Not quite Egyptians?

So continuing my search for Native North African components, I use the Dogon as the West African pole. The Dogon are a people of Mali, living in the Sahel region not far from the southern "shore" of the Sahara. They speak the Dogon language, presumed but not universally accepted as, a Niger-Congo language. So they are likely related, perhaps central to, the West African Neolithic Revolution Core.
Any source for slaves carried by caravans to the North must have come from here.
For the first run I used 24 Dogon as the pole, all Masai and all Basques:

Fst:
"Dogon24" to Basque 168 (to "Yoruba24" previously 166)
Basque to Masai 97 (98 in "Yoruba24" run)
Masai to "Dogon24" 42 (to "Yoruba24" 35)
So results are very similar to the "Yoruba24" run using an otherwise identical set-up. Suggestive of great similarity of the Dogon and Yoruba, due to common West African Neolithic descent. Interestingly, "Dogon24" seems more distant to Masai and Basques than "Yoruba24".

Now using only 5 Dogon individuals:

Fst
"Dogon5" to Basque 179 (to "Yoruba5" 180)
Basque to Masai 113 (112 in "Yoruba5" run)
Masai to "Dogon5" 55 (to "Yoruba5" 53)
Results are somewhat similar as well. Dogon and Yoruba are interchangeable as poles. Reducing individual numbers in either pole leads to major changes in components. I don't think the "West-African" in North Africans is derived from West African Neolithic populations. It must be native to North Africa.

So how can more be found about it?
Previously I used population isolates, with little or no relation to populations analysed, as "childless" poles to "fish out" unknown components.
Now I'm going to be more straightforward. I'll use restricted poles, each comprised of only 5 individuals, from perhaps slightly more related populations, together with full-set ones just a bit more distant. Here are the poles used:
1) "Dogon5" Five random Dogon individuals - I named the component "Nortwest Africans". Dogon are West Africans, but I believe the restricted pole captured instead such a hidden component
2) All 150 or so Yoruba - "West African". Yoruba serve to "focus" the "Dogon5" pole into capturing the hidden element since the 150+ Yoruba will pull the actual West African I think.
3) "Sandawe5" similarly to "Dogon5" - named "Nile Core Component" or NC. I don't know what's the relation of Sandawe to possible Green Saharan populations, but it doesn't matter since it's intended as a pole for NC anyway. They seem to be just a Masai-like East African population, but I want them to pick something else here, since the much more numerous Masai pole is meant to pull the East African elementf
4) All 100+ Masai - named "East African". They serve the same function vs "Sandawe5" as Yoruba vs "Dogon5": focusing the lens into the desired independent component if it exists (some of the poles in previous blindly supervised runs got nothing)
5) All Basques plus all Lithuanians: named "Mesopotamian Core" or MPC. They are meant to be representative of Anatolian/Mesopotamian/Levantine Core expansion into the region.
6) All San-Namibia: to pick out Subsaharan African Forager elements.

I included some control pops and individuals. FRNA has French and North African ancestry. Tigrinya is ancestraly from Eritrea. Assyria1 and 2 are Assyrian Christians.
Results are very similar to previous blindly supervised runs with different set-ups.
Unsupervised runs tend to pick more composed components centred in Bedouin/Saudis and Mozabite/Tunisians instead, but with lots of MPC as well.
Bedouin and Palestinians may have high NC elements due to early spread of NE Green Saharan incipient pastoralists into the Arabian Peninsula. Pastoralist lifestyles seem to have been important in the evolution of the Green Saharan Neolithic cores from a much earlier stage compared to the MPC Neolithic perhaps giving them from an early stage more of a comparative advantage for marginal soils.
I suspect all four populations derive at least partially from the Green Sahara incipient Neolithic.
1) The Nile Core matured earlier and fused with Neolithic intruders from the North, and would later expand into the same region.
2) Native Northwest Africans lived in a Mediterranean climate but held the Fertile Crescent onslaught well and thus may not have been much behind. They fused with the MPC element and possibly then had a minor expansion into Iberia. I suspect from some recent runs that these are really a Western wing of the Northern Green Sahara pastoralists/incipient Neolithics. There may be an exotic forager element here too, early divergent but sufficiently distinct from the Pygmies and San (whose pole seems to have picked up Pygmy elements quite well). Both elements may be lumped together here.
3) West Africans were protected by a difficult tropical climate from Fertile Crescenters whose crops weren't adapted. They took a longer time to reach a Neolithic critical expansion point maybe for the same reason.
4) East Africans saw some small Fertile Crescent intrusion and admixture, but were also somewhat protected by envirnmental factors
These groups may also have unseen important Forager admixture. This would explain why Pygmies cluster so tightly in PCA and yet have a homogeneous large "West African" element.

