so far as to attempt to model the admixture in the Horn of Africa with reference populations and found the admixture to be good fits for models such as the following:

[10]

Anuaks, South Sudanese etc. carry the AEA/ Nilo-Saharan component/ it's the majority of their admixture so they indeed if you discount their Niger-Congo admixture are a good fit for the admixture in the Horn. 

These results are honestly corroborated even more by PCA plots (Principal Component Analysis) such as even the one shared by Hodgson et al. :

[1]

.

or the one shared by Pagani from which Hodgson et al. got its Horner samples from:

[2]

.

[2.2]

In fact, every PCA plot/ cluster with Horners present displays that Ethiopian Semitic speakers and Agaw/ Central-Cushitic speakers have a somewhat noticeably greater pull towards "Eurasians" than Somalis, Wolaytas and certain Oromos do. Which is generally in line with Pickrell's findings where they have somewhat more Middle Eastern input than Somalis or Wolaytas (with Somalis having somewhat more than Wolaytas).

These results are further corroborated by a very recent & very thorough study (Gudrasani et al.) on African genetics where the authors use three different methods to identify Eurasian admixture in the African continent and they in Methods 1 & 2 find pretty much the same results Pickrell did with only somewhat more heightened Eurasian admixture among the Horner populations via Method 3:

[12]

The Horn populations are not nearly as pre-historic Middle Eastern to Non-African admixed as Hodgson et al. or Shriner et al. posit and the proof is not only in their own data (i.e. Lower Ks of admixture runs, fst distance etc.) but also various other studies such as with Shriner et al. which has proved extremely unreliable if one has even remotely become familiar with studies on ancient genomes which completely disprove its assertions.

Horners generally cluster the way populations with their levels of admixture do. Amharas & Tigrinyas being practically 50%~ Middle Eastern influenced tend to cluster as perhaps near pefect intermediates between the populations of West Asia & populations such as the South Sudanese and Niger-Congo speakers (perhaps with just a slightly greater pull towards the South Sudanese/ Nilotic populations) and Somalis show just an ever so slightly greater pull toward the South Sudanese/ Nilotic populations as they are just practically 40%~ Middle Eastern influenced in contrast and about 60-62%~  East African/ "Nilo-Saharan". Hodgson et al. apparently thinks we should plot at the very fringe of the Maghrebi populations or almost with them given the practically 60%~ Non-African score it gives us based on its mixed component, also given that Maghrebis are essentially 20-30%~ African (they do indeed admit the admixture levels in Moroccans & the like, but merely do not notice the admixture in those isolated Tunisians).

On another note; other studies including Pagani et al. & Gudrasani et al. often do come up with the sort of mixed components of the type that Ethio-Somali & Maghrebi are. I.e. Pagani et al. at the higher Ks in its run could be said to have found a mixed component in the Hadza:

 

[2]

Observe the Hadza in the visual image of everyone's admixture; notice tht they're almost entirely made up of an orange component. The Hadza in truth are mixed and even Gurdasani et al. finds similar results in them but still notes their mixed nature:

[12]

They look like a population made up by only one component (or predominantly by one component) however in Gudrasani et al.'s three runs for Eurasian ancestry they come out much like they do in Pickrell et al. with relatively 5 to 6%~ Eurasian admixture (particular pre-historic Middle Eastern admixture) and of course the rest of their components are ones like AEA (Ancestral East African/ "Nilo-Saharan"),  as well as certain varieties of Khoisan and "Pygmy". 

Luckily unlike Hodgosn et al. or Shriner et al.; studies like Pickrell et al. & Gudrasani et al. had the good sense to note the mixed nature of the populations who came up with such dominant components at the higher Ks via further analysis. In fact the components these "not real" components are made up of are not entirely "pure" in any sense. Southwest Asian or Mediterranean are ultimately (as we've learned via ancient genomic tests on the Neolithic Near Eastern farmers of Europe) mixed components as well in the sense that they seem to be some sort of interaction between West Eurasians somewhat similar to the WHGs/ EFs (Western European Hunter-Gatherers/ European Foragers) of Europe and what Lazaridis et al. and Fu et al. believe maybe a "Basal Eurasian" population; a population that did not participate in the forming of an "autosomal clade" between other Eurasians. I.e. between the ancestors of unmixed West Eurasians like Loschbour and the ancestors of East Eurasians (Han Chinese, Onge etc.)-> basically "Out of Africa isolates" who broke from other OoAs early on; at least that's the running theory for now.

