Basal Eurasian in Kostenki14

This one's a strange find from last year that was recently followed up on by Haak et al. 2015, it's the idea that Kostenki14, an ancient (~36,000-38,000 BP) West Eurasian (Russia) Upper Paleolithic individual actually shows the Qausi-African Basal Eurasian component. 

This is quite strange in that for now this has only been found in Early European Farmers who were more or less Neolithic West Asians with a certain degree of Western European Hunter-Gatherer (native European component) ancestry (~30% or less).

When the findings in Seguin-Orlando et al. 2014 to which we owe that diagram above first came out, David Reich who had a key part in Lazaridis et al. as well as Haak et al. went so far as to suggest that Kostenki14's sample was contaminated & that these results perhaps couldn't be relied upon (last paragraph). 

Haak et al. which he had an important role in finally decided to incorporate Kostenki14 and the subject of his Basal Eurasian admixture into their study and for example share the following points:

"The hypothesis of Basal Eurasian ancestry in Kostenki14 needs to be further tested, as the negative D(Mbuti, Han; Loschbour, Kostenki14) statistic could also reflect gene flow between Han<->Loschbour a priori plausible, as these populations are much younger than Kostenki14 and may share intra-Eurasian genetic drift that Kostenki14 lacks because of its age. The possibility of later gene flow between Europeans and eastern non-Africans must be further tested with additional ancient samples from Upper Paleolithic Europe and Asia."

Frankly they're skeptical and even went so far as to suggest that this isn't the same affinity we find in Early European Farmers with ancestors from the Near East; claiming that this in some models even looks like a lineage that split before the split of the Basal Eurasian in West Asians & Early European Farmers from West Asia:

Other models include Kostenki14 sharing in the Basal Eurasian that was in the Early Farmers & many European & West Asian populations today which I frankly find unlikely however they note that no model making Kostenki14 out to be a single branch off fits; as in Kostenk14 can't fit as a simple break off from "West Eurasian Upper Paleolithic" or anything of the sort, instead a 2-way branch for the time being (like Basal Eurasian + WEUP) makes more sense.

Ultimately the study leaves you with honestly not many answers at the very end, we need more data, ancient genomes from East Eurasians might be able to explain this, this could be Kostenki14 being the extremely old individual he is showing affinities for populations whose divergence he long precedes etc etc. And frankly we may need more ancient samples from his timeline and area to make more sense of this find.

I personally find it implausible that this is the same affinity found in Early European Farmers given that Haak et al. itself did a study on the Steppe, relatively not too far off from Kostenki14's location and none of the Eastern European Hunter-Gatherers in the area prior to the arrival of Armenian-like West Asian ancestry in the area showed signs of Basal Eurasian admixture, Western European Hunter-Gatherers across the rest of Europe west of the Pontic-Caspian Steppe also show no signs of such admixture until mixture with the Early European Farmers whose genome is predominantly West Asian ensued.

Anyway, all that can be said at this point is that further study is required & I suppose this is intriguing to say the least.

Reference List:

1. Massive migration from the steppe is a source for Indo-European languages in Europe, Haak et al. 2015

2. Genomic structure in Europeans dating back at least 36,200 years, Seguin-Orlando et al. 2014

Notes:

1. You're welcome to see the author of Eurogenes' take on all this from months ago...

Massive migration from the steppe

The newest study aimed at ancient European population genetics is quite a treat to say the least. I thought it deserved an extra blurb post on its own while I'm still reading it.

It has some profound new things to say about European population genetics but for the moment I'll let its abstract do the talking:

"We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies1-8 and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe."

Eastern Europe's pre-history is not exactly the same as the story you'd find in the rest of Europe. Here it seems more as though the region of Eastern Europe around the Steppe was inhabited by Eastern European Hunter-Gatherers (EHG) who seem to be a mix between Ancient North Eurasians (~40%) & the hunter-gatherer (~60%) populations you'd have found in the rest of Europe-> Western European Hunter-Gatherers. 

 "All samples from Russia have affinity to the ~24,000 year old MA1, the type specimen for the Ancient North Eurasians (ANE) who contributed to both Europeans and Native Americans. The two hunter-gatherers from Russia (Karelia in the northwest of the country and Samara on the steppe near the Urals) form an “eastern European hunter-gatherer” (EHG) cluster at one end of a hunter-gatherer cline across Europe; people of hunter-gatherer ancestry from Luxembourg, Spain, and Hungary sit at the opposite “western European hunter-gatherer” (WHG) end, while the hunter-gatherers from Sweden (SHG) are intermediate."

Scandinavian Hunter-Gatherers such as Motala12 are essentially Western-European Hunter-Gatherers with a certain amount of Ancient North Eurasian ancestry. Lazaridis et al. in its supplemental demonstrates the gene flow into Motala12:

Of course, EHGs have a higher proportion of gene flow from Ancient North Eurasians than Motala12 did hence why Scandinavian Hunter-Gatherers (SHG) sit between Western European Hunter-Gatherers & Eastern European Hunter-Gatherers. The Karelia Hunter-Gatherer as the paper points outs seems to look intermediate between MA-1 (ANE) & Loschbour (WHG).

