Friday, 29 April 2011

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.

Thursday, 28 April 2011

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...

Wednesday, 27 April 2011

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.

Saturday, 23 April 2011

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.

Thursday, 21 April 2011

Wednesday, 20 April 2011

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.

Tuesday, 19 April 2011

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.

Sunday, 17 April 2011

Unsupervised Northern Eurasia+new samples part 1

I've rerun my previous unsupervised analysis of Northern Eurasia at K=7 with the new data. First part is about East Asia. I have a new Korean sample and two Philippine ones both from the Visayas.
Results are basically identical, I'm only providing the new ones and a few reference populations. The colours are different and the bars have components in different positions.

The spreadsheet will follow at the end of both parts.


Korea1 is from Southeast South Korea.
Both Philippines samples are from the Visayas.
Philippines2 has some known minor Spanish ancestry.

The purple component peaks in Fertile Crescent populations. Red in Papuans. Pink in Siberians and dark blue in Amerindians. I believe as I said previously that yellow and light blue are somehow related to the two cores of the Chinese Neolithic (Yellow and Yangtze Rivers), a "Siberian" related expansion, explaining the presence of these elements in the populations analysed.

Part II of the same run will present the new data for the West.
Yesterday's spreadsheet.

Saturday, 16 April 2011

First Results

I've done a supervised run on some of the samples I've been receiving. The set up was identical to a previous one, with three poles, Amerindian (unadmixed Totonac+Surui+Karitiana); Siberian (Unadmixed Nganasan); and Fertile Crescent (Egyptians). Results are basically identical, so I'm only publishing the new data:


I've named individuals with ancestry from one region of a country with a regional tag (N North, C Central, NW Nortwest etc). Individuals with mixed ancestry from a single country were given IDs with that country's name.
Some ancestry info:
CAsia is from Central Asia
Russian1 comes from North/Central Russia, Urals.
SEFI is a Swedish-speaking Finn
SwedenNorway has about 50/50 ancestry from either country
UKDK likewise UK and Denmark
CEuro has mostly German with some Polish and Ukrainian
SWFrance1 and CPortugal1 come from mountainous regions of their countries
PonticCaspian is mostly Gagauz with some North Ossetian
USA2 has major Amerindian ancestry
FRCA1 is French Canadian with colonial ancestry and also Faroe Islander
Brazil1 is a White Brazilian of colonial ancestry. No known recent Amerindian ancestors.

Considerations.
For some reason, just as in previous runs, if Fertile Crescent-like segments are pulled away by a suitable pole, Europeans with ancestry from the North or from mountainous regions have a small but detectable amount of DNA segments clustering with those of Amerindians. Other segments cluster with those of nearby Siberians. Samples from more Central/Southern or presumably fertile regions show such segments to a much smaller degree, being almost completely attracted to the Fertile Crescent pole.
I'm sorry for anyone not included this time, I didn't want to include too many recently mixed samples and also couldn't include individuals with major ancestry not covered by the poles. I'll run a more inclusive analysis soon.

Still accepting all non-recently admixed samples from the same country, even non-European ones. I have two Philippine samples already and would welcome more East, Southeast Asian ones.
I'm now considering more mixed samples as well as long as ancestry is well defined.

Tuesday, 12 April 2011

Narrowing the Submission Window

I have received a number of samples already in the last few days. Please don't send the files attached straightaway, only ancestral information you feel comfortable sharing.

Everyone who already received a reply will have their samples analyzed in a repeat of a few experiments I've done here previously, to be published probably during the weekend.

I can't accept any more recently mixed samples from multiple origins right now, but promise a new opportunity later.

I'm narrowing the window, since I want to retry the approach with first just a few extra dozen samples of known ancestry. I'm only accepting for now:
1. Samples with 3 or 4 grandparents ancestrally from a single country/region.
2. Samples with two clear ancestral origins if one of them is unusual and absent from my current populations. For instance someone with an Indonesian grandparent but 3 European ones would be eligible.
3. Any sample with likely more than 5% Amerindian admixture may also be acceptable, case by case.

