Inferences that can be made from a Sudanese Arab's Gedmatch results

A while back I said I'd be sharing the various genomic results of both a Sudanese Arab man & a Nubian woman who were commercially tested (via 23andme) because this would allow for the utilization of more SNPs when dealing with analyses like admixture or PCAs.

The reason I wanted to do this was because while Dobon et al. 2015 sampled a lot of Nubians & Sudanese Arabs for about 200,000 SNPs which should allow for high quality analyses; they utilized a bad genotyping chip / a chip that overlaps in SNPs badly with the chips used for sequencing genomes in other datasets.

For example, the admixture analysis above from Dobon et al. 2015, if I recall correctly, and was told by one of the study's researchers via email was that it only utilized about 15,000 SNPs and, indeed, the decent enough PCAs I shared in my post about Dobon et al. also used such a low number of SNPs.

It's usually preferable for PCAs like the one below, for example, to utilize 100,000 SNPs or more for high quality results:

The PCAs I shared are good enough and the inferences that can be made from them like Bejas seeming as though they are intermediates between certain Horn Africans (Somalis, Habeshas, Wolaytas, Oromos) & Sudanese Arabs + Nubians aren't wrong at all. [note]

On the other hand, when dealing with analyses like admixture analyses which become increasingly unstable & therefore unreliable with the lower number of SNPs you use; such a low number of genetic markers is problematic.

So what I essentially wanted to do was circumvent this issue by taking two people who were not tested in this study and whom were sampled for anything between 500,000 to 1,000,000 SNPs (like at 23andme) & run them through some admixture analyses in order to  reliably compare them to modern populations in terms of for example just how much ancestry they may share with Somalis & Habeshas.

I'm happy to say the data very much supports what was noticeable via the PCAs I shared that were ultimately owed to David Wesolowski who runs the Eurogenes genome blog and project.

Basically, what the results for Eurogenes K=36 suggest is that Horn Africans such as Somalis & Tigrinyas in terms of more recent ancestry; are closer to one another which explains why in various PCAs like the one below; we cluster off together rather than either population clustering with Sudanese populations instead:

More recent ancestry being ancestry I suppose more along the lines of like the last few thousand years: in terms of such ancestry its obvious most Horn Africans of Cushitic & Ethiopian Semitic speaking populations are closer to each other than either is to Sudanese Arab or Nubian groups as the PCAs suggest and this Sudanese Arab's admixture results do as well.

Although another inference that can be made is that it seems quite evident lots of likely post-Neolithic ancestry is shared between Horn African groups like Somalis & Northern Sudanese groups like Sudanese Arabs.
I say this once again based on these Eurogenes K=36 results. Firstly it must be noted that these results were acquired via Gedmatch which allowed me to utilize David Wesolowski's K=36 admixture calculator; however, these results are skewed to some extent by the notorious calculator effect.

This is why for example, the Eritrean Tigrinya, this Sudanese Arab chap & I are showing "East African" which is actually a Maasai peaking / seemingly based component from what I understand. In the original table David made for this analysis; things are more fine tuned and not effected by the calculator effect and Somalis alongside Tigrinyas are missing components like "East African".

However, the Northeast African component here peaks in Somalis & is somewhat similar to the "Ethio-Somali" component or the "Lowland East Cushitic" component. And of course, even if it is now being shown via a calculator effect; the "East African" component carries with it Horn African-related ancestry.

This Sudanese Arab along with Dobon et al.'s Nubians & Sudanese Arabs as the global PCA below including them (that's a bit messy because of the low number of SNPs utilized) suggests- :

-is on a rather fundamental scale very similar to Horn African populations & essentially a mixture between West Euraisan ancestry and African ancestry related to the kind of ancestry that forms the non-Niger-Congo-related ancestry in populations such as Dinkas. [note]

In fact, in this regard he is somewhat more similar to Tigrinyas than I am as he is closer to them in West Eurasian ancestry levels than Somalis are as you can see below:

 However, the difference seems to be that he has some much more "recent" West Eurasian-derived ancestry than either Somalis or Tigrinyas do, as evidenced by his higher "Arabian", "Near Eastern" & "Eastern Mediterranean" scores than either me or my Tigrinya colleague. [note]

Another distinction seems to be that he has much much recent Nilo-Saharan speaker-related ancestry evidenced by his "Central African" score (peaks in South Sudanese, if I recall correctly) which also explains why, in various admixture analyses available at Gedmatch, he consistently displays Niger-Congo-related ancestry which is present in contemporary South Sudanese populations and seemingly also populations like Darfurians.