Even Nilo-Saharan/ Ancestral East African as I call it; demonstrates a certain amount of mixture with other divergent African populations via the mtDNA of the populations it peaks in who demonstrate L0 markers for example whilst actually at the lower Ks demonstrating a small amount of Khoisan/ Khoesan admixture:

[1]

Simply observe populations with a substantial amount of the "Nilo-Saharan" component at everything from K=3 to K=5 (before the the "Nilo-Saharan"/ AEA component is introduced) and the small amount of Khoisan admixture they show... As brought to my attention by a friend; one of the people who worked on Lazaridis et al. said they might eventually be publishing a paper that confirms the idea that Niger-Congo speakers as their uniparental markers (Y DNA + mtDNA markers) [13] [14] [15] imply; are made up of some divergent & perhaps likely pre-historic African populations [-]. Most of the components that make up "Ethio-Somali" themselves will very likely be thoroughly redefined once we have ancient DNA from the Middle East & East Africa that fits with the sequenced.

Ancestral Components like "Ethio-Somali" take this up a notch though by being a mixture of these much more ancient mixtures (this is ultimately what makes it "not real"/ "less real"/ it is certainly not some "pure" component, especially not a Non-African one). The populations that form components like it often do because they've been isolated for some time (i.e. those Tunisians) and then create in a sense; their own distinct cluster. At least that is the case at times... 

It is not a "real component" and the populations of the Horn are by no means 60%~ or more Non-African/ Near Eastern but it is correct that there is non-negligible admixture in the horn with an ultimate and likely very pre-historic origin in the Middle East-> the study doesalso have some ups that I took the time to note.

Reference list:

1. Early Back-to-Africa Migration into the Horn of Africa, Hodgson et al.

2. Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool, Pagani et al.

2.2 . Pagani et al, Supplemental Data

3. Genomic Ancestry of North Africans Supports Back-to-Africa Migration, Henn et al.

4. Ancient human genomes suggest three ancestral populations for present-day Europeans, Lazaridis et al.

5. Genome-Wide and Paternal Diversity Reveal a Recent Origin of Human Populations in North Africa, Fadhlaouli-Zid et al.

6. Genome flux and stasis in a five millennium transect of European prehistory, Gamba et al.

7. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Raghavan et al.

8. Genome-wide genotype and sequence-based reconstruction of the 140,000 year history of modern human ancestry, Shriner et al.

8.2 . Shriner et al. , supplementary data. 

9. Reconstructing Indian population history, Reich et al.

10. Genome Sequence of 45,000-year-old modern human from western Siberia, Fu et al.

11. Ancient west Eurasian ancestry in southern and eastern Africa, Pickrell et al.

12. The African Genome Variation Project shapes medical genetics in Africa, Gurdasani et al.

13. mtDNA analysis of Nile River Valley populations: A genetic corridor or a barrier to migration?, Krings et al.

14. The expansion of mtDNA haplogroup L3 within and out of Africa, Soares et al.

15. Ethiopian Mitochondrial DNA Heritage: Tracking Gene Flow Across and Around the Gate of Tears, Kivisild et al.

Notes:

1. It's humorous to note that mere layman sources like the Harappa ancestry project for one actually notice the same admixture levels posed by Gudrasani et al. & Pickrell et al. whilst being awfully close to the admixture levels posited by Pagani et al. (the very study Hodgson et al. gets its samples from). Harappa, Dodecad, MDLP etc. all note about 35 to 40%~ Middle Eastern admixture in Somalis for example and about 48 to 51%~ Middle Eastern admixture in Tigrinyas and Amharas (not entirely sure in the case of MDLP). Funny... Even supposed layman know more than this study does...

2. Make no mistake; Modern Nilotes (Dinka, Anuak et al.) & Peninsula Arabians are by no  means an accurate representation of the pre-historic peoples who mixed seemingly episodically to create Horners-> both groups predominantly for one have Niger-Congo admixture (non-negligibly; especially in the case of the Nilotic groups).  And of course there's the case of Modern Peninsula Arabians not seeming to be a good fit for the Uniparental markers in the Horn. It's all a little complex but they're just essentially; the closest living populations to those pre-historic peoples.

3. However as a friend brought to my attention, the L0 in the Horn or AEA carrying populations is likely not "Khoisan" admixture despite what shows up at the lower Ks. I'll merely quote him for good measure:

"Also, I wouldn't say AEA has "Khoisan" admixture, since the L0 haplogroup is over 100,000 years old and East Africans carry different L0 lineages compared to the southern African Khoisan. It's a very distant relation, and you'll find more recent mtDNA relations shared with West Africans. Certain L2, L3 sublineages have common ancestry with West African lineages, and almost all of the L0 in the Horn belongs to L0a, which is also found in West Africa. Non-L0a L0 lineages are mainly found south of the Horn."