"Middle Neolithic Europeans from Germany, Spain, Hungary, and Sweden from the period ~4,000-3,000 BCE are intermediate between the earlier farmers and the WHG, suggesting an increase of WHG ancestry throughout much of Europe. By contrast, in Russia, the later Yamnaya steppe herders of ~3,000 BCE plot between the EHG and the Near East / Caucasus, suggesting a decrease of EHG ancestry during the same time period."

In the rest of Europe the Early European Farmers who were predominantly West Asian (Early Neolithic Farmer) but had a certain great proportion of Western European Hunter-Gather ancestry were seeing a resurgence of WHG ancestry however at this same juncture in time the situation in Far Eastern Europe/ the Steppe was that there was a decline in Eastern European Hunter-Gatherer ancestry & the appearance of West Asian-Caucasian-like ancestry.

The paper specifically outlines this West Asian influence as "Armenian-like" in other passages. Eventually they discover that Middle Neolithic Europeans from the rest of Europe (i.e. Germany & Spain) plot essentially between WHGs & earlier Farmers; suggesting an increase in WHG ancestry by the Middle Neolithic. While Late Neolithic & Bronze Age samples from the rest of Europe sit between the Yamnaya (Steppe nomadic pastoralist population) & Early to Middle Neolithic Europeans who are clearly distinct from this Yamnaya population that as the paper notes looks like it's drawing ancestry from a Caucasian-like population as well as EHGs.

You can see the straddling the Late Neolithic population does between the Yamnaya the Early to Middle Neolithic populations to the south of the PCA (Principal Component Analysis). 

What implications does this have for Europe as a whole? Well, what the title of this post implies, which is that Europeans as a whole trace a very substantial segment of their ancestry back to the Pontic-Caspian Steppe (Yamnaya) for one:

There is less of this Steppe derived ancestry in Southern Europeans such as Tuscans, Spaniards, Greeks, Albanians & Sardinians but for other populations such as Lithuanians, Norwegians, Icelanders & Scots; it seems to make up far more of their ancestry than Early European Farmer (Early Neolithic) & WHG do.

The paper as it says also believes this massive migration from the Steppe to corroborate a Steppe origin hypothesis for at least some Indo-European languages:

"These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe."

Frankly, this study also has astounding things to share about the history of Y-Haplogroups R1b & R1a but for more on that I would guide you toward more focused and knowledgeable hands than mine when it comes down to European population genetics. For the time being; this is good progress for the Kurgan Hypothesis.

This is all very staggering frankly. For one it shows that Europeans acquired West Asian ancesty via more than one migration into the general zone of Europe, one from Early Neolithic Farmers who were ancestral to Early European Farmers & another that was intrusive to the Steppe. 

Europe Proper

In their series, the first peoples of Central Europe to show signs of Yamnaya ancestry are the peoples of the Corded Ware Culture at around ~2500 BCE. As they noted, Corded Ware share elements of material culture with the Yamnaya. Their genetic evidence shows clear indications of a migration from the East of Europe to the West, that the Corded Ware are a monument to, as you can see in the chart results above; Corded Ware individuals trace the vast majority of their ancestry back to the Pontic-Caspian Steppe and only some to Early European Farmers & un-mixed Western-European Hunter-Gatherers.

"By extending our model to a three way mixture of WHG, Early Neolithic and Yamnaya, we estimate that the ancestry of the Corded Ware was 79% Yamnaya-like, 4% WHG, and 17% Early Neolithic (Fig. 3)."

The Steppe ancestry in Europe also seems to be key in spreading ANE across the continent, though its been known for a while now that the spread of Indo-European languages likely aided in the spreading of Ancient North Eurasian ancestry across Europe. If we are to use Haak et al.'s model, the Ancient North Eurasian ancestry in Tuscans for example would be entirely derived from the Pontic-Caspian Steppe, the rest of their ancestry is Early European Farmer.

"Further data are needed to determine whether the steppe ancestry arrived in southern Europe at the time of the Late Neolithic / Bronze Age, or is due to migrations in historical times from northern Europe."

Out of the three-way model Haak et al. has mapped out (Yamnaya + WHG + EEF) it's clear that Steppe ancestry (Yamnaya) is what brings ANE to at least many Europeans. At any rate it seems clear that for Europe in particular; the spreading of Indo-European languages had a key part in spreading Ancient North Eurasian ancestry.

"Our results support a view of European pre-history punctuated by two major migrations: first, the arrival of first farmers during the Early Neolithic from the Near East, and second of Yamnaya pastoralists during the Late Neolithic from the steppe (Extended Data Fig. 5). Our data further show that both migrations were followed by resurgences of the previous inhabitants: first, during the Middle Neolithic, when hunter-gatherer ancestry rose again after its Early Neolithic decline, and then between the Late Neolithic and the present, when farmer and hunter-gatherer ancestry rose after its Late Neolithic decline. This second resurgence must have started during the Late Neolithic/Bronze Age period itself, as the Bell Beaker and Unetice groups had reduced Yamnaya ancestry compared to the earlier Corded Ware, and comparable levels to that in some present-day Europeans (Fig. 3)."