I won't include any samples submitted from now on, even if eligible, in my first runs. I'll repeat the runs later with the newer samples.

Regards

Sunday, 10 April 2011

Face to face with Europe's First Peoples?

In 1884, Roland Bonaparte, a French member of the Society of Geography, made a trip to Northern Scandinavia, a frigid area unsuited to any kind of agriculture. There lived the Sami, a Reindeer-herder people who likely inhabited a much greater area of the peninsula until Medieval times.
He had an Anthropological interest, and said some sensible things together with lots of nonsense like many contemporaries. Here are the photos he took, some using newly developed colour photography techniques (the colours are real) of contemporary Sami peoples still mostly with thousand-year old lifestyles in the late 19th century.
There's also this photo (it's 130 years old and obviously in the Public Domain, but I'll link it instead of "using" it).

Today Sami look more often like this, or this.

Let's assume the Neolithic Replacement hypothesis holds, and that the Sami might be Europe's last Native Peoples. They are the genuine descendants of the Cro-Magnon, related to the authors of these and these works of Art, admired by Picasso himself, who said "after Altamira, all is decadence" (thinking his own ancestors had painted them, but certainly truthfully). They had perhaps the most effective contemporary stone tools in the World. Some of them maybe invented a new lifestyle away from land during the last Ice Age, living in the Ice floats of the Atlantic hunting seals, whales and fishing. They possibly made it to the empty American Continents with only Stone Age technology. Today, in Europe, they're maybe reduced to the Sami (admixed in varying degrees with Scandinavian and Finnish Fertile Crescenters) and a few percent in some populations' genome, their probable former diversity largely lost for ever. Such is the power of a Neolithic Revolution.

Call for Samples

ADMIXTURE's quite sensitive to the variability present in its sample data in order to be more precise about relationships. Representative samples from certain regions would definitely improve the resolution, particularly for smaller components.

Thus I'm asking for 23andme genotype files. Complete anonymity is guaranteed. No health information will be collected from samples, only ancestral info. I will identify each individual only by a tag with country of birth of grandparents and if provided regional origin as well. I do think ADMIXTURE's powerful enough for at least some regional resolution. So if a participant only wants to declare country of birth of his/hers 4 grandparents, that's enough but if you could provide regional origin as well (ie Cornwall, Munster, Bavaria) it would be much more useful.
I'm very interested in samples from Europe, like Ireland (particularly the Western part), UK (all, but more Cornwall, Wales, Scotland Highlands), Finland, Scandinavia (especially Norway), Iceland, Switzerland, Austria (especially Tirol), Slovakia, Carpathians in general (regions of Romania, Poland, etc), Germany, Ukraine, Iberia and France (especially Alps, Massif Central, Pyrenees) with regional identification. Plus people from the Americas with significant known Amerindian ancestry (tribe or regional-tagged please). Also any mountain or island region in the world not represented in my current sample. I know I'm naming several regions with few participants in other projects. So I'm not even mentioning Madagascar, Sami, Indonesia, or Australian samples with known or possible aboriginal origin.
Since I'm anticipating a slow start, I'll probably accept any sample that is tagged with certain regional origin of each grandparent. I'll be making an announcement at 23andme tomorrow (I'm Diogenes412 over there).

So what do I offer? ADMIXTURE analysis in possible Neolithic/Forager element runs I've been publishing. In the future I may be doing more regional and historically more recent stuff as well, if possible.

You can email me at artemisproject.diogenes@gmail.com (or through the blog's email).

Regards

Saturday, 9 April 2011

Native Americans, Native Europeans, Native Siberians

Trying to confirm previous runs showing "Amerindian" in North/West Europeans and in the Caucasus, I ran a more conventional supervised analysis. I set up the following poles:
1. Egyptians once again representing the Fertile Crescent.
2. Nganasans, comprising the 5 less admixed individuals, but keeping the rest in the analysis (but out of the pole)
3. Totonac+Surui+Karitiana: I included 3 especially recently unadmixed populations. Amerindians suffered from severe founding effects. The analysis is not too different using only one of them as the pole, but it's more chunky since some original diversity is lost if only one group is considered..