The "East African component" based ancestry in Horn Africans while seemingly related to the non-Niger-Congo ancestry in Nilo-Saharan speakers such as Dinkas; isn't exactly like them & is seemingly mostly to entirely pre-historic in origin / extremely ancient hence why we lack the likely ancient & substantial Niger-Congo-related ancestry present in populations like Dinkas; our non-West Eurasian ancestry is not derived from them.

However, in this Sudanese Arab's case it does seem as though he derives actual ancestry from groups like the South Sudanese rather than pre-historic populations similar to much of the ancestry in them. This is quite understandable as many Sudanese Arabs used to be actual Nilo-Saharan speakers prior to their Arabization, and Nubians are Nilo-Saharan speakers.

As for the signals of perhaps post-Neolithic Horn African-related / Somali-like ancestry showing in this Sudanese Arab, I would have liked to see the results of a Nubian in these kinds of analyses but what this likely suggests to me is that this is due to ancestry from actual early to not so early Cushites being present in Sudanese Arabs & Nubians. [note]

As it is suggested via both archaeological and linguistic studies; in many cases, some of the earliest inhabitants of Northern Sudan (as early as the Neolithic) were in fact people of Cushitic speaking origins who were eventually assimilated by the Nilo-Saharan speaking ancestors of populations like Nubians just a few thousand years ago. [2] [3]

The Kerma culture's people are suggested by some linguists to have been Cushitic speakers

Then there's of course the strong & long-time presence of actual Cushitic speakers seemingly closely related to Horn African populations such as Bejas [note] who are, in some cases, thought to be a relic of not just Sudan's early Cushitic speaking nature but also that the ancestors of Horn African Cushitic speakers originally migrated into the Horn from northerly regions such as Sudan.

Further linguistic, archaeoligical & genomic study is needed to confirm these possibilities of shared ancestry from just say the last few thousand years or so between Nubians and Somalis for example (the sampling of ancient genomes would be the most ideal)...

Northeast Africa

Nevertheless, for now those are the best inferences I can make using this one man as a proxy for Dobon et al.'s various samples whom he seems representative of. Granted, one should recall that at least in terms of admixture levels (proportions of West Eurasian and African ancestry); Sudanese Arabs and Nubians seem quite heterogeneous.

For now my bet would be that Nubians for example are a mixture between earlier Cushitic or generally Afro-Asiatic speaking peoples perhaps genetically similar to Somalis, populations perhaps similar to Copts from earlier periods of Egypt & populations similar to contemporary Nilo-Saharan populations such as Dinkas with Sudanese Arabs being all that + some later Arabian-related gene flow. [note]

Only further genomic study of these groups will tell and what I wrote in the above paragraph is honestly just an educated guess on my part based on our current data.

Reference List:

1. The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape, Dobon et al.

2. The Origins and Development of African Livestock: Archaeology, Genetics, Linguistics and Ethnography

3. Links between Cushitic, Omotic, Chadic and the position of Kujarge, by Roger Blench

Notes:

1. Eurogenes ANE K=7 mostly inflates the ENF & WHG-UHG scores of people who've been run through it (Northwest Africans turning up as over 20% WHG-UHG as opposed to the more fine-tuned K=8's ~15% values) though its ENF scores are not inflated by much (Somalis hopping from 41% in K=8 to 42% in K=7). This is because the run was honestly mostly designed to spot ANE-related ancestry & not as much care was put into the other components. [note] Sub-Saharan African is just a result of me adding the "East African" & "West African" components in ANE K=7 together to neaten things up.

3. A friend more knowledgeable than I in this particular subject's notes on the Niger-Congo-related admixture in groups like the South Sudanese: Link to note

Northwestern Neolithic Anatolians were essentially "EEF" with less "WHG"

Well, it seems David wasn't wrong when he worked on the extremely low coverage genome of a farmer from Neolithic Northwestern Anatolia as we now have proof with far more samples from the recent Mathieson et al. 2015 to back up what he noticed.