 This would have it that Europe has experienced not one but so far as we know; two migrations from West Asia, one into Eastern European Hunter-Gatherers (themselves a mix between Ancient North Eurasians & Western European Hunter-Gatherers) from a Caucasian-like source and the other from Early Neolithic Farmers who intermixed accordingly with Western European Hunter-Gatherers. The part West East/ Near Eastern & part EHG Yamnaya pastoralists then proved to progenitors to a large scale (massive) migration into the rest of Europe, roughly around ~2500 BCE. This also posits that Basal Eurasian ancestry entered Europe in a much more complex way than Lazaridis et al.'s first posited in 2013.

 As a whole Wolfgang Haak and others have a lot more to say & for the time being I would advise following the Eurogenes blog for good updates on things we're learning from it, however I believed a few excerpts and shares as to where this paper is going for now was worth sharing. Needless to say; the Steppe/ Eastern Europe has had a profound part in shaping the genetic landscape of modern Europe.

Reference List:

1. Massive migration from the steppe is a source for Indo-European languages in Europe, Haak et al. 2015

2. Supplemental Data for Lazaridis et al.

Notes:

1. If the West Asian population that makes up a segment of the ancestry in the Yamnaya pastoralists was Armenian-like then they must've indeed had Ancient North Eurasian ancestry? Armenians are mostly Early Neolithic Farmer + for now what looks to be ~10-15% ANE ancestry and a negligible segment of WHG ancestry. 

If this Near Eastern/ West Asian population was Armenian-like then a certain amount of the ANE in Europe today is owed to a pre-historic West Asian population. Although one must remember that the EHGs they mixed with were much heavier on ANE ancestry than Armenians are and the mixture between these Armenian-like West Asians & Eastern European Hunter-Gatherers as this paper says; diluted the ANE ancestry in the Steppe. 

Update:

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

Basal Eurasian

During the Neolithic farmers from West Asia came to Europe and brought with them agriculture & in time began intermixing with the local hunter-gatherer groups on the continent like what Lazaridis et al. 2013-2014 refers to as "West European Hunter-Gatherers". [1]

These farmers also brought with them one quite divergent theoretical ancestral component which was initially discovered through the studying of their genomes and that would be Basal Eurasian.

Now, something to quickly recall and/or understand before I go on and explain what Basal Eurasian is would be what's strewn out on the diagram above from Lazaridis et al. 2013... 

And what is strew out on it is that virtually all Out-of-Africa populations [note] from modern Eastern Non-Africans & West Eurasians to pre-historic groups such as Ancient North Eurasians and Eastern European Hunter-Gatherers (the non-Basal Eurasian ancestry in modern West Eurasians); predominantly descend from one incredibly ancient & seemingly bottle-necked Homo Sapien Sapien population of ultimately African origins. [note]

These African origins are demonstrable in terms of autosomal DNA such as how the "Non-African" ancestral group of all Out-of-Africa populations fitting as sharing a "root" with African populations such as Mbuti pygmies (like in the diagram above) or even through Haplogroups where all the mtDNA markers outside of Africa descend from the seemingly East African but definitely African Haplogroup L3- :

Theoretical spreading of Haplogroup L3

-or through observing how all Out-of-Africa Y-DNA Haplogroups (including Y-DNA E in Africa) are descended from one ancestor dubbed "Halogroup CT" which in turn is descended from Haplogroup BT which is then descended from Haplogroup A with A & BT being African Haplogroups.

A Haplogroup "leaf" that demonstrates Haplogroup A's basal position among all other Y-DNA Haplogroups

The Out-of-Africa model while we still need to study how exactly how it happened like if there were numerous dispersal events out of Africa or just one; is essentially a genetic fact and also an archaeological fact in that the earliest remains of our species and genus exist in Africa and not Eurasia.

This is all relevant because within the story of the Homo Sapien Sapien family tree; Basal Eurasians are, for now ,thought to be a group that apparently cut-off from the original ancestral group to all Out-of-Africa groups and then became supposedly isolated from other "Non-Africans" who seemingly continued to remain as "one group" that in time diverged into supposedly two or many branches.

I'm sharing this diagram again because it really explains Basal Eurasian to perfection. And I'll explain how as you hopefully observe it alongside this text... Once again I'll say that there was one seemingly bottle-necked group that all Out-of-Africa groups descend from and then, supposedly, Basal Eurasians cut off from this group and as does seemingly another group.

Basal Eurasians supposedly remained genetically isolated from this other group and the various divergent groups in Africa while this other group continued to go on and diversify in time into the non-Basal Eurasian Out-of-Africa genetic diversity we see today. 

Regardless of how the branching happened & how many complex mixtures formed various modern populations; eventually the ancestors of East Asians, Oceanians, Southeast Asians & the non-Basal Eurasian ancestors of West Asians, Europeans and South Asians formed from this other group that eventually diversified.

This may sound weird to some... How on Earth did Basal Eurasians not over what could have been a  period of over 60,000 years not also diversify into separate branches like the separation we see between Eastern Non-Africans Vs. Ancient North Eurasians & European Hunter-Gatherers for example?

Well, the thing to understand for now is that Basal Eurasian is really just a sort of statistical concept. A way of explaining why Early European Farmers (and various Out-of-Africa ancestry carrying groups that seem to carry the same kind of "West Asian / Near Eastern" ancestry they carried) don't fit well as fully descending from a common ancestral clade with groups like Eastern Non-Africans, Ancient North Eurasians and European Hunter-Gatherers.