Results:


Caucasus sample
North European sample



Lets assume the Solutrean Hypothesis is correct, as suggested by ADMIXTURE's results (except the Solutreans can't be properly called the ancestors of modern Europeans).
It's somewhat strange that Amerindians fall 100% in their own pole, since I suspect they also received significant gene flow from Siberians proper (Y and mit haplogroups seem to indicate such a scenario). However those severe founding effects during the Atlantic crossing by the Ice Cap led to a highly distinctive population reaching the other side. It is indeed likely that Northern Europeans and Caucasus valley populations harbour gene variants present in the original "Western Siberian" or Cro-Magnon populations and which were lost due to drift in the Atlantic crossing by the ice cap. Thus ADMIXTURE tend to assume the Amerindians are the "unadmixed" population (similar to what it did to Sardinians in unsupervised mode). This may be why the Amerindian modal component can be found in strange places in Eurasia, since that may really be about Eastern Siberian less common variants that also suffered from drift during the crossing into America via Beringia.
So I suspect Amerindians may really be the admixed population, whose parent populations are the West "Siberians"/Solutreans/Native Europeans going by the Atlantic ice cap and on the other hand East or proper Siberians entering through Beringia. Both populations having undergone drift, but especially the ones coming from Europe, and producing an "offspring" population that can be related to ADMIXTURE to both groups but, being so distinctive, is assumed to be the "parent".
This may be why the "Amerindian" component is quite chunky when analysed with the Amerindian proper populations, and quite uniform and more widespread when analysed without them, with a "blind pole" instead fishing them out independently. In addition, maybe Spaniards and Basques don't present so much "Forager A" component in Amerindian containing runs due to founding effects in Northern Europe, when Solutrians expanded there from their Iberian refugium at the end of the Ice Age >10.000 years ago. So Northern Europeans would share the first founding effects with Amerindians, unlike Iberian Solutrians and those distinctive signatures make those segments easier to spot in an analysis including Amerindians?
Still affinities of "Forager A" segments in Europeans and those in Amerindians are sufficiently clear for them to be grouped together every run, more or less chunkily.
Spreadsheet
Yesterday's blind analysis spreadsheet.

Thursday, 7 April 2011

West "Siberians" and East "Siberians"

This is what I'm henceforth calling a (partially) Blindly Supervised Analysis, of Europeans and Caucasians versus the "Siberian Belt" peoples (excluding the East Asians).
The set-up was very simple. I set up the following poles on the populations presented (no other populations were included in the run).

1. Egyptians as the Fertile Crescent Pole. This was not blind, but ADMIXTURE did pick up the Fertile Crescent element blindly before. Egyptians have both much "Mesopotamian" and "Nile Core" elements, and I would find it very odd if they had any "Forager A" indeed (unlike the Druze who may have residual segments since they have so much mtDNA X), so they're a good choice. Naturally "Egyptian-ness" in this setting means only Fertile Crescent (Western Eurasian) affinity.
2. San-NB (Namibian Sans): blind pole - will not correspond to the actual component found, but instead used to "fish out" an unknown component. Obviously none of these populations are specially related to the San.
3. Mbuti Pygmy: another blind pole
4. !kung: blind pole
5. Hadza: blind pole
6. Yoruba: I included it because Mexicans have a small but significant chunk of West African ancestry. I don't expect much from Yoruba pole in Fertile Crescenters since there's Egyptian

Results:

So:
1. San is about possible West "Siberian"/Amerindian/European Aboriginal components
2. Mbuti Pygmy didn't pick up much
3. !kung: I think this picked up specially "concentrated" "Nile Core" segments
4. Hadza is Eastern "Siberian" or Siberian proper and is prevalent in actual Siberians
5. Egyptian is really the Fertile Crescent Neolithic components
6. Yoruba is picking West African segments in Mexicans, and maybe also some "Nile Core" segments also found in Yorubas but maybe less frequently in Egyptians (not all the Egyptian, especially ancient, variability is represented in the individuals used as the pole)

Percentages are a bit different from other runs since all runs depend on the individuals actually present in the data. But there's a tight correlation. All the data I fed ADMIXTURE is the populations represented in the graph plus pole populations.