What he noticed can be surmised via the PCA (Principal Component Analysis) / autosomal DNA based cluster above where the Barcin / Neolithic Northwestern Anatolian farmer whose genome he analyzed looked like she was essentially an Early European Farmer with less Western European Hunter-Gatherer-related ancestry.

As you can see in the PCA above where Mathieson et al. 2015's Anatolian Neolithic samples are present; they essentially cluster with Neolithic Europeans (F.e. Middle Neolithic) / Early European Farmers but pull farther away from Western European Hunter-Gatherers than they do.

This is all quite interesting as it suggests now that the Neolithic Farmers who entered Europe from West Asia (specifically Anatolia and into the Balkans) during Neolithic period already carried Western European Hunter-Gatherer-related ancestry.

These farmers who brought agriculture to Europe then stocked up on more WHG-related ancestry once they got to Europe (from mixing with the continent's local earlier forager inhabitants) resulting in individuals like the Stuttgart farmer who're more WHG-related in ancestry than these Anatolian Farmers from around 7,000 years ago.

Scope of Matheison et al.'s samples

The next step would obviously be acquiring more and more ancient DNA from West Asia. For now, it's difficult to assume all of Neolithic Anatolia was like these Barcin Farmers who lived so close to the Balkans & the Bosphoros (perhaps this explains their WHG-related ancestry visible outside of "ENF"?). 

It would be truly intriguing if Neolithic Anatolian farmers from areas such as Eastern or Central Anatolia also proved to be very EEF-like and not distinct from their Barcin Farmer neighbors.

However I suppose the old "EEF + ANE + WHG" model has been shaken up once again and Europeans are for now looking to basically be "Anatolian Neolithic-related + Yamnaya-related + WHG-related" on a as displayed above in charts from Mathieson et al. 2015.

With the Pontic Caspian Steppe side of Europeans being part Caucasian-like & part Eastern European Hunter-Gatherer-related which as this paper notes has a certain extra relation to Ancient North Eurasians like MA-1 that makes modeling Europeans as part "ANE" possible, and finally the Neolithic Farmers who came to Europe seemingly from Anatolia would've been part this component & part WHG-related.

The plot thickens with the more ancient DNA we get and there are still unanswered questions like the exact source of West Asian-related ancestry in Bronze Age Steppe Pastoralists like the Yamnaya & what exactly "Basal Eurasian" really could be. 

Reference List:

1. Eight thousand years of natural selection in Europe, Mathieson et al. 2015 

Recommended reads:

Eight thousand years of natural selection in Europe - take 2

New version of paper of Iain Mathieson: Eight thousand years of natural selection

All Modern Africans are part Eurasian? We should probably be a bit cautious

In light of a recent study that sampled a 4,500 year old Southwestern Ethiopian (labeled "Mota" for the cave he was found in) we now have data suggesting that Africans all around other than the obvious already known cases like Horn Africans & various Southeast Africans; supposedly have non-negligible Eurasian ancestry.

Truthfully, upon really taking a look at this paper's various results... I must personally advise some caution and say that I'm not 100% convinced that this Eurasian ancestry in all these groups is real. Why? Well, it's mostly but not entirely the scope as well as the levels. 

Every population from Hunter-Gatherer Pygmies like Mbutis & Biakas [note] down to farmer groups like the Yoruba or pastoralists like Anuaks are all supposedly about ~6-8% Eurasian (supposedly even West Eurasian?)? What's suspicious about this is the general homogeneous amount found all across in all these populations that prior to this study showed no strong Eurasian affinities other than some signs of Neanderthal ancestry or a hint here and there in some admixture runs in only some of them, if I recall correctly. [2]

But what large scale event occurred that spread Eurasian ancestry at such a homogeneous level to so many culturally & genetically distinct as well as geographically far removed from one another populations? This doesn't entirely even make sense. 

It can make some sense when observing some populations like Yorubas showing prior signs of Neanderthal ancestry and then the presence of markers like mtDNA U in West Africa but all across Africa? From Nilo-Saharan speakers like the South Sudanese ("Sudanese" samples) to Niger-Congo speakers like South African Bantu speakers and at a roughly equal level?

I mean there's nothing shocking about Eurasian ancestry showing up in groups like the Nama whom we know have both South Cushitic pastoralist & European admixture or in the Maasai who are substantially South Cushitic (and perhaps even part East Cushitic?) admixed or in Horn Africans but in these other populations it's surprising but would to my mind be more acceptable if these levels varied more.