Eastern Non-Africans, Ancient North Eurasians and European Hunter-Gatherers share a lot of genetic drift and ancestry with each other and we discovered as well that Ust-Ishim, a man who died over 40,000 years ago; existed in a genetic state that preceded their divergence even if he diverged from the ancestors of these groups before or around when they were diverging from each other. [2]

As I explain here; Ust-Ishim is "basal" to all Out-of-Africa groups whether modern ones like Eastern Non-Africans such as the Andamanese Onge or the East Asian-related ancestry in the Karitiana Native American population or ancient Out-of-Africa groups such as Ancient North Eurasians & European Hunter-Gatherers.

Ust-Ishim is quite literally physical evidence that these groups descend from a common ancestral clade and continued to share genetic drift with each other until a few tens of thousands of years ago where they for now supposedly diverged into two separate branches, one ancestral to the Eastern Non-Africans & another ancestral to Ancient North Eurasians & European Hunter-Gatherers.

And while this branching may eventually grow a good degree more complex with more and more ancient DNA being studied; the point to get here is that modern Europeans and West Asians (including those West Asians lacking African admixture); do not fit into this model.

They don't fit properly as a "down-stream" development from what Ust-Ishim was in the way an Andamanese islander or a Western European Hunter-Gatherer would. This in the researchers' eyes implies an element in them that preceded Ust-Ishim's genetic state and whom Ust-Ishim is not "basal" to as the diagram shared above from Haak et al. 2015 clearly stipulates. [3]

[2]

We don't have actual ancient DNA data from West Asia or North Africa or anywhere that could truly explain what Basal Eurasian honestly is so we for now have to work with this current statistically based concept. [note]

Because the thing is; Basal Eurasian doesn't look "African" as some including I once might have implied but rather still clearly looks as though the original Out-of-Africa group that Lazaridis et al. 2013-2014 dubs the first "Non-Africans" are indeed ancestral to it, but then it clearly doesn't seem to be a downstream development from Ust-Ishim and lacks the extra shared genetic drift and ancestry between Eastern Non-Africans and groups like Ancient North Eurasians.

So I'll say what I've said quite often; we need more ancient DNA data to truly understand what Basal Eurasian was but what I explained above is essentially the current academic view...

 That view being that it is a highly divergent Out-of-Africa lineage that diverged from the Homo Sapien Sapien ancestors of Eastern Non-Africans and groups such as Ancient North Eurasians and European Hunter-Gatherers before they ever diverged from one another. Making it more distinct from them than they are from each other as well.

As for its "modern spread"... It ultimately looks to be associated with having West Asian/Near Eastern related ancestry like the non-West European Hunter-Gatherer related ancestry in Early European Farmers or the non-East African related ancestry in some Bedouins as I mention here. 

The Eurogenes K=8 admixture run is one of the best show of how much of such "Near Eastern" ancestry various global populations have

Such ancestry as you can see in the spreadsheet linked to with the above text is found all over the world from East Africa to the Sahel region among Fulanis to North Africa to Europe, Central Asia, South Asia and finally what looks to be its homeland of West Asia or the general Middle East / Near East region.

All these groups carrying such West Asian / Near Eastern-related ancestry through various different migrations and distinct influences throughout Human history ultimately carry Basal Eurasian ancestry as Basal Eurasian seems to be part of the ancestral package this West Asian / Near Eastern-related ancestry carries with it.

Reference List:

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

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

3. Massive migration from the steppe is a source for Indo-European languages in Europe, Haak et al.

Notes:

1. There was indeed and older and more long version of this post on Basal Eurasian at the exact same page you're reading this one but I felt it was over-bloated and perhaps even boasted some inaccuracies here and there so here's a much more short and straight forward post explaining Basal Eurasian.

2. If you saw the "[note]" at the end of the fourth paragraph then here are your links: [-] , [-] , [-]. African populations carrying substantial West Eurasian ancestry like various Horn Africans would indeed carry more Neanderthal ancestry than Yorubas though, evidenced by how in the first study linked to; Maasais are noted to carry notably more Neanderthal ancestry than Yorubas due to their Eurasian ancestry which they ultimately acquired via Cushitic admixture.

3. From what I can tell; Haak et al. didn't include groups like Papuans in its analysis when it made that statement about Ust-Ishim being basal to European Hunter-Gatherers and Eastern Non-Africans so I contacted Iosif Lazaridis who was involved in the study and he essentially confirmed that Ust-Ishim would indeed be basal to Eastern Non-Africans like Papuans or Australian Aborigines as well, though he noted that the Denisovan admixture in these groups can complicate such models.

Recommended reads:

1. A decent forum discussion about Basal Eurasians

Cushitic Admixture Levels: Somalis as a proxy

As has been mentioned on this blog in the past, Somalis often form a Cushitic or pseudo-Cushitic component, dubbed that way mostly because it peaks in them (Lowland East Cushitic speakers) and then peaks in other Horners (Cushitic & Ethiopian Semitic speaking alike) who obviously would share a lot of much more recent post-Neolithic ancestry with Somalis. 

This blog post is simply going to outline the interesting findings of "Cushitic levels in Horners" if Somalis are used as a proxy for Cushitic and essentially this is what Hodgson et al. & Shriner et al. find:

Hodgson et al. essentially gives Somalis a pseudo-Cushitic cluster they dub "Ethio-Somali" which hits a level of about ~57% in the Somalian Somali samples, there's also the question of the Nilo-Saharan admixture clearly shared between the Horner populations as well as Cushitic admixed groups such as Ari Cultivators & the Maasai that you can also find in the paper.