FST
E African to W African 28
E African to NC 57
E African to NW African 50
W African to NW African 64
W African to NC 93
NW African to NC 81
E African to MPC 123
W African to MPC 187
NW African to MPC 150
NC to MPC 125
African F to MPC 280
African F to NC 179
African F to E African 116
African F to NW African 168
African F to W African 116 (same as for E African)

Fst is somewhat distorted by seeding individuals, but since they're only 5, it should have some vague validity. It's interesting NW Africans are seemingly both considerably less like the San/Pygmies and the MPC than E Africans.
Note that E African's fst values are being affected by the very many (100+) Masai who seeded the pole, and thus the smallish Northern element in the Masai is pushing fst closer to MPC and away from African F, so that it seems to be closer to MPC than the NC. The high number of individuals shouldn't be a problem for the Yoruba pole since it is more representative of the actual corresponding core population.
NC is considerably closer to MPC than W African, and fst is including some "East Asian" in the MPC pole populations used, as well as NC being based on the Sandawe pole. If corrected for genetic distance "Subsaharan African" contributions to Middle Easterners are not that dissimilar to those reported by various papers.

A thought: Why do Druze and Assyrians have less of this NC component? Is it because they have been more recently isolated due to their different culture and religion? Or have they from ancient times been more isolated from outside influences due to environmental (eg mountains) or cultural idiosyncrasies and thus have kept distinctive cultures/religions?

spreadsheet

Next I'll expand this into Europe and rest of ME to see if it holds together.

Sahara: Pump and Valve of Africa (and Eurasia)?

The title is provocative, but I just want to draw attention to Razib's comment on the new paper.
In addition I want to clarify I intend to go further on why there are so many discrepancies in the Masai vs Yoruba North African runs soon. This may be confusing to many, but I believe results are telling us something.
One reason is due to different pole sizes. I have very many Yoruba in my database (some 150) and in some runs I used only 5 in others 24 of them, creating quite different results versus the full set in supervised mode. ADMIXTURE stretches small poles a lot more than large ones, sometimes making them about something different from the pole individual's population.

This indicates there may have been a Northwest African aboriginal population quite distinct from modern West and East Africans, but related to them. This component even sometimes appears as if more distant from Eurasians than West Africans themselves...

Also high absorption levels in a Mediterranean climate environment IMO indicates some incipient level of Neolithic adaptation in this people before partial replacement by Mesopotamian/Anatolian/Levant and Northeast African Neolithics.

Searching for Native North Africans, Part II: EastAfrican-Americans

I'm short on time, so I'm only presenting for now the Masai restricted-pole results and some experiments with 53 African-American samples.

I used either the full set or just five individuals as poles in each run. I didn't use 24 vs 5 since I assure you for the following analysis the behaviour of poles comprising all individuals vs 24 is basically the same.

Fst: 164
This is the straightforward result against which all other runs should be compared. Yoruba are historically a good proxy for the West-African parent population of African-Americans. White-Utahns are obviously a near perfect proxy for the other ancestor population. There is also a little bit of Amerindian but I decided to ignore it since it's so small, and after realising in the Mexican run that small component poles can act quite strangely in such experimental set-ups.

Here's what happens when the Yoruba pole is reduced to just five individuals:

Fst:167
Not much change. Yoruba here are representative of West African ancestors and a valid full-set pole.