F.e. if the South Sudanese were like ~3% and Yorubas were like ~7% & things just varied altogether then these results would seem a bit more plausible to me as it would mean there was some very ancient Eurasian expansions into Africa (plenty of evidence for such) that just so happened to hit these populations in different ways and likely at different times and then understandably resulted in different levels of Eurasian admixture.

But then Mbutis are ~6%, Yorubas are ~7% , Southern African Bantus are ~7% & the South Sudanese are ~6.5%... I must ask how? Why such extremely close levels? I'm not going to come out and say these results are 100% moot but I must say that one should be a little suspicious of them.

Perhaps this is due to Mota containing some form of a very archaic African element that all these populations lack? [note] This could perhaps shift them all away from Mota and towards Eurasians at a roughly equal rate? I'm really just shooting in the dark here as I'm generally just in shock over this study's results.

All I can say at this point is that further study is required... More ancient genomes from Africa, more from Eurasia and I'll be excited to see what we get when people like David who runs Eurogenes or Kurd over at Anthrogenica get their hands on this sample and start comparing him more and more to modern populations.

A lot more still needs to be learned and tested but for now this study's claim that these groups have Eurasian admixture is what the data we currently have is saying...

Reference List:

1. Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, Llorente et al. (the study's text is pay-walled but the supplementary information which contains most of what you'll need anyway is free)

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

Notes:

1. Maju seemed skeptical about the validity of these results at his blog as well... 

Ancient Ethiopian Genome has some interesting things to share

Well, it seems we no longer have to utilize modern Africans as a reference for a completely "African" population (from a genetic point of view) with essentially no "Eurasian" input as we now have an ancient genome from Southwest Ethiopia that's about 4,500 years old and he has interesting things to share about modern Africans.

"Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry."

They're not joking about that last emboldened part either. Yorubas and various African populations thought to completely lack "Eurasian" / Out-of-Africa ancestry are in fact anything between 5 to 10% Eurasian (seemingly West Eurasian) based on comparing them to Mota (the name for this ancient individual being based on the the "Mota cave" which he was found in) and ancient Eurasians like Early European Farmers whom I talk about here.

Basically every population from Mbuti pygmies to Yorubas to Kenyan Bantus now demonstrates non-negligible non-African / Euraisan / Out-of-Africa ancestry. It seems that yet again, we were misguided to use modern samples to try and fully understand Human history.

The reason we now have these estimates is because Mota seems to utterly lack any signs of Eurasian ancestry; signs that Yorubas among other groups have shown in the past like Yorubas showing non-zero Neanderthal ancestry levels [2] whilst Mota unlike various modern Africans utterly lacks any signs of Neanderthal ancestry.

This really shakes up and complicates African genetics and slightly back-ups statements I've made in other areas of the internet somewhat based on what geneticists like David Reich have said; even populations like Yorubas thought to be mostly "pure" due to ADMIXTURE analyses like the following one from an old study- :

[3]

- are not in fact "pure" but clearly somewhat complex mixtures like many Eurasian and other African populations like Horn Africans, various Southeast Africans, Central Asians, Europeans and so on. [note] We will of course need more ancient genomes from Africa in the future to add to and further comprehend what these results show as well as even back them up but for now; that's what we have.

But for now that's all I'll be saying about this paper until I've gotten around to reading it more thoroughly than my current skimming of it.

I also highly recommend going through the study yourself or at least it's currently available supplementary information.

Reference list:

1. Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, Llorente et al.

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

3. The genome-wide structure of the Jewish people, Behar et al.

Notes:

1. Mota belong to Y-DNA E1b1 & mtDNA L3x2a

2. Seems to be a lot of news on this study in the mass media...

3. A fruitful discussion about this study is ensuing here.

4. One interesting thing to note is that when Mota & the Druze are used to asses how "Eurasian" all of these populations are; the West Eurasian ancestry in Horn Africans increases but then decreases (something that doesn't happen to other populations like Yorubas and Mbutis) when Mota & Early European Farmers (LBK) are used...