However Hodgson et al. incorrectly finds Omotic admixture in Somalian Somalis who actually seemingly lack it, in fact the Omotic levels in populations like Ari Cultivators go down once you do what a fellow ethnic Somali did with his own old ADMIXTURE run and remove the more inbred Ari Blacksmiths, a recent study is working to show that Ari Cultivators are essentially a less inbred edition of their Blacksmith counterparts [-] however the Cushitic admixture noted to be in them while likely lower than is purported in Hodgson et al.; is very likely quite real as it is not the only study to note such admixture.

I ultimately adjusted Hodgson et al.'s Omotic levels by adding that Somali's likely very accurate (the best we have) Omotic levels  for each Horner population and then where Hodgson et al. & Shriner et al. really do pull through and do some good work is that they note the extra/ newer West Asian admixture Agaw & Ḥabesha populations have over Somalis.

Hodgson et al. notes about ~12% new Arabian/ Southwest Asian-like admixture in Agaws and a certain amount of Caucasian-like (dubbed "Eurasian") admixture at a rate lower than 5%:

 I merely selected the highest bound possible by their calculations and gave Xamir Agaws ~16% new West Asian admixture over Somalis but their levels could be anything between 12 to 16% (the exact proportion of newer Caucasian-like admixture is not shared as it is below a level of 5% as is stated in the earlier table).

For Ḥabeshas it's more clear cut and we get ~7-8% new Caucasian-like admixture & ~16% new Arabian/ Southwest Asian-like admixture. Somalis show small visually visible but clearly lower than ~5%  (as they do not show up in this table from Hodgson et al.) levels of this new West Asian admixture, whether or not they actually have such admixture and this is more of them simply reacting to ancestry carried by populations very close to them is up to one's own interpretation but they have very little if any of this admixture; ~1-4% at most hence that chart throws in a safe high bound of ~3%.

This coupled with the Omotic in Ḥabeshas & Xamir Agaws would essentially make Tigrinyas for example ~64% Cushitic if Somalis were to be used as a proxy for Cushitic/  that much ancestry is clearly much more recent likely post-Neolithic ancestry shared with Somalis. It's higher for Xamir Agaws at ~75% & lower for Amharas (due to their higher Omotic admixture) at ~60% roughly.

Though, Hodgson et al. notes a low below 5% Maghrebi-like influence in non-Somalis (it's only visually visible) at K=12 after Ethio-Somali's appearance and while this is a mixed component with a strong African influence, one can perhaps give the values in these populations a very low negligible ~1-3% lower bound for those results of shared ancestry above.


Shriner et al. finds similar results and manages to add another population into the mix:

The study finds higher levels of shared ancestry between these Horner populations than Hodgson et al. does though notably not by much at all. One very notable thing about Shriner is that it gets the Omotic levels of each population quite right and notes none in Somalian Somalis & the levels in the other populations were actually only ~1% or so different from the levels in that Somali's ADMIXTURE run. Didn't really need adjusting in this case.

Its Omotic levels are only inaccurate for the Ethiopian Somali samples (~8%) however they have two outliers who skew the average  quite a bit even in that Somali's run, their removal would neaten things up a bit.

Supplemental data for ADMIXTURE components in populations, Shriner et al.

It finds lower new West Asian admixture levels in each population (~2% less in Ḥabeshas, much less in Xamir Agaws/ "Afars") & it kindly adds Beta Israels/ Ethiopian Jews to the mix. It kindly gives us the exact numbers for each component though it has a large proportion of "unassigned" admixture in each population. 

It's strange that the ~6% non Arabian/ Southwest Asian-like admixture in Amharas it notes is "Berber" & not "Levantine-Caucasian" which is what they find in Tigrinyas, it's likely an error as there is no radical difference of any sort between Amharas & Tigrinyas, perhaps just their Omotic levels but that's mostly it.

Beyond that it's just the same pattern of a mixed West Asian ancestry + East African ancestry cluster/ component in Somalis (~56%) + "Nilo-Saharan" which seems to make up the bulk or entirety of the shared ancestry between Horners & Cushitic admixed populations in this paper as well.

However one should note that Somalis are not to be taken for an exact example of "Cushites". Somalis themselves show signs of acquiring some admixture that other much older examples of Cushites may have not had. 

For one, Somalis in mostly all runs will show some sense of a Mediterranean & Caucasian (or one of the two) influence in runs where the Maasai or Datooga (groups with South Cushitic pastoralist admixture; these being the groups to have spread the West Eurasian ancestry in Southern & Southeastern Africa noted by Pickrell et al.) or Ari Cultivators (unknown Cushitic admixture) do not ever show such influences, to my knowledge the Borana also lack such influences. However this influence is clearly gobbled up in the Somalis' Cushitic-esque clusters/ components: dubbed Ethio-Somali in Hodgson et al. & Lowland East Cushitic in Shriner et al.