Now all Masai as the pole.

Fst: 108
Such discrepancies suggest what's already well known. The Masai are not good proxies for the parent population of African-Americans.

Using five Masai as the African pole:

Fst: 123

Genetic distance between components is now considerably closer to the actual one, and much of the divergence is due to unavoidable weighting in of the 5 Masai used. Admixture proportions are now basically the same. The pole was stretched and here it appears to be almost wholly dominated by the hidden West-African component.

In my previous "Chinese Mexican" experiment the "Chinese24" pole underestimated the actual admixture proportions and "Chinese5" grew correcting it. Here the larger Masai pole overestimates it, and "Masai5" shrinks to correct it.
Naturally this is easier with just two populations, since there's no extra-component to be "eaten-up".

Now back to North Africa
.
All Masai, all Yoruba and all Basque as 3 poles:

Fst:
"Masai" to "Yoruba": 38
"Masai" to "Basque": 117
"Yoruba" to "Basque": 163
(distances are slightly different to those of "Yoruba24" since I used all Yoruba here and Yoruba are a poor substitute in this case I believe)

Only 5 Masai as the "Masai5" pole, remaining poles full-set:

Fst:
"Masai" to "Yoruba": 82
"Masai" to "Basque": 99
"Yoruba" to "Basque": 182
Tunisians are similar to Northern Moroccans. These are the two large fertile areas and mostly agricultural; while other sampled populations live in regions with some fertile but other less fertile areas more suited to pastoralism.
Moroccan-Jews mostly lose their "Yoruba"-like component.
So Masai are likely not a good proxy for the component it's picking up here...
That's all I'll imply by now. Don't pay too close attention to fst since it's possible the pole's inadequacy made them eat up quite a bit of the other components. Masai have some Northern admixture making this more likely.

I don't have more time right now, so tomorrow I'll try to go further...
I should warn you I think in a very probability-based manner and all I need to jump is to feel a significantly higher probability in the validity of a trick/interpretation. I don't play the "wrong"/"certain" game. Good bets are valid even if sometimes "erroneous", because they can add up (as long as they don't bankrupt you). I won't tie my hands up for fear of being wrong.

I soon may have to review my early replacement from Egypt model for North Africa. Native Northwest Africans may also have had incipient Neolithic capabilities just as Northeast Africans... Maybe other Green Saharan melting pot populations shared them too. The Green Sahara may well have been an incipient Neolithic Eden. West Africans, East Africans, the Nile Core, and aboriginal Northwest Africans may all be the sons of another Neolithic Eve.

Also Dienekes comments on a new paper possibly relevant.

So take these experiments with a pinch of salt right now. It's only food for thought...

Searching for Native North Africans, Part I: Chinese Mexicans

Being a skeptic of the "Slave theory" of demographic change in established peasant populations at the Malthusian limit (that is excluding frontier situations with a land surplus like those in the New World) I've long suspected that West and East-African-like admixture in North Africans was really about a substrate (semi-)forager/pastoralist Western Green Saharan population and a Neolithic expansion from Egypt. Indeed I think the Tuareg may very well be at least a population with a large component corresponding to this ancient no longer extant in an unadmixed form group of people.

Seeking evidence about Native North Africans I've been thinking about ways to uncover evidence about them indirectly using some supervised mode tricks I've been developing.

First I ran a supervised analysis of Mexicans. I used historically appropriate pole populations: all my 12 Spaniard samples, all 24 Totonac representing Mesoamerican Amerindians, and 68 Yoruba representing the bit of West African present in this population. The Mexican samples were 58. I didn't use recent individual samples in any of the runs since results are highly experimental:

ADMIXTURE's own Fst estimates:
"Spanish" to "Yoruba": 164
"Spanish" to "Totonac24": 170
"Yoruba" to "Totonac24": 258
ADMIXTURE always mixes some bits of components up, it's a statistical tool, so it doesn't matter for this purpose if these are exactly correct or not.
Results are in line with other studies.