The Druze have a small amount of "African" ancestry, if I recall correctly at about ~3% or some such (some of this may in light of this recent find carry Eurasian ancestry?) so perhaps this causes the sudden lowering in Horn Africans in respect to when LBKs are used or perhaps it's the greater European Hunter-Gatherer-related ancestry in LBKs? It's an interesting thing to note, I suppose.

Ancient North Eurasian

Ancient North Eurasian is an ancestral component now somewhat common in population genetics... It was originally discovered through the genome of a Siberian boy who died over 20,000 years ago referred to as either Mal'ta boy or MA-1 and was backed up as being a real entity in pre-historic Eurasia through other ancient genomes like that of Afontova Gora-2. [1]

It's discovery really shook up a lot of things like our understanding of the origins of Europeans, Native Americans and even groups such as Central Asians, South Asians and various West Asians who seem to carry either Ancient North Eurasian or Ancient North Eurasian-related ancestry.

Lazaridis et al. 2013-2014 seemed to suggest that Europeans were basally a three-way mixture between Ancient North Eurasians / MA-1 related peoples, what they dubbed Western European Hunter-Gatherers based on the ancient genomes of various Mesolithic Hunter-Gatherers from Europe like Loschbour and then finally Early European Farmers who began entering Europe around the Neolithic from West Asia. 

Since then that model's become rather obsolete and has been replaced by one where all of the supposed Ancient North Eurasian ancestry in Europe is owed to the spread of the Indo-European languages by pastoralist peoples from the Pontic-Caspian Steppe. 

These pastoralists were carrying with them a foray of different ancestries from what looks to be Caucasian-like ancestry rich in what looks to be Ancient North Eurasian-related & West Asian ancestry and what is for now referred to by chaps like Wolfgang Haak of Haak et al. 2015 as "Eastern European Hunter-Gatherers (EHGs)". [2] 

EHGs almost fit as a mixture between Ancient North Eurasians & Western European Hunter-Gatherers but instead don't entirely look to be the result of such a mixture. Though as David Wesolowski who runs the Eurogenes genome blog and ancestry project once remarked in the quote below- :

"It depends how you define EHG, ANE and WHG, and the concept of pure components.
They can all be distinct pops, or EHG can be a mix of ANE and WHG, or even WHG can be a mix of EHG and something as yet unsampled."

-it's honestly rather iffy and tricky modeling these pre-historic groups with wildly different time stamps on them (Mesolithic for WHGs and EHGs and Paleolithic for ANEs) as mixtures of one another.

But David seems to assume groups like EHGs and WHGs are likely a mixture between groups that preceded them perhaps like Ancient North Eurasians and some other groups as yet unsampled. The cold hard truth of the matter is that we require more samples of pre-historic Hunter-Gatherer groups across West Eurasia to really understand what EHG and WHG are and how exactly they're connected to ANE because the current models seem inadequate.

 It could just be that Eastern European Hunter-Gatherers are somehow extra related to Ancient North Eurasians or somehow partially descended from them and something Western European Hunter-Gatherer related. We'd need more ancient genomes across time and space in Europe and other parts of Eurasia to truly grasp this with any kind of conclusive detail.

Early Neolithic = Early European Farmer

Although one thing is resolved for now... A group of "pure" Ancient North Eurasians didn't come and contribute Ancient North Eurasian ancestry to the ancestors of modern Europeans; this Ancient North Eurasian-related ancestry is ultimately owed to expansions from the Steppe. Whether EHGs are "WHG + ANE" or related to MA-1 in some other way or not.

Though it is worth-noting that the non-EHG and "Caucasian-like" ancestry in Pontic Caspian Steppe pastoralists like the Yamnaya did also carry Ancient North Eurasian-related ancestry and in this case; not seemingly owed to Eastern European Hunter-Gatherer ancestry. 

The redder a place or its "outline" is; the richer in ANE-related ancestry it is

In the end though what looks to be Ancient North Eurasian ancestry or Ancient North Eurasian-related like EHG ancestry is found all over Eurasia from Siberia to South Asia or Western Europe to Central Asia. In a modern context it tends to peak in Siberian groups like Kets [3] or various modern South Asians and in West Eurasia peaks in the Caucasus region.