Hodgson et al.'s own run at K=5 shows an example of this admixture where Somalis show more Northern West Asian-like affinities in the form of the "European" component while the Maasai & Ari Cultivators don't (though the Maasai may show a slight hint):

Various independent ADMIXTURE runs have found very much the same data. I.e. in Dodecad's globe13 Somalis will show Mediterranean while the Maasai & Ari Cultivators simply do not. In Eurogenes K=15 (a run honestly not meant for Horners though) Somalis will show West & East Mediterranean affinities like other Horners do but the Maasai & Datooga alongside Ari Cultivators do not. 

The Datooga plot in PCA plots (Principal Component Analysis) much closer to Horners and are more South Cushitic admixed seemingly than the Maasai which if I recall correctly; Tishkoff et al. had at ~50% Cushitic (as do Hodgson et al. among other papers, roughly):

Eurogenes World PCA Plot

It's the same story in other runs (virtually all really) such as in MDLP where Somalis will show Mediterranean & Caucasian affinities like other Horners do whilst the Maasai & the like do not. Same goes for HarrapWorld's run where Somalis will show Caucasian & Mediterranean affinities while Ari Cultivators (unknown Cushitic input) & the Maasai will not:

 All this says is that Somalis likely acquired some form of a new West Asian influence the South Cushites who contributed to the Maasai, Datooga & even some Southern African Khoisan peoples simple did not have and the Cushites who contributed gene flow to Ari Cultivators clearly lacked this influence as well.

However this West Asian contribution as is likely-> is very ancient and would obviously predate the influence in Xamir Agaws & Ḥabeshas. It also says something that this admixture is nevertheless still absorbed into the respective Cushitic components in Hodgson & Shriner (Hodgson even noticing it at K=5 as a more Northern West Asian & non-Arabian/ Southwest Asian affinity) so that does indeed say a lot about how old it is.

It takes time for clusters like Ethio-Somali, Omotic & Maghrebi which are inherently mixed and made up of older more basal components to form, the populations they peak in had to have been genetically isolated for a very long time, they're also often inbred.

Nevertheless, this merely points out that Somalis are not to be taken as a perfect example of "Cushites" or some form of preserved "purity"-> it merely simplified those charts (making Somalis 100% Cushitic) to show what proportion of ancestry in other Horners is clearly shared with Somalis.

For Ḥabeshas it's clearly ~60 to 70% of their ancestry and ~65 to 80% for Agaws (Beta Israel + Xamir). So not only are Horners very much made up of the same basal components (West Asian/ Early Neolithic Farmer ancestry + East African) with a greater fundamental similarity than you'll find between Europeans or West Asians at large but they all seem to share the majority of their more "recent" (within the larger context of Human existence) likely post-Neolithic ancestry.

Reference List:

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

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

3. The Genetic Structure and History of Africans and African Americans, Tishkoff et al.

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

Notes:

1. A colleague I correspond with often tends to assume the ~8 to 10% new West Asian admixture Ḥabeshas have over Xamir Agaws and even to a smaller extent over Western Agaws like Beta Israels who only made a linguistic shift to Ethiopian Semitic over the last few centuries (they were originally Agaw speakers:  [-] , [-] ) is likely owed to what they gained from shifting to Semitic.

Linguistic shifts often bring with them a certain degree of admixture from the population that brought the language branch or family to the area. I.e. Turks have a certain proportion of East Asian-like admixture likely gained from shifting to Turkic however Turkics/ Central Asians as of late have been found to have admixture such as ANE in large proportions [-] along with some ENF/ West Asian ancestry & WHG so some of the ANE & WHG in Turks is likely also owed to the peoples who shifted them to Turkic. 

I find the model that some of the extra West Asian in Ḥabeshas (~10% or less) is owed to shifting to Semitic to be quite likely but we can't be 100% sure.

Note for those who don't know: Ḥabeshas used to be Agaw/ Central-Cushitic speakers as is noticeable via the Agaw substratum in their languages (shifting to Semitic likely around ~3,000 BP [-]). If Agaws were used as a proxy for "Cushitic" then Ḥabeshas would more or less come out ~90% Cushitic (give or take).

2.  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 (IIRC) 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 would in such a plot however the data is relatively the same. Thank you very much to the author of Eurogenes for it nonetheless.

3. The basal components that seem to make up the majority of the ancestry in Horners (ENF (Early Neolithic Farmer) / EEFs without WHG admixture + East African) are for now rather weakly and poorly defined, to really get a grasp on them we'll need ancient genomes from the West Asia + North Africa & East Africa.

Update (28/5/2015):

1. Link to the update.

The Omotic Cluster: A Horn Specific Cluster

The Omotic component which I sort of disseminated in this post seems to be unique in that its spread doesn't really leave the Horn of Africa.

The component for the time being peaks in Ari Blacksmiths (90 to 100%~) and after them in Ari Cultivators, these peoples essentially being speakers of an Omotic language for now of the Afro-Asiatic language family hence the naming of the component though one study (Hodgson et al. [1]) has opted to call it Ethiopic, noting its spread only in the Horn region.