It also doesn't matter much how many Totonac samples are used as a pole, since these are close to the actual parent population(s). Here is the same run using only 5 Totonac:

"Spanish" to "Yoruba": 168
"Spanish" to "Totonac5": 182
"Yoruba" to "Totonac5": 255
Results and fst distances aren't very different. I actually believe these restricted pole results may be closer to the truth since the Amerindian pole is less dominated by the Totonac and more by the Mexican samples' actual Amerindian ancestors.

Now imagine Amerindians were no longer present as unadmixed populations to sample directly. We might know or discover however that this parent population of Mexicans was somewhat similar to the East Asians. So we might try to use say, Beijing-Chinese samples as the proxy for the actual parent population (I used only 24 BJG-Chinese just as Totonac):

"Spanish" to "Yoruba": 160
"Spanish" to "BJG-Chinese24": 117
"Yoruba" to "BJGChinese24": 210
So, genetic distances and admixture proportions change quite a bit, suggesting as known that BJG-Chinese are not the parent population. The pole was stretched by the 24 Chinese seeding it.

So what would happen by doing the same as in the Totonac runs, restricting the Chinese samples to five?

"Spanish" to "Yoruba": 181
"Spanish" to "BJG-Chinese5": 113
"Yoruba" to "BJGChinese5": 188
As sometimes happens with inadequate poles, the poles ate up some unrelated segments in this run. But results suddenly became more in line with the Totonac ones. The pole isn't as distorted with 5 as it is with 24 Chinese and it becomes more dominated by the Mexicans East Asian-like ancestors.

Note how genetic distances don't change much with Totonac24 vs Totonac5. They do change a lot with the restriction of the inadequate BJG-Chinese pole. ADMIXTURE is trying to tell us Mexicans aren't really descended from the Chinese.

Now applying these techniques to North African populations. I used all my Basque samples (24), 61 Masai and 24 Yoruba as poles:

Fst:
Basque to "Yoruba24": 166
Basque to Masai: 98
Masai to "Yoruba24": 35

With only five Yoruba as pole:

Fst
Basque to "Yoruba5": 180
Basque to Masai: 112
Masai to "Yoruba5": 53
There is change. The situation is a bit more like Mexicans with BJG-Chinese than with Totonac I think. Basque is now closer to "Yoruba5" just as Masai is more distant. This could be absorption due to the inadequate pole just as in the Chinese5 pole experiment.

So Yoruba are clearly somewhat related but I think also distinct from the Northwest African substract. Perhaps West Africans, East Africans and ancient North Africans are all populations born of a Green Sahara melting pot.
Tomorrow I'll run a control, and do the same using Niger-Congo-speaking Sahel populations. And the same for the Maasai pole. And then it gets even more complicated but hopefully revealing.

More Egyptian than the Egyptians themselves

Next I ran a supervised run of North Africans. The poles were:

1) Masai
2) Yoruba
3) Basque
4) Egyptian

The population with about 50/50% Basque-Egyptian are Moroccan Jews.

Again populations from more agriculturally productive regions (Tunisia and N Morocco) lack significant Subsaharan segments as expected. Desert regions tend to present them in a chunky way which I ascribe not to slavery but to recent movement of desert tribe members anciently less affected by Neolithic migrations (Tuareg and others) into the coast and cities.

It's noteworthy how Tunisians have all 100% affinity to Egyptians versus other pole populations. If affected by Subsaharan Caravan Slave trade, we would expect to see West African segments. As it is, segments apparently Subsaharan African in some other runs are all attracted to the Egyptian pole.
As for North Moroccans, much of the same applies, except that here some Northern influence is visible as well.
South Moroccan heterogeneity may be regional, due to fertile versus more desertic areas.
W Saharan's low homogeneous West-African-like elements may be aboriginal or otherwise ancient.

Together with my previous run, it appears to me that an Early Neolithic wave from the Nile spread West even as Egypt itself continued to receive Northeastern influences. This wave would maybe carry Berber languages. Later a second Nile wave would spread not only West but all over the Near East and Mediterranean.