I did not remove admixed individuals, which should make this outcome less likely not more. I'm coming to the conclusion there is no way I can run ADMIXTURE with Europeans and Caucasians and Amerindians without some "Amerindian" appearing in both. With the Cypriots and Druze as FC pole it's more chunky but it's there. With Egyptians it's more even. In some runs Basques and Spaniards have much of it, in others less so. But Northern Europeans always have it as expected in a Neolithic (near) total replacement model, since they're the periphery of the expansion.
Chuvashes, Russians and Turks always come with "regular Siberian" admixture in all runs. I don't know how else to explain these results. Supervised, unsupervised, they're there. ADMIXTURE may not be that sensitive with small components. But I can't imagine why it would make "noise" consistently in the very same direction. "Noise" by definition is non discriminating. I think the Solutrean Hypothesis deserves greater consideration.

Amerindians almost certainly did cross Beringia. But just maybe, they were going the "wrong" way...

Unsupervised North Eurasia Run Part II: Big Brother?

These are the remaining populations from yesterday's unsupervised Euro/Caucasus/Siberia/Amerindian/East Asian run.

East Asians all cluster very close to both Siberians and Amerindians in World-wide PCA. I'm growing to believe that the Chinese Yellow River/Yangtze River Millet/Rice Neolithic Revolution is about an expansion of Siberian-like peoples independently adopting Agriculture. This would again happen elsewhere once or twice (according to whether Mesoamerican and Peruvian agriculture are truly independent of one another or not) in the Americas.
But the most successful "Siberian"-derived Neolithic is definitely the East Asian one. Expanding not only across East Asia, but also into the Pacific (from Taiwan, ultimately from China's Yangtze valley?) and marginally into India and it's Ocean up to uninhabited Madagascar (before the Bantu could get there with their better adapted Tropical crops, mix with them at around 50/50, while less admixed people remained in the Highlands).
In this unsupervised run there appear to be two main components, one centred in the North, peaking in the Japanese and another in the South, peaking in the Iban. Singapore Chinese and Chinese Americans are mostly from South/Southwest China itself.
These may correspond to two Core Populations, and I think a model similar to the Fertile Crescent one is likely, with an earlier maturation of Millet-based agriculture in a previously Siberian-like forager population living in the Yellow River area and it's expansion South to the Yangtze River but not much further due to mis-adaptation of Millet to warmer/wetter climates. Another wave perhaps from the Yangtze River valley with Rice, a much more productive cereal, into Southeast Asia and Taiwan (and from there onwards), and also expanding into the North and into Japan. As in the Fertile Crescent, this second wave would face higher drag, and absorb more and more First wave elements as it travelled, explaining perhaps low "Second wave" in the Japanese (which may have only successfully settled Japan from Korea after getting Rice). I think I can perhaps see a third reexpansion of the Northern Core, maybe related to the early adoption of Fertile Crescent-derived Wheat?
Another point is why didn't the Chinese occupy Siberian lands before the Russians did so? Again I think the answer may lie with Rye, a much better cereal for the Eastern Siberian climate and soil types. And probably also the development/adoption of Pastoralist lifestyles in marginal lands.
I'll review the model with a supervised analysis later, since these unsupervised modal populations might be artificial (though relationships should hold).

