The East African Cluster

The East African cluster/component (which I used to dub AEA/ Ancestral East African) is an ancestral component that peaks mostly, for the time being, in populations such as the Dinka, Anuak, Gumuz & generally South Sudanese populations, most of whom are speakers of Nilo-Saharan languages (a family which Old Nubian whom some of you maybe familiar with is a member of) and it is often dubbed "The Nilo-Saharan" component as a result.

The ADMIXTURE run from Hodgson et al. 2014 does, as many studies do, notices the existence of this cluster, it's the light blue one that is duly named Nilo-Saharan by them. 

At the lower Ks of this run and in many other runs, both those arranged by more layman sources as well as peer-reviewed studies; this component makes up a great degree of the ancestry in Horn Africans as well who are sort of the next peak of it in East Africa although we lack North Sudanese samples (Nubians, Sudanese Arabs, Beja etc.) for the time being.

This component tends to make up ~60% of the ancestry in Somalis & for example ~50% of the ancestry in Ḥabeshas such as Tigray-Tigrinyas. It also has a certain spread in West Asia & North Africa, most North Africans (Egyptians, Berbers) often prove to be almost ~20% East African [3], the rest of their African admixture being "Niger-Congo", a component of West-Central African origins that can be found all over Africa except, mostly, the Horn of Africa in varying degrees while peaking in Niger-Congo speakers.

The East African cluster exists in Levantines right down to Ashkenazi Jews & Negev Bedouin at a rate of about ~1-15% and in Arabians themselves as you can observe in Hodgson et al. itself at a rate of ~5-15% [4] [1]. Much of its presence in these populations given its spread seems quite extensively ancient (its ancient nature is likely even greater in North Africans) and this component's spread is not to be conflated with the Arab Slave Trade though some of its spread might be owed to this.

Mainland East Africa

Yemenite Jews for one are likely similar to some of the Christian populations of the rest of West Asia & Egypt; in that they are a perhaps decent representation of  the pre-Islamic inhabitants of their respective homeland (in this case; Yemen), seemingly avoiding a good degree of the admixture incurred by their Muslim counterparts [8], it says a lot that they too have this component at a rate of ~5-15%. It's also quite prevalent in Southeast Africa, making up a non-negligible segment of the ancestry in various Southeast African Bantu speaking peoples as well as the Hadza, and so on.

What makes this component intriguing however is not its spread, though its main geographic concentration (East Africa) is key. It's that this component and its carriers tend to show a greater affinity for Eurasians or rather; Out of Africa Populations than other African populations do.

Above is a PCA plot (Principal Component Analysis) from Pagani et al. , a study focused on the Horn of Africa populations. In this PCA/ cluster you can see that Anuaks & the South Sudanese samples have a greater pull towards West Asians & North Africans as well as Europeans (CEU) than Yorubans who are a Niger-Congo speaking West African ethnic group do (though the pull is small) despite the fact that Anuaks and such have anything between ~10-30% Niger-Congo input (makes up almost the entirety of the Yoruba).


As many of you might know by now if you've been keeping up with this blog, Out of Africa populations in general are thought to have expanded out of East Africa or at least share more of a lineage with East Africans over other Africans, this is noticeable in that every single mtDNA Haplogroup outside of Africa traces back to mtDNA L3 which is an East African marker.

A theoretical spread of how L3 spread

The Y-Chromosome Haplogroups of all Out of Africa populations also trace back to CT which is for now thought to be East African although its ancestors BT & Haplogroup A (Anuaks, Dinkas etc. are rich in Haplogroup A and rich in L3 markers) are clearly African.

It seems to be this general East African (their ancestors honestly could have been anywhere in Africa, it's just that their lineage is mainly pulling toward East Africans as we know them today) origin postulated for Out of Africa Populations that seems to give modern East Africans a certain affinity for them that other Africans lack or have less of.

However the East African cluster is most likely not a pure representation of the cluster, for example, the Proto-Eurasians (the first and ancestral OoA population) descend from. Carriers of this component including those whose ancestry it covers at a rate of ~70-80% (Anuaks etc. have a certain degree of Niger-Congo admixture) show markers such as L2 and so on that are signals perhaps for more divergent African ancestry in them and likely in their component.

The component also at the lower Ks even shows a meager "Khoisan"-like influence that you can see for yourself in Hodgson's own plot by observing the populations it peaks in at K=3 (numbers on the side) to K=5.

It even has a very small Eurasian/Out of Africa element that tends to show in these populations at the very lowest Ks (K=2 etc.).

It can only be assumed that if these more divergent influences (excluding the small Eurasian element) were not likely present in it (we'll need ancient genomes from East Africa to truly understand the component); the component's affinity for Eurasians would become even more potent. It could perhaps even seem Eurasian itself as a result... It could possibly be assumed that there is a very ancient East African cluster within it, noted by lineages such as L3 while the rest is more divergent African input marked by other markers such as L0 & L2.

Nevertheless, its current affinity for Eurasians brought about by the richness for example of lineages such as L3 in its carriers is quite evident. It shows in terms of whole-genome-wide variance as well as Fst distances.

The Ethiopic (Omotic) component is a mixed cluster made up of this East African component or predominantly, then pretty much something related to the Arabian & Khoisan clusters in that Fst distance table above so its greater closeness to Eurasia is explained mostly by direct and non-negligible West Asian input (~15%) but notice how Nilo-Saharan (East African component we're discussing here) is closer to all of the Eurasian clusters than Niger-Congo, Pygmy & Khoisan are.

Now, Fst distance can be influenced by a variety of factors, i.e. populations with small sizes can enjoy a higher incidence of genetic drift which will raise their Fst distance from other populations (it's ultimately not a 100% reliable way to gauge "distance") but then the thing is; even the Niger-Congo component likely shares in very ancient East African input.

Niger-Congo carriers such as Yorubans will often show L3 and as you can see their component has a certain affinity for Nilo-Saharan that "Pygmy" & "Khoisan" lack and they too prove closer to Eurasians than lets say the Khoisan do even when we utilize whole genome data to look at the estimated divergence dates between these populations:

The Yoruba are much less divergent in this respect from the French & the Han than San/Khoisan are. This is perhaps due to their ancient East African input which is shared to some extent between their Niger-Congo component and lets say your average Anuak's Nilo-Saharan component. David Reich himself once suggested that Niger-Congo Africans could be made up of divergent African lineages.

It's quite likely to me that components such as East African/ Nilo-Saharan & Niger-Congo will crumble into other components once we have ancient genomes from all over Africa to work with, much like what happened with Europe and our current knowledge of the three-way mixture nature of Europeans [7]. One of the components it will be made up of will likely be a specifically East African cluster with what might be a very strong affinity for Eurasians (Out of Africa Populations) given the origins of Eurasians as a whole. For now, only time & waiting will tell.

For the time being we just know that this cluster has what can be assumed to be a somewhat greater affinity for Eurasians than other African clusters as displayed above.

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.

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

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

5. Genetic history of an archaic hominin group from Denisova Cave in Siberia, Reich et al.

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

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

8. Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture, Haber et al.

Notes:

1. Rummage through the Ethio-Helix blog's pages (the links I shared) on Haplogroups in East Africa, the author sets things up quite well in terms of interactivity and shares links to each of the studies he got the marker percentages from so everything he's sharing is entirely reliable, no worries. It's a good blog in mostly all other respects too so I recommend it.

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.