Debunking Mozabites and Company - again

As a first step towards uncovering structure in Fertile Crescent populations, I have run a few unsupervised runs of the region's populations. In these you generally get Mozabite, Saudi or Bedouin, and Druze or Armenian modal components. Egypt generally comes out as a population combining all elements available in largish amounts. This could have two explanations. Either Egypt is where Mozabites, Saudis and Druze all arranged to have a party by the Nile, or Egypt is actually the Mother of them all (there's likely a Father as well) and ADMIXTURE is simply rendering different levels of parental admixture into distinct components. This would happen because Egypt itself has a dominant non-African component mixed with an important African one. Since this component doesn't exist unadmixed anymore, at K=2 with Yoruba and say Basques, you do get an African vs non-African division in the populations, but it's lost at higher Ks, suggesting Yoruba or Masai are not good proxies for it.
In a previous run, I found evidence of a native NorthEast African element in the region.

So I've decided to study North Africa alone for a start. I'll study the Saudi and Druze dominant components later.

Firstly unsupervised run of North Africans with Masai, Yoruba and Basques. I've removed a few problematic Masai and Tunisian individuals, who form their own component:

Notice how regions with especially fertile soils (Tunisia and North Morocco) have little "West African" whereas more desert areas have larger such components. Many such segments are confined to a few individuals, indicating admixture possibly with desert tribes such as Tuareg. I believe such West African segments are actually aboriginal western Green Sahara foragers and semiforagers, largely replaced by the Nile Wave.
Notice also how even in Morocco you get a lot of East African, just like in Egypt, even though southern populations are exclusively West African.

Genetic Distance estimates (Fst):
Nile 1st Wave to East African 84
Nile 1st Wave to Basque 51
Nile 1st Wave to West African 124
Basque to East African 127
Basque to West African 177
East African to West African 44


So what's happening here? The Nile component, higher in Tunisians and many Moroccans than in Egyptians themselves, has actually more affinity to East African than to geographically closer West Africans. It also may have a lot of Basque-like (Mesopotamian Core) admixture.

My point is: Mozabites and other North Africans plot in MDS distantly to Subsaharan Africans but much closer than their low affinity to West Africans would predict, as shown in this run. I think this is due to a Neolithic North Eastern African migration. In other words, for North Africa it's maybe more due to a more recent "Out of Egypt" than due to an ancient "Out of Africa" event.

Next I'll look into North Africans in supervised mode.

The Fertile Crescent variation: a model

Up to this point, I've been concentrating on "macroscopic" ADMIXTURE runs defining the affinity of populations in the Fertile Crescent zone, from Scandinavia to North Africa to West Asia.
I've presented runs proposing a two core Neolithic Replacement model, with a Northern "Mesopotamian" Core best preserved today in North Europeans; and a Northeast African Southern "Nile" Core today inexistent as the predominant component in any population, but important in North Africa, also in the Near East and to a lesser extent, in Southern Europe. These runs, as a bonus, also revealed a "Siberian"-like small component in peripheral and mountain populations, very suggestive of aboriginal DNA absorption.
I still think this model is a very coherent first approach to intra-Fertile Crescent variation. However as always, the picture becomes more complex as one digs further, in a more "microscopic" way.