Some minor elements of note:
1. There is a Papuan-like "Coastal Migration" element in Japanese I think might correspond to the aboriginal Japanese (Ainu and related populations to the South), which may have also Siberian admixture?
2. You can see Amerindian-like very tiny elements in some Southeast Asians. I think since the Chinese Neolithic was probably a "Siberian" development, these may have been carried south by the Neolithic waves since I don't think they'd be aboriginal. Indeed this element together with more conventional Nganasan-modal green one, can be found to some extent in all East Asians, up to the Chukchi living in the Bering Straight.
3. There is a small Fertile Crescent element in Thais, Khmer and other Southeast Asians. I've seen it repeatedly under different conditions and set-ups. There is a large Fertile Crescent element in all Indians, and I've seen it eslewhere in an ADMIXTURE run including East Bengalis. Maybe Burmans have it as well and it extends here. It may have arrived before the Northeastern Waves, since it is a minority component. Interestingly, it is quite larger than the Papuan-derived "Coastal Migration" component. I suspect low adaptability to wet and hot conditions of Fertile Crescent crops meant it could not penetrate most ecosystems of the region thoroughly. Yet it seems it was latter easily swamped out by the Chinese probably Yangtze River-derived wave. Yet this did not happen in India, or in the Melanesians, Papuans, despite long contact with the East Asian Neolithic. Papuans have contemporary documented independent Agriculture in the highlands of New Guinea. South Indians don't, yet the genetic result of high "Papuan" containing Tongans and Samoans and South Indians appears similar...

Still, these results are preliminary ones, I'll do a supervised run later on...

The "Siberian Belt": unsupervised run

Trying to find clues to the origin of "Forager A", the non-Fertile Crescent element in Europeans and Caucasians, I decided to run an unsupervised analysis of all Northern Eurasian populations. I don't have much faith in components from unsupervised mode actually corresponding to closely related ancestral populations just because ADMIXTURE decided on it's own it's so. Still unsupervised runs are great to get a picture of relationships.
I also included the San, since I wanted to see if they were actually related to "Forager A", Hadza, Mbuti Pygmy, !kung, and Papuans, Melanesians. And why not, also the East Asian populations because of the proposed Altai language family and it's tenuously possible links to Korean and Japanese. And since I was at it, I also threw in those often forgotten populations of the "Siberian" belt, Amerindians.

Remember this is an unsupervised run. Some noise <1% is expected, but I think >1% consistent components across similar populations are significant. I won't immediately name the components ADMIXTURE came up with. Also, these are kind of chunky, particularly for smaller components, so this is just a simple experiment I wanted to share, to get hints about what "Forager A" might actually be, and also for my future East Asian Neolithic run.

These were included to clear any doubts of "San" relatedness of Euro aborigines.
"Forager A" is definitely a Siberian-like population, only aboriginal to Europe, and mostly replaced by the Fertile Crescent expansion I think.
I don't think this means that "Forager A" is about Amerindian women or slaves brought to Europe a few centuries ago by the way... At least it's hard to explain how they would get to Dagestan.
I think "Forager A" is likely "Siberian"-like. As for closer affinities among "Siberians" it could be drift/founding effects making more distantly related populations seem closer? Seems unlikely and there are other theories considered unlikely as well...
"Yoruba" in Druze and others is I think attracting a bit of the Nile Core Component (Northeast African) by the way, since these could be distantly related via the Green Sahara.

This is an unsupervised run though. It is quite chunky. These are small elements.
For now, I'll just say that "Forager A", if thats what unsupervised ADMIXTURE is picking up, looks interesting indeed.
I'll also be doing a supervised, hopefully more homogeneous run.

I also ran East Asian populations in the same run, I'll present them in the next post tomorrow.

Tuesday, 5 April 2011

Adam and Eve

Sadly I don't have Iraqi people's genotypes to analyse with ADMIXTURE, still I expect a pretty boring "Mesopotamian Core" + a lot of "Nile Core" admixture. Sumerians and Akkadians? Certainly much more complex than that, still an attractive thought.
What follows is a highly speculative simplified narrative for the benefit of readers not familiar with some of these theories, which have been advanced before by others. Some could turn out correct, others wrong, but in general I think there is something in it. Something prevented the vast majority of Forager groups from developing this lifestyle, that once properly matured, allowed for demographic change in a scale (only recently completed with the settlement of Australia 200 years ago), such as Mankind may not have known ever since "Out-of-Africa some 50-100.000 years before.