You can observe its peaking in the Ari populations in Hodgson et al.'s ADMIXTURE run (names of the components) or even Shriner et al.'s (component that peaks in the Ari Blacksmiths) but here is perhaps a more detailed showing of the Omotic component's proportions within these two populations from an old run created by an ethnic Somali:

Omotic Levels of the Ari

 His run is somewhat more adept at spotting Omotic admixture in populations than the runs in the studies as he removes the most inbred of the Ari and as one colleage points outs- :

  "I would guess if a component is based on shared genetics with your immediate family rather than a more ancient family ("population"), alleles that are not really characteristic of a particular region might show up in other regions, for reasons other than shared ancestry"

- this can perhaps prevent a skewing of results and show Omotic's spread better in the Horner populations (the majority of Cushitic & Ethiopian Semitic speakers) however I wold place his results for the Ari under some scrutiny. For one, his results maybe somewhat inflated. For one, his average in the case of the Cultivators at about 86%~ doesn't fit with their 17%~ Ethio-Somali admixture from Hodgson et al. and they show comparable levels in Shriner et al. in the case of Lowland East Cushitic; both these component's serve to map the Cushitic input in Ari Cultivators along perhaps with the Nilo-Saharan/ East African input in them in both studies that's also present in Horners outside of the Ethio-Somali mixed cluster/ component.

So while this run is quite adept it definitely has its discrepancies-> it's "West Eurasian"/ West Asian admixture scores at K=5 are definitely deflated for each of the populations and don't at all fit with most ADMIXTURE run's levels of admixture or the work of rather reliable studies like Gudrasani et al. or Pickrell et al. [2] [3] in the case of Horner admixture so I would advise a focus not on the exact percentages and numbers but more on the relative levels and climes of the admixture components (this group has more than that group and so on).

Now, what this run and studies such as Shriner et al. Pagani et al. & Hodgson et al. show us is that "Horners" (the Cushitic & Ethiopian Semitic populations that make up the majority of the Horn of Africa) or at least many of them have experienced gene flow from Omotics/ peoples genetically similar to Aris. It's clear that the component for the time being is tied to people who speak within the Omotic branch of the Afro-Asiatic language family. [4] [5]

For one, among "Horners" it peaks among the one group that actually speaks an Omotic language, it's total peak are Ari Blacksmiths and their Cushitic admixed kin the Ari Cultivators. So it can only really be assumed that the Omotics in the Horn (not necessarily Aris) could have somewhat genetically contributed to the populations specifically of Ethiopia (the very heart of the Horn region) however there seems to be no influence of Omotic in Somalia/ among non-Ethiopian ethnic Somalis.

Simply observe the levels of Omotic/ Ethiopic admixture among various autosomal DNA tested Horner ethnic groups/ populations: 

Horner Omotic Levels 1.0

However those are our levels with the outliers among each population set not removed. These are the results with the very few "outliers" removed:

Horner Omotic Levels 2.0

The "High" line just shows you the level of admixture the one person among each population set that had the most Omotic ancestry (the group's "High") with the "Low" line obviously doing the opposite. Ethnic Somalis from Somalia (North-Centralites if we're being exact) pretty much have none while their Ethiopian brethren also practically lack Omotic admixture with only a 2%~ negligible average whilst a good number of Ethiopian Somalis actually seemed to lack Omotic admixture as well.

The mixed component (a mix of seemingly non-ANE & WHG admixed West Asian ancestry + East African + Khoisan) however interestingly when we ignore Wolaytas who are Omotic speakers and thus arguably would be expected to have a large proportion of this component anyway; peaks mostly in Oromos.

However Oromos have many subgroupings among them with the Borana being the least West Asian admixed among all Horners tested so far, one group being very similar to Somalis in terms of admixture levels (Oromo B) & one being very Agaw (Beta Israel & Xamir Agaw) like, they're not exactly like Somalis who are a rather inbred and genetically "homogeneous" ethnic group.

After them it's Amharas alongside Beta Israels ("Ethiopian Jews") and then other than in Somalis it's at its lowest in Tigray-Tigrinyas as well as Xamir Agaws. Since there's in truth no genetic difference between Tigrinyas in Eritrea & Tigrinyas in Ethiopia (they're essentially the same ethnic group) and since one Eritrean Tigrinya is actually among the samples used in that Somali's ADMIXTURE run and he shows the same Omotic levels as Ethiopian Tigrinyas-> it can only be assumed the component has a spread in Eritrea as well among at least the Ḥabesha population there that makes up more than half the country.

How exactly Omotic spread to Agaw & Ethiopian Semitic populations (who were originally Agaw speakers given the Agaw substratum in their languages and the rise of Ethiopian Semitic at around roughly 800 to 1000 BC [6]) is unknown to me of course beyond the obvious being that they mixed with and interacted with Omotic peoples. Perhaps it was the ones to their west in regions of Ethiopia such as the modern "Beninshangul Gumuz Region".

The Gumuz are actually another population with Omotic input but interestingly; the Gumuz lack some of the heavier West Asian admixture in the Omotic component. I.e. Observe the "West Eurasian" (West Asian) admixture levels across East Africa from Pickrell et al. :

Note: The "Afar" in these studies are in fact Xamir Agaws.

The Gumuz as you can see in that Somali's run and Hodgson et al.'s run; have a significant amount of Omotic/ Ethiopic input. Although they just don't have the levels of West Asian admixture you would expect from peoples with their Omotic levels. Ari Blacksmiths who are practically 95 to 100% Omotic are about 15-16%~ West Asian however the Gumuz are just about relatively 1-2%~ in Pickrell  and actually show no West Asian admixure in that Somali's run at K=5 however as I said; his West Asian admixture levels are quite deflated, no doubt due to a different method for identifying such admixture which seems to have inflated the African levels in many groups and deflated their Eurasian levels.