So I'm restating my model in a more detailed manner. My confidence is not extremely high, but I think this is the simpler model to explain patterns.
1) The first Neolithic people in the World are born in the Mesopotamia/Levant/Anatolia around 10.000BC
2) Europe like all of Northern Eurasia (and the Americas) is inhabited by Siberian/Amerindian-akin foragers
3) Most of Africa is inhabited by San/Pygmy-akin foragers
4) Climate change leads to the Green Sahara, a savanna-like environment with very large lakes and river valleys, inhabited by peoples existing in a gradient of DNA variation, much as Siberians/Amerindians. To the west, these people are more West-African-like, to the East more East-African-like. In the Northeast and Nile valley a related people, similar but distinct to both modern West and East Africans, develops incipient Neolithic capabilities.
5) Mesopotamians reach a critical point in their Neolithic evolution. They then expand in all directions namely: Western Anatolia and Europe; Caucasus and Steppe river valleys; Iran plateau and India; and also Southwest Asia and into the Nile itself. Due to prolonged genetic and environmental contact with neighbouring peoples, replacement is incomplete, especially in the more developed Nile valley. Replacement is largely complete in Europe and the Northwest of the Subcontinent though.
6) Thus a western subset of the Mesopotamian/Anatolian/Levantine core expands into the Med and Atlantic regions; and up the Balkans into the fertile Central European river valleys. A Northeastern subset into the Caucasus and Steppe. And a related Eastern subset into Iran and India.
7) The Nile populations are absorbed by invading Southwestern subset Mesopotamian populations. This new hybrid population reaches a balance around 6000BC and then expands into the Green Sahara absorbing West and East-African-like foragers and semi-foragers in the process. Berber languages are born in the area.
8)The Sahara dries up and refugees with variable Neolithic capabilities flee to North Africa, the Sahel region, East Africa and back to the Nile valley.
9) All the environmental stress and ensuing selection of organizational and food producing strategies leads to the evolution of a more advanced Neolithic lifestyle in Egypt. Food surpluses become more abundant. A new more efficient critical point is reached and a new Neolithic wave is born, carrying Afro-Asiatic tongues. It expands from Egypt in all directions. Egyptian Civilization is born.
10) Afro-Asiatic speakers migrate into Mesopotamia itself, as well as Anatolia and all over the Mediterranean following the routes of earlier Anatolian migrations. Sumerian becomes extinct and is replaced by Akkadian.
10) At some point (first or second Nile wave) North Africans spill into Iberia, blending with majority Anatolian elements mostly into fertile coastal regions in the West and South of the peninsula.
12) The West and East Anatolian (Mesopotamian) waves clash in the Northern European plains. The resulting melting pot of seeds, ideas and genes is archaelogically known as the Corded Ware culture. A new Neolithic lifestyle adapted to cold and sandy soils is born, depending on Rye monoculture and other innovations. This people then expand into Scandinavia, British Isles, and to a smaller degree into Western France and Iberia, blending with Wheat-planting West Wave Basque-like peoples but bypassing the modern Basque country. Militarized elites bring the horse from the steppe simultaneously or following later. In the opposite direction, movements into Siberia, and directly from the Steppe into India begin.

Dienekes has new unsupervised results. Bear in mind that unsupervised mode fails to detect components corresponding to ancient but currently inexistent populations (such as ancient Northeast and Northwest Africans) and that it tends to represent admixed clines containing the majority component and such unrecognized minority components as a series of closely related spuriously independent components.
My above model is quite in accordance with his results. I will be exploring FC structure further with supervised runs.

"Rapid, global demographic expansions after the origins of agriculture"

Dienekes and Razib comment on a new paper.
"Who are we? Where do we come from?" -a Paradigm Shift shapes up

Unsupervised Northern Eurasia+new samples part 3

In this last part of the unsupervised run I'll present results of New World populations and participants, and some South Asians I introduced into the run without South Asian populations (to avoid the artificial Irula modal component).




Mexico1 and Mexico2 are demonstrative of the high variability still found in Mexicans, a young population in terms of ethnogenesis from mostly Spaniards and Neolithic Amerindians, with a little West African as well. Unlike ancient admixture events in the Old World which are mostly stabilized with little variation between components in different individuals. Same can be said of Dominican Republic samples (Hispaniola1 and 2) even though here the West African component is larger and the Amerindian smaller. EUDR has major ancestry directly from Europe. You can also see likely continuing admixture in populations with exclusively aboriginal self-identification.

GeUSA has half German ancestry. Some of the USAs are mostly colonial but colonialUSA1 will remain the only one with such a tag since its hard to find Americans without either some colonial or non-colonial ancestry. USA6 is African-American, another very young New World population drawing from diverse Neolithic Core Areas, still with very different admixture levels between individuals.
Afrikaner1 is a White South African sample of Afrikaner ancestry. The Cape has a Mediterranean climate little suited for Bantu crops, but ideal for Fertile Crescent ones. This may explain why Dutch farmers managed to settle and flourish in the forager/pastoralist (San and Khoikhoi)) inhabited area unlike Europeans in other regions of Africa, who had few food producing advantages and local disease resistance over the West African Neolithics.

