September 14, 2012

Inter-relationships between Dodecad K7b and K12b components

In a previous post I used leave-one-out to show how components inferred by ADMIXTURE could be related to each other.

One of the "problems" with ADMIXTURE and related analyses is that as the number of components K increases, additional components are formed by merging and/or splitting of components at lower K.

But, it turns out that thanks to the supervised mode, we can look at how components at different K are related to each other: we can treat, e.g., the K=12 ancestral populations as test data with the K=7 ancestral populations as references and vice versa.

I carried out precisely this procedure for my K7b/K12b components.

Below are the K12b components expressed as mixtures of the K7b ones:

And, the K7b ones expressed as mixtures of the K12b ones:

I have also calculated f3 statistics (ussing threepop) for all population triples using the  K7b/K12b calculators. Most of the mixes inferred by ADMIXTURE appear significant, although I didn't hand-check each one. I report the significant ones below:

Population f3(A; B, C) s.e. Z-score

Atlantic_Baltic_K7b;Atlantic_Med_K12b,North_European_K12b -0.00287483 2.64051e-05 -108.874
African_K7b;East_African_K12b,Sub_Saharan_K12b -0.00241502 2.3253e-05 -103.858
East_Asian_K7b;East_Asian_K12b,Southeast_Asian_K12b -0.00218574 2.17614e-05 -100.441
Caucasus_K12b;West_Asian_K7b,Southern_K7b -0.00317634 4.12205e-05 -77.0573
West_Asian_K7b;Gedrosia_K12b,Caucasus_K12b -0.00209044 3.14454e-05 -66.4785
Siberian_K7b;East_Asian_K12b,Siberian_K12b -0.00166911 2.60228e-05 -64.1403
South_Asian_K7b;Gedrosia_K12b,South_Asian_K12b -0.00195015 3.35149e-05 -58.1876
East_Asian_K12b;East_Asian_K7b,Siberian_K7b -0.00191747 3.49244e-05 -54.9034
Atlantic_Baltic_K7b;Southern_K7b,North_European_K12b -0.00181747 3.63948e-05 -49.9377
East_African_K12b;Southern_K7b,African_K7b -0.00412496 0.000101701 -40.5598
Atlantic_Med_K12b;Southern_K7b,Atlantic_Baltic_K7b -0.00138679 3.68608e-05 -37.6222
East_Asian_K7b;Southeast_Asian_K12b,Siberian_K7b -0.00127133 3.92998e-05 -32.3495
Northwest_African_K12b;Southern_K7b,Sub_Saharan_K12b -0.00272013 0.000110067 -24.7133
Northwest_African_K12b;Southern_K7b,African_K7b -0.00255262 0.000107527 -23.7394
East_African_K12b;African_K7b,Atlantic_Med_K12b -0.00237833 0.000107306 -22.1639
East_African_K12b;African_K7b,Caucasus_K12b -0.00217732 0.000101003 -21.557
Caucasus_K12b;West_Asian_K7b,Atlantic_Med_K12b -0.000977923 4.573e-05 -21.3847
Caucasus_K12b;West_Asian_K7b,Northwest_African_K12b -0.00100154 4.86387e-05 -20.5915
East_African_K12b;Southern_K7b,Sub_Saharan_K12b -0.00247983 0.000122139 -20.3034
Caucasus_K12b;Southern_K7b,Gedrosia_K12b -0.00112749 5.91335e-05 -19.0669
East_Asian_K12b;Southeast_Asian_K12b,Siberian_K7b -0.00100305 5.44851e-05 -18.4097
Atlantic_Baltic_K7b;North_European_K12b,Caucasus_K12b -0.000534432 2.98199e-05 -17.922
Southern_K7b;Southwest_Asian_K12b,Atlantic_Med_K12b -0.000683711 4.08148e-05 -16.7515
East_Asian_K12b;East_Asian_K7b,Siberian_K12b -0.000651854 4.01206e-05 -16.2474
African_K7b;Gedrosia_K12b,Sub_Saharan_K12b -0.000738345 4.5676e-05 -16.1648
African_K7b;Southern_K7b,Sub_Saharan_K12b -0.000769896 4.8516e-05 -15.8689
South_Asian_K7b;South_Asian_K12b,Northwest_African_K12b -0.000598387 3.84069e-05 -15.5802
African_K7b;Sub_Saharan_K12b,Northwest_African_K12b -0.000602378 4.07154e-05 -14.7948
East_African_K12b;African_K7b,Southwest_Asian_K12b -0.00141216 0.000102079 -13.834
African_K7b;Sub_Saharan_K12b,North_European_K12b -0.000663712 4.87314e-05 -13.6198
African_K7b;South_Asian_K7b,Sub_Saharan_K12b -0.000598399 4.51811e-05 -13.2445
Southern_K7b;Southwest_Asian_K12b,Northwest_African_K12b -0.000577559 4.50096e-05 -12.8319
Siberian_K7b;East_Asian_K7b,Siberian_K12b -0.000403499 3.17418e-05 -12.7119
Atlantic_Baltic_K7b;West_Asian_K7b,Atlantic_Med_K12b -0.000520714 4.41022e-05 -11.807
East_African_K12b;African_K7b,Atlantic_Baltic_K7b -0.00122819 0.000106897 -11.4895
African_K7b;Sub_Saharan_K12b,Siberian_K7b -0.00051246 4.93477e-05 -10.3847
East_African_K12b;African_K7b,North_European_K12b -0.00103911 0.000106816 -9.72802
African_K7b;Sub_Saharan_K12b,Southeast_Asian_K12b -0.000469707 4.98071e-05 -9.43052
African_K7b;East_Asian_K12b,Sub_Saharan_K12b -0.000461359 4.9918e-05 -9.24235
Gedrosia_K12b;South_Asian_K7b,West_Asian_K7b -0.00047115 5.11259e-05 -9.2155
South_Asian_K7b;East_African_K12b,South_Asian_K12b -0.000384664 4.18056e-05 -9.20125
African_K7b;Sub_Saharan_K12b,Caucasus_K12b -0.000430657 4.69419e-05 -9.17425
African_K7b;Sub_Saharan_K12b,Southwest_Asian_K12b -0.000421792 4.64037e-05 -9.08962
Atlantic_Baltic_K7b;North_European_K12b,Northwest_African_K12b -0.000328259 3.62081e-05 -9.06589
African_K7b;Sub_Saharan_K12b,East_Asian_K7b -0.000446564 4.9569e-05 -9.00895
African_K7b;Sub_Saharan_K12b,Siberian_K12b -0.000437012 4.88062e-05 -8.95404
Northwest_African_K12b;African_K7b,Atlantic_Med_K12b -0.00115555 0.000131897 -8.76101
African_K7b;West_Asian_K7b,Sub_Saharan_K12b -0.000397507 4.57534e-05 -8.68804
African_K7b;Sub_Saharan_K12b,Atlantic_Baltic_K7b -0.000418044 4.81379e-05 -8.68431
African_K7b;South_Asian_K12b,Sub_Saharan_K12b -0.000393516 4.57123e-05 -8.60853
South_Asian_K7b;South_Asian_K12b,Southwest_Asian_K12b -0.000290753 3.88373e-05 -7.48644
South_Asian_K7b;West_Asian_K7b,South_Asian_K12b -0.000228331 3.63783e-05 -6.27657
Atlantic_Med_K12b;Southern_K7b,North_European_K12b -0.000329428 5.28014e-05 -6.239
East_African_K12b;Gedrosia_K12b,African_K7b -0.000596188 0.000102434 -5.8202
African_K7b;Sub_Saharan_K12b,Atlantic_Med_K12b -0.00023116 4.95629e-05 -4.66397
South_Asian_K7b;South_Asian_K12b,Atlantic_Med_K12b -0.000172605 4.09236e-05 -4.21775
Siberian_K12b;Atlantic_Med_K12b,Siberian_K7b -0.000166672 4.4065e-05 -3.78243
East_African_K12b;West_Asian_K7b,African_K7b -0.00034931 0.000103503 -3.37489
Atlantic_Baltic_K7b;Atlantic_Med_K12b,Siberian_K7b -0.000226988 7.32706e-05 -3.09795