It also really helped redefine our understanding of the origins of Native Americans who like many populations on this planet are now understood not to be some "pure" separate branch of the Homo Sapien Sapien family tree but a mixture of sorts like Europeans. In their case the mixture seems to be between Ancient North Eurasians and East Asian-related ancestry. [4]

If I had to quickly dive into where the component stands in Eurasia; it's essentially closest to Eastern & Western European Hunter-Gatherer and seems to share as geneticists suggest; a sort of earlier root with these components like it does with Western European Hunter-Gatherer in that Lazaridis et al. 2013 diagram I shared.

Though as I said; we really need more samples from across Eurasia (West Eurasia, Siberia, Central Asia, South Asia etc.) from various time periods to really understand the true nature of groups like Ancient North Eurasians, Western European Hunter-Gatherers and Eastern European Hunter-Gatherers because as it stands; things stand on somewhat unsure and confused ground.

For all we know; what looks to be non-Steppe derived "ANE" ancestry in groups like South Asians, Central Asians and West Asians may not be owed to some sort of "pure" Ancient North Eurasian group like we once thought was the case for Europeans...

It could instead mean that these groups owe their Ancient North Eurasian-related ancestry to Eurasian Hunter-Gatherer groups somehow related to Ancient North Eurasians or who carry ANE ancestry themselves in some way or other; more ancient DNA analysis is needed... I say this a lot and before this blog post is over will say it again because it can't be emphasized enough.

This uncertainty I highlighted above is essentially why I insist on sometimes writing "Ancient North Eurasian-related ancestry" rather than undoubtedly assuming some of these non-European populations have direct ANE ancestry.

Eurasia

Nevertheless, for the time being what we dub "Ancient North Eurasian" is highly divergent from Western European Hunter-Gatherers despite the seemingly closer relations between ANEs and European Hunter-Gatherers when compared to Eastern Non-African groups, to a point where Native Americans will often seem more similar or closer to Mal'ta boy than Europeans are like in analyses such as IBS:


MA-1 IBS


This being the case despite the fact that the East Asian-related ancestry that makes up the rest of Native Americans' ancestry is less related to Ancient North Eurasians like Mal'ta boy / MA-1 than the European Hunter-Gatherer ancestry in Europeans is, though Europeans might be shifted away a bit by the highly divergent Basal Eurasian component in their West Asian / Near Eastern-related ancestry.


Eurogenes K=8 is a good representation of the levels of Ancient North Eurasian-related ancestry found across various global populations


Nevertheless, ANE is a pretty distinct ancestral cluster of its own with what seems to be a very large spread across Eurasia of either ANE or ANE-related ancestry showing up in small amounts even in some East Asian populations as well as somewhat in Egyptians, a Northeast African population.

Reference List:

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

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

3. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry, Flegontov et al.

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

Notes:

1. What shows up as Ancient North Eurasian in East African groups like the Gumuz or Anuaks in the K=8 admixture analysis isn't actually ANE ancestry. From what David once told me; it's essentially some sort of archaic Eurasian element these groups demonstrate that just won't fit into the runs other clusters/components. 

These East African cluster rich groups in my experience do tend to show an odd as of yet unexplained very small Eurasian / Out-of-Africa (related to Non-African populations) element in various runs especially at K=2; just don't make much of it for the time being. 

2. I've put a little time into formally explaining components like Ancient North Eurasian or the Near Eastern / West Asian ancestry (Early Neolithic Farmer) in Early European Farmers because many I've encountered who've just gotten recently interested in population genetics sometimes might need a more straightforward explanation for what these components are / what we for now understand of them without having more ancient samples to paint a better picture so here are your explanations.

3. The world map that shows various ANE levels across the globe via the colors green and red is owed to a chap David/the author Eurogenes refers to as Sergey as mentioned here. And the MA-1 IBS spreadsheet if you're wondering is owed to David.

4. This is a direct note quoted from David/ the author Eurogenes I'm sharing because it's rather interesting: [-]

ASI = Ancestral South Indian, you can learn a little about it here. It's essentially a "South Indian" centered Andamanese & perhaps also Australo-Melanesian related component though we'll need ancient DNA from South Asia to really grasp it as for now it's not even "purely" made up of such ancestry and as David notes; is "mixed" in that it carries ancestry like Ancient North Eurasian-related ancestry. That's because all the models of it we have for now are based on modern South Asians who are all mostly a mixture between West Asian-related, ANE-related, Pontic Caspian Steppe-derived & "ASI" ancestry.  The only way to get a good and unmixed edition of it would be sufficient ancient DNA from South Asia where it can be found in such a state. 