Many people have advanced theories on the origins of agriculture. It's a very hard life, and it now seems it only pays back initially as a form of insurance, since grains can be stored, and planting planned, unlike meat, fish and gathered fruits.
It looks like before 10.000 years B.C Mesopotamia was much longer than today, extending to the very mouth of the Persian Gulf, almost all the way to India. It was likely an extremely rich environment for hunter-gatherers, with marches full of game, and several large grain grasses covering large areas, allowing for high densities of settled foragers, unlike most of the World. However the very unstable climatic situation at the end of the Ice Age must have meant that this rich environment was under constant change with maybe devastating floods and dry periods alternating: ideal circumstances for the birth of future planning, namely the planting of wild seeds in the empty soil after the calamities. Women largely gathered the plant-derived food, and men hunted and fished, just as in current forager groups. So Eve ate the fruits of Knowledge, of future planning and worrying, of continuous, high levels of cooperation between non directly related people, and doomed all of her children to a life of increasing control over destiny, but also slavery to the soil, rather than direct daily dependency on Nature's bounty.
After the Flood of this original Eden
Mesopotamians were put in even greater stress, and likely life as we know it began.

Something similar may have happened in the Green Sahara. A vastly rich environment full of game and rivers and large lakes, the Saharan desert probably allowed for high densities of hunter-gatherers in some areas, such as the Nile River. Then desertification started, beginning with the Eastern Desert, people cramming into an already full Nile valley. Similar pressures had similar results, and probably in mutual influence from an already expanding Mesopotamia, the Nile Core was born.

Turkey, a major centre in the maturation of the Mesopotamian Core, was in a previous post.
One Jordanian has obvious recent East African admixture, also to a lesser extent a Palestinian.
Areas with higher Nile Core occur in all countries, maybe in more fertile areas, maybe closer to the coast, further South, or all three combined. Some Mongol/Turkic influence can be seen in Syrians, even though far less than in Turks. "Coastal Migration" elements are either ancient Roma-like admixture or, less likely, a very old aboriginal signature.
Druze are an "Island-like" population with little outside influence. Their isolation (they live in mountainous areas) may have determined their smaller Nile Core element and their peculiar religion and culture, rather than the reverse.
Many Saudis, most Bedouins, and some Yemenis live or have until recently lived as pastoralist nomads. Unlike settled agricultural peoples, nomads receive a lot more admixture from elites and slaves. It's hard to draw consistent rent from pastoralist groups, and slaves are generally much better treated and have more social mobility in such societies. It's interesting to note the Mongol-like small element in these populations. The widespread but residual "Coastal Migration" element in Yemenis could very well be IMO aboriginal.
Differences in Mesopotamian Core and Masai-like ("Nilo-Saharan?") elements in Egyptians may betray a Southern versus Nile Delta origin. There is an obvious cline among Ethiopians, with larger "Mesopotamian Core" segments correlating with large "Nile Core" ones suggesting an Egyptian wave southwards after admixture with Mesopotamians. However larger percentual Nile Core versus Mesopotamian in Ethiopians versus Egyptians may imply a presence of the Nile Core there before this wave. This is also observable in North Africans, and may correspond to another earlier Egyptian wave, affecting only North Africa and East Africa, before large scale admixture with the Mesopotamian element in Egypt itself. Or maybe related Sahara desertification refugees?
Three Lybians have recent East African-like admixture. This may be happening in individuals with Nomadic ancestry, but may be typical of local desert groups such as the Tuareg. Tunisians are quite homogeneous as expected for an especially densely settled and fertile area in the region.
I'm not presenting graphs of the other North Africans as they're very similar, except for South Moroccans, who seem to have a very balanced "West African" pole-attracted element I think is native. Algerians have some similar unbalanced elements I think are about admixture with desert tribes.
North Moroccans are similar to Tunisians, without desert nomad elements, as the fertility of the region would predict.