Nevertheless their levels of West Asian admixture are a bit too low for peoples possessing their proportions of Omotic/ Ethiopic input. It's the same effect in Hodgson et al. as you might have noticed where they barely even show "Arabian" the way Ari Blacksmiths and Cultivators do before the formation of the Ethiopic component at K=11/ 11.

This low level West Asian influence as a friend brought to my attention as well as suggested; might mean that the Gumuz interacted with Omotics long before these Horner groups did. Likely at a time when Omotics had far less West Asian input?

The Omotic cluster/ component's mixed nature ultimately makes the Gumuz the most East African population to be tested so far. By East African I am referring to the "Nilo-Saharan" cluster in Hodgson et al. , a component that is also often dubbed East African (EA) in other ADMIXTURE runs and studies whilst I and some others I'm familiar with used to often call it "Ancestral East African" (AEA). The Gumuz are by all accounts predominantly made up of this component as all of their non-Omotic derived ancestry is EA, the rest which comes with Omotic is a small West Asian influence that is practically negligible along with a slightly non-negligible Khoisan influence which comes with Omotic/ Ethiopic.


Ethnic Somalis lack input from Omotics very likely because Somalia or at least North-Central Somalia very likely never had an Omotic presence for Somalis in those areas to interact with. Nevertheless one sub-cluster of Somalis; Sab Somalis who have their own sub-languages such as Tunni, Jiido, Garre & Maay were all identified to have a strong Oromoid influence in their languages, one Somali linguist who actually had a good part in establishing them as totally separate languages from from Standard/ "North Somali" even argued that their Oromo influence goes as far as being a substratum. Their languages also lack pharyngeal sounds... A phenomenon found in Oromo & Sidamic languages (they lack them as well) however Somali, Saho & Afar (fellow "East Cushitic" languages) are very heavy on pharyngeal sounds.[6]

One ethnic Somali on 23andme.com also encountered a half Ogadeni Garre who was straddling in a PCA plot (Principal Component Analysis/ a cluster like this one) between him and Borana Oromos whilst the guy had no Niger-Congo input or anything of the sort that would "pull him south" of standard inbred Somalis like the chap on 23andme.com. This all might mean that these Sab Somalis who are very often traditionally sedentary farmers or agro-pastoralists could very well have Omotic input via Oromo populations similar to the Borana who for one have Omotic admixture; which would give Omotic a certain spread in Somalia as well, though there are some small Ḥabesha and Oromo minorities all over the country anyway, some of whom have been around for centuries.

The Sab are counted under the "Raḥanweyn & Digil":

Beyond the Horn of Africa; I would assume it could also be found in parts of Kenya where the Borana live. Other than that; it's a generally Horn specific cluster, showing only extremely low "noise" levels in non-Horn populations.

Reference List:

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

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

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

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

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

6. Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East, Kitchen et al.

7. Culture & Customs of Somalia, Mohammed Diriye Abdullahi, page 9

Notes:

1. A good part of Diriye's book is based on some outdated information on history, anthropology and so on (using terms such as "Hamitic") and I wouldn't make much of any of it beyond his comments on linguistics (concerning those sub-languages of "Macro-Somali") albeit I'm skeptical as to whether or not what these languages have is a clear influence from Oromoid or actual susbtratums.

2. If you'd like some ethnic maps of the Horn of Africa, knock yourself out: [Eritrea] , [Ethiopia] , ["Greater Somalia"] , [Djibouti 1, Djibouti 2]

3. Make of Kitchen et al.'s linguistic ideas about Semitic what you will but it is generally accepted that the Ethiopian Semitic languages arose after a single introduction of South Semitic at around 800 to 1000 BC with no prior evidence (inscriptions etc.) of them before that. The Ethiopian Semitic languages carrying an Agaw/ Central-Cushitic substratum (showing that the speakers once spoke Agaw languages) is also a well-known fact.

4. To their credit, Shriner et al. actually did also find that Somalis lack Omotic admixture as you can see via their supplemental.Whilst showing that Ethiopian Somalis have a certain amount albeit their levels for them are arguably quite inflated and probably skewed even further by two "outliers" among the Ethiopian Somali samples who had some pretty high Omotic levels.

Updates:

That Somali's run for the Ari populations (in terms of Omotiv levels) are likely pretty solid at least in the sense that he was onto the right idea about removing the inbred samples. In fact an upcoming study with its abstract shown at a recent conference (have a look) seemed to be focused on this exact same subject and it aims to show that Ari Cultivators are essentially a less inbred edition of Ari Blacksmiths.

As a result Ari Cultivators probably to some extent have less Omotic due to being less inbred however the "Ethio-Somali" (Cushitic influence) in them seems to indeed be real, for one it's noticeable in how they are notably more West Asian than their Blacksmith counterparts. 

One should also note that Omotics such as the Ari have a rather distinct Y DNA profile that you can see in Plaster et al. (Variation in Y chromosome, mitochondrial DNA and labels of identity in Ethiopia) or have it more comfortably simplified for your viewing at the Ethio Helix blog. I'd highly recommend that blog btw.