Recommended reads:

1. A decent forum discussion about Eastern European Hunter-Gatherers

Is the Eastern Non-African situation more complex?

A recent study based on cranio-metric data essentially proposed something quite preposterous once genetics is taken into account and that's the following:

"Our results support a model in which extant Australo-Melanesians are descendants of an initial dispersal out of Africa by early anatomically modern humans, while all other populations are descendants of a later migration wave. Our results have implications for understanding the complexity of modern human origins and diversity."

It's preposterous because it's quite obvious at this point that Eastern Non-African (ENA) populations (I formerly referred to them collectively as "East Eurasians") at large share a lot of drift with West Eurasians or at least with the non-African & non-Basal Eurasian ancestry in West Eurasians like the African ancestry in Arabians or the Basal Eurasian in all West Eurasians. [1] [6]

This shared drift and closeness between Eastern Non-Africans and West Eurasians whether ancient or modern is seemingly owed to the fact that all Out-of-Africa populations are essentially descended from an extremely ancient pre-historic bottle-necked population like the following diagram from Lazaridis et al. 2013 [2] displays:

There seems to be little doubt in terms of autosomal DNA about this fact and their Haplogroups somewhat support this as well. Then there's the fact that Haak et al. [3] from what I recall proved Ust-Ishim [4] occupies a basal position to Eastern Non-African groups like the Andamanese Onge and East Asians alongside European Hunter-Gatherers groups such as Western European Hunter-Gatherers as the quote below stipulates:

"Ust’-Ishim was inferred to occupy a basal position to eastern non-African and European hunter-gatherer populations but not to modern Europeans, which was interpreted as due to admixture from a population occupying an even more basal position to Europeans"

This in a vague sense means that Ust-Ishim was in a state that Western European Hunter-Gatherers, East Asians and groups like the Onge are ultimately only "downstream" from as in they diverged from a shared state quite like Ust-Ishim regardless of whether or not he was alive around the time when the ancestors of Eastern Non-Africans, Ancient North Eurasians & Western Hunter-Gatherer-related groups diverged.

The Out-of-Africa model in terms of how it exactly happened and whether or not there were various slow dispersals rather than one is not entirely known from what I recall but one thing's for sure:

All of the ancestry in Europeans including their Basal Eurasian ancestry and all of the Homo Sapien Sapien ancestry in Eastern Non-Africans; ultimately diverged from seemingly one bottle-necked population (the original "Non-African" group in Lazaridis et al.'s diagram) and all of the Homo Sapien Sapien ancestry in Eastern Non-African groups like the Onge or even Papuans is seemingly a downstream development from the state Ust-Ishim was in.

[3]

So some idea where a distinct group of ancient Africans left the continent for Eurasia and then made it to areas like Melanesia and Australia with a second migration carrying the distinct ancestors of Europeans and East Asians is just not in line with the genetic data and that's what's ultimately most relevant in making such inferences about populations and their relations to each other; genetics.

Another big issue for this model is simple, in truth. Australo-Melanesians, Andamanese and East Asians are seemingly closer to each other than they either is to Europeans often prompting various population geneticists to lump them into a sort of "clade" with one another like "Eastern Non-African" in Lazaridis et al. 2013 or similarly in Kay Prüfer et al. 2014 [5] as I touch upon here.

Australian Aborigine man

The argument perhaps being that they share extra ancestry with each other that they don't share with Ancient North Eurasians or Western European Hunter-Gatherers, suggesting that there's another extra node in the Out-of-Africa family tree that they ultimately diverged from like you see in that Lazaridis et al. table where the East Asian-related ancestry in Native Americans like Karitianas seemingly comes from the same "ENA" node as Onges.

The question I'm merely posing here is simple; will things grow more complicated for this supposed node or part of  the Out-of-Africa family tree?

This is a possible outcome in my humble opinion especially once we get ancient DNA data from across Oceania, Southeast Asia & East Asia.