Here is the spreadsheet:
Included is the Fst distance estimate by ADMIXTURE. Please note that even though some of these are accurate ("Nilo-Saharan?" vs "West African"), some like "Forager A" are not, since together with all Forager A fragments ADMIXTURE weights in all the more numerous San individuals inside the pole into the component. I actually now think Forager A is a more Siberian than a San like population, I'll present data soon. ADMIXTURE probably picked them up into "San" because it's clearly not Nganasan, further still from other Siberian poles, and the San pole was "childless", while the Nganasan pole had chunks of Chuvash, Russians and others to play with. More on that later.
spreadsheet

Caucasians and Iranians

The Caucasus range and whereabouts is another region where the "Forager A" (picked up by the San pole) element is concentrated. After a few more interesting populations at the individual level, I will present some runs trying to find out more about this, but for now I can say already that it's probably even less related to actual San than ancient Mesopotamians were related to the Chukchi. Foragers groups very likely existed in a genetic continuum worldwide, with few exceptions.

It's noteworthy once again how "Forager A" (and also ("Coastal Migration") disappears in high "Nile Core" areas, especially in populations south of the main Caucasian range, like Georgians. Also Georgian Jews lack it entirely.
In populations North of the highest peaks of the Caucasus, like the Adygei, which were likely spared the full force of the Nile wave by geography, these components are more frequent. This area is where Coastal Migration foragers begin to disappear and "Siberian"-like elements become more frequent. It may have been the route for earlier dispersal of the "Siberian" belt of forager peoples around the World.

Lezgins are an ethnic group from Dagestan and Azerbaijan. Urkarah and Stalskoe are Mountain valley Caucasian towns in Dagestan.
Just as in the West Caucasus, you can see some Siberian/Central Asian Nomadic influence as Turkic and Mongol and other pastoralists made their way into the Middle East.

Armenian-b show all the signs of being mountain people. They have more forager and less second wave components.
Kurds and Iranians now have "Coastal Migration" (attracted to the Papuan+Melanesian pole) as their aboriginal element. In India this component then increases to levels I don't think would exist without an indigenous incipient Neolithic.
You can also see how the "Nile Core" element starts decreasing in Iran. Just as in the West, the high drag of a wave travelling over already Neolithic lands can be observed here.