As for the South Asian samples. I welcome samples from the area, was a little surprised to get 3 Tamil Brahmins. SIndia1 is mostly Tamil from Sri Lanka. UKIND is British with some Indian ancestry.
Interestingly the Fertile Crescent element in the Tamil samples isn't very different here.
The remaining components I tend to believe are artificial. Ancient South Indians (ASI) were likely a Coastal Migration derived population. Yet Papuans are separated by seas, thousands of kilometres and tens of thousands of years and the genetic affinity may not be close enough, so this ASI component is IMO being split artificially between the remaining poles. This shouldn't be considered evidence of admixture with the pole modal populations though. It possibly simply means that ASI is somewhat distantly intermediate between them. I'll look closer to South Asian populations later.
But before I want to search for finer structure in the Fertile Crescent Cores.

Here's the spreadsheet. Don't take small components literally, especially in an unsupervised run. They may be real, but also noise or may be replacing something different not represented in the other 6 components.

Unsupervised Northern Eurasia+new samples part 2

This is part 2 of the unsupervised North Eurasian Run. Just as any unsupervised run including such diverse populations, you can expect a lot of noise, especially when evaluating single individuals versus large n populations.
So don't see meaning in every single small component you may find in one or two individuals. It is most likely just noise. Still you can see some patterns, and I'd like to call attention to the dark blue (peaks in Amerindians) and pink (Nganasan) elements. This is an unsupervised run, all I did was decide on the populations and individuals to be analysed and how many components I wanted to ADMIXTURE to figure out. In an unsupervised run I can't tell ADMIXTURE "find this versus that" as in supervised. It finds what it does on its own. And yet results are globally pretty similar to these.




FRNA has French and North African ancestry.
FRMA French and Madagascar/South Asian
Tigrinya is from Eritrea.

Some considerations
Unsupervised mode in my opinion tends to overestimate/make up smaller components which is why I don't like it much. It clusters segments without an historically informed departing point and tends to amalgamate more exotic variation with some of the dominant component. It is also more chunky and less reliable IMO than some of my blindly supervised results.
Green in Med populations I think corresponds to the Nile Core Element (ancient Northeast African, which doesn't exist "unadmixed" anymore) which is likely intermediate between the Mesopotamian Core and very anciently related also to West and East African maybe through the Green Sahara of thousands of years ago. In the Tigrinya sample the Yoruba modal component is likewise drawing on East not West African elements.
Red and light blue elements in more Eastern populations are likely representative of assimilated Coastal Migration elements. In Europeans they are most likely noise, even though at least in some Romanians they might indicate Roma admixture.
Yellow segments could be interpreted as Central Asian elements but their unevenness and presence in unlikely places (Spain) may mean its just noise.

My point in presenting this unsupervised run is to prove ADMIXTURE does find what can be interpreted as both Fertile Crescent replacement and Amerindian-like residual segments in Northern Europe and the Caucasus on its own at the adequate K.
One very interesting new indication of the new samples is the near complete absence of Siberian/Amerindian-like segments in Germany. Germany was an entry point for early Neolithic colonization of much of Northern Europe, the Danubian Wing of the 1st Wave up the Balkans, Danube and Rhein valleys from Western Anatolia -other sources were likely the Med-Atlantic Wave via Iberia and British Isles also from Western Anatolia and the Wave from Eastern Anatolia via the Caucasus and the Ukranian/South Russian river valleys.
This region has (in West/South Germany) excedingly fertile river valleys, congenial to wheat/barley agriculture. Residual forager elements are expected to reach a nadir here. And the results speak for themselves.

Tomorrow I'll present New World data, and also the results of a few South Asian samples I threw in the analysis without my South Asian populations to keep them company. Their results are a bit artificial I think, but still revealing.