This grouping may even collapse to some extent and make it seem more like Eastern Non-Africans are partially descended from separate Out-of-Africa nodes downstream of Ust-Ishim that merely intermixed to some great extent in pre-history hence their closer affinity to each other over pre-historic West Eurasians like Western European Hunter-Gatherers; a model I've come to suspect but that could be entirely wrong. [note]

[6]

For now I'd say one thing is for sure... Papuans, Australian Aborigines, the Andamanese; these groups are closest to East Asians and Polynesians when it comes to the Human family tree but how this will make sense someday within the Out-of-Africa family tree in general like whether or not this Eastern Non-African clade will remain for the most part is what could be shifty but the greater closeness between these groups is not going to change.

Reference List:

1. Testing modern human out-of-Africa dispersal models and implications for modern human origins, Reyes-Centeno et al.

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

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

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

5. The complete genome sequence of a Neanderthal from the Altai Mountains, Kay Prüfer et al.

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

Notes:

1. The non Non-Homo-Sapien-Sapien ancestry in Eastern Non-Africans I'm referring to would be both Neanderthal & Denisovan admixture.

2. 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 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.

3. Hodgson et al. (the sixth reference) is not relevant in anyway here except in showing those parties interested; direct proof that groups such as Arabians have African admixture. You can basically consult any of its admixture analyses to see that proven for you or even observe Lazaridis et al.'s K=20 admixture analysis to see the same kind of data where ancestry related to the ancestry in groups like Dinkas and Yorubas surfaces in various "Arab" populations including Peninsular Arabians.

4. There's also the fact that Eastern Non-African groups haven't been as focused on in population genetics as West Eurasians so a good amount of their lack of strong differentiation might be due to this...

Early Neolithic Farmer: The West Asian ancestry in Early European Farmers

 I've often shared results from the Eurogenes K=8 admixture run where the "Early Neolithic Farmer / Near Eastern"component turns up or perhaps referred to pre-historic "West Asian" ancestry and I'd like to take this opportunity to quickly explain what this component is.

It's simply as Iosif Lazaridis of Harvard Med ultimately says in that email reply to me above. It's what you would get if you account for the Western European Hunter-Gatherer-related ancestry in Early European Farmers or what looks to be the non-African ancestry in the Bedouin B samples often tossed around between various studies who are Bedouins from Negev.

Israel's South District, roughly coterminous with the Negev

Long story short; Farmers from West Asia migrated to Europe during the Neolithic and intermixed with the Hunter-Gatherer groups present there like what Lazaridis et al. 2013-2014 [1] dubs "Western European Hunter-Gatherers". 

These farmers as we've recently learned through observing some low coverage data on a Neolithic Anatolian Farmer; might have been carrying some Western European Hunter-Gatherer-related ancestry before entering Europe and then acquired more of such ancestry within Europe itself.

The rest of their ancestry was what Iosif Lazaridis refers to as "Near Eastern" or David Wesolowski who runs the Eurogenes genome blog and ancestry project refers to as either "Near Eastern" or "Early Neolithic Farmer". 

(Above are groups this component tends to peak in)

For the time being it's a shaky model for what certain parts of West Asia among other neighboring regions might have predominantly looked like in terms of Non-African ancestry. 

It's shaky because it's ultimately based around the non-African ancestry in Bedouin Bs who seem to lack Ancient North Eurasian / Mal'ta boy-related ancestry or the kind of Western European Hunter-Gatherer-related ancestry that appears in Early European Farmers. [note]

The component seems to carry an excess of the illusive Basal Eurasian component along with what in my humble opinion is probably ancestry related to groups like Western European Hunter-Gatherers but honestly; we'll need ancient DNA data from West Asia, North Africa & perhaps even East Africa to fully grasp "Early Neolithic Farmer" or "Near Eastern" as well as Basal Eurasian.

West Eurasia

For now any parties curious about this component should just understand it for being what is described above and as being a "West Eurasian" component seemingly native to West Asia that's been found in pre-historic groups like Early European Farmers and Pontic-Caspian Steppe pastoralists such as the Yamnaya. [2]

Its current modern spread is far and wide where it can be found in various distinct populations all over the world from Fulanis in the African Sahel to Tamils in the Indian subcontinent; signifying shared pre-historic ancestry presumably from West Asia or the general "Middle East" region between these numerous distinct Homo Sapien Sapien populations.

We'll know more someday and have a much keener understanding of pre-historic West Asia and neighboring regions once we have adequate ancient DNA samples from the region and other regions adjacent to it but for now; that's mostly all that needs grasping in respect to this component and what it is.

Reference List:

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

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