Monday, 4 April 2011

A New World

Assuming the model and run are valid, Europe is where the Northwestern Nile Core wave finally runs out of steam. Perhaps coming out of Turkey through the Balkans, and through the Mediterranean village to village links established by their predecessors, it finally dilutes itself so much into the established Mesopotamian Core element that it ceases to be detectable, at least by this method. I suspect "Nile-Core acculturated" Mesopotamians from Southern Europe continued to carry some of the innovations well into Northern Europe, but this is harder to detect in autossomes due to higher similarity between the incomers and the settled. Dominant groups tend to spread Y-DNA far further than autossomes though.
Radiating from the Southeastern Corner of the Mediterranean, this people may have an even greater influence in Y-DNA explaining a large part of the current distribution haplogroups E1b1b and J1c3 and perhaps others, some of which may now be more frequent out of Egypt due to founding effects. Also maybe the tiny percentage of L mt-DNA in Europe.
Speculating, the Spaniard with the high Nile Core element may come from the coast, maybe the Mediterranean Coast of Spain. The Italian with low Nile element maybe from an Alpine valley?
I don't know what the Pygmy pole is picking up in Europe but it's definitely not Pygmy. I think it's probably nothing much, but I named it "Forager B?" rather than naming it "noise".
Hunter-gatherer tribes in Europe were likely much closer to each other than in Africa, even though much more different over the same distances than a Neolithic Core component. Siberians don't easily get their own ethnic component in ADMIXTURE runs as San and Pygmies do. Still don't know if "Pygmy" (Forager B?) and Hadza represent anything at all, most likely not.
Basques have no or only a small "Nile Core" element. They lack many of the more colourful elements found in residual amounts in both Spaniards and the French. In general a good question is are groups with different languages/cultures/religions from their related neighbours more isolated because of said language/culture/religion, or do they have less subsequent outside influence and different cultural paths because they were isolated for other reasons (like geography) from the start? This could also explain why the Druze and others have relatively less of a "second wave" element.
I suspect not many Southern, Mediterranean French were genotyped into this set, maybe there's one?
Cypriots are quite homogeneous, lacking extra elements to the Neolithic ones, as expected in an island population close to the source-areas.
Askhenazi Jews have residual "Siberian" elements, bringing Khazars to mind, but probably mostly due to their Eastern European origins.
Romanians have much "Evenki+Yakut" maybe due to their proximity to the steppe. Some of these individuals appear to have significant levels of Roma admixture.
Sardinians are a very homogeneous population, with no extra-Neolithic elements, and can serve as a "template" for other Southern Europeans. No wonder ADMIXTURE often considers them an "unadmixed" population.
Hungarian tribes were more Nganasan-like than Evenki-Yakut-like, coming from Western Siberia, and you can see this here.
Don't know why Orcadians have visible Nganasan here.
Utah whites likely consist of New England-derived settlers of mostly British but with also significant German, Dutch, Irish ancestry. The larger Nganasan segments (larger than in Orcadians, and I suspect, even larger than mainland Britons, you see in several may indicate residual Native American ancestry? I don't know why ADMIXTURE would choose Nganasan to pick up Amerindian segments. Drift making them randomly slightly more like them than Evenki? Chukchi was already taken as the Mesopotamian pole, since it doesn't exist in ME/Europeans (I think something similar may have happened to "San" and others. Maybe Evenki+Yakut was "stretched" too much towards Mongolian/East Asian groups.
"Siberian" elements in Finns, Balts and Russians are I think most likely aboriginal.
These I think are Northern Russians. Central Russians might look more like Byelorussians.
Fertile Crescenters and their crops and ways didn't find Siberia very inviting at first. Then Rye, a Middle Eastern grain that often grew there as a pest in the middle of more productive ones, started to be planted widely, probably in the Corded Ware zone, and the East Slavs perhaps radiated from there into the East. It's possible that armed with this new productive food tech and maybe some other innovations for colder climates, they were finally able to go all the way to Vladivostok.

Turks and Tuscans: the impact of the wave from the Nile?

As promised I'm releasing individual, intra-population data for my Dual Core run. It is remarkably uniform within each population, and clines within them are smooth and can be explained easily. This may not be the best solution ADMIXTURE can provide, but I remain convinced it's the most informative so far for Neolithic relationships.
Note how "Evenki+Yakut" is nearly absent in a few individuals and has absolutely no relation with the Nile Core wave component. The model doesn't predict any correlation since the Nile component arrived thousands of years before Turkic nomads presumably brought the Evenki+Yakut and the Nganasan element into Anatolians. The Turkic element, being a lot more recent (hundreds vs thousands of years) is much more uneven.
Note how "Forager A" diminishes in areas with more of the Nile Core wave component. This is actually a prediction of the model. Nile valley derived agriculturalists would have arrived into Tuscany via a sea route, following the coastal village to village route settled by their predecessors in the First Mesopotamian Western (Vasconic) wave. Their demographic impact would reduce both the Forager A and the first wave Mesopotamian elements even further due to greater demographic densities possible with the new Nile Core capabilities. On the other hand, areas further up North, or inside the peninsula, particularly in the hilly interior, would be less affected. I don't know where from Tuscans in this set with high "Forager A" come from but I'd be willing to bet they are ancestrally from further North, away from the coast or from hilly/mountainous regions such as the Apennines.
In Italy it appears the Nile River wave is loosing steam?, perhaps as it absorbs more and more Mesopotamian elements, perhaps also concurrently as Mesopotamians begin to learn new techniques, adopt new seeds and ways more readily, and absorb other capabilities in less dramatic ways? Second Neolithic waves would have higher drag in the model, since they're expanding against already Neolithic, even if less advanced, people.

"Forager A", or whatever the "San" component is (can't think of any other explanation for it but I'd welcome suggestions) is much more homogeneous in populations to the North. I'll publish more populations next and then the spreadsheet with all of them.