This leads to a very simple way of gauging whether an ancestral population is better seen as admixed or not: count the number of times it appears before the semi-colon, and subtract the number of times it appears after the semi-colon. This may not be a perfect measure, but it captures the basic idea. When I do this, I get:

[1,] East_African_K12b      7
[2,] African_K7b            7
[3,] South_Asian_K7b        4
[4,] Atlantic_Baltic_K7b    3
[5,] East_Asian_K12b        0
[6,] Caucasus_K12b          0
[7,] Northwest_African_K12b -2
[8,] East_Asian_K7b         -2
[9,] Siberian_K12b          -3
[10,] Southeast_Asian_K12b   -4
[11,] Gedrosia_K12b          -4
[12,] Siberian_K7b           -4
[13,] Southwest_Asian_K12b   -5
[14,] South_Asian_K12b       -7
[15,] North_European_K12b    -7
[16,] West_Asian_K7b         -7
[17,] Southern_K7b           -8
[18,] Atlantic_Med_K12b      -8
[19,] Sub_Saharan_K12b       -19

I think this looks reasonable; the components at the bottom usually appear contributing to the admixture of other populations, and the components at the top usually appear admixed in terms of the other components. Of course admixed components may be themselves be useful if they represent regional mixes (such as teh East African), but this is certainly a good way to supplement and interpret ADMIXTURE analysis.

pconroy said...

Interesting analysis!

I guess you could interpret the results also to be the relative time-depth of admixture of a given component?

I wonder does that yield results that match archaeology...

Slumbery said...

Dienekes

You said multiple time that Caucasus is West Asian + Southern, but what there is an other result of the this analysis that seems to complicate the matter. Gedrosia seems to be almost entirely a subset of West Asian and West Asian comes out as an about even mixture of Caucasus + Gedrosia (actually with more Gedrosia).

A possible interpretation that Gedrosia is a less admixed and Caucasus is a strongly admixed successor of the "West Asian" ancestral population. However this would place the "homeland" of the West Asian into the East (East from Anatolia and the Armenian Highland), possibly in the current Iran.

I think this is also supported by the G2a origin theory. You seem to support the idea that the source of G2a is the Armenian Highland, but the Neolithic G2a immigrant in Europe did not have West Asian at all. They were Southern. I think the idea that the West Asian homeland is in Anatolia or even Northwest Iran is not compatible with the idea that the G2a population came from this region. The prehistoric (before 5000 BP) West Asian migration had to start somewhere East from this area. (However it is possible that it happened right after G2a left, let's say around 7000 BP or so and after that moved forward from here.)

eurologist said...

Slumbery,

I largely agree with you: there is a much older connection with South/Central Asia dating back to the first settlement of Europe and the Gravettian. This cannot be neglected - it connects Europe to (very roughly) Pakistan and north of it, where most of the important haplogroups either originated or passed through from further East.

IMO, "Gedrosia" signifies remnants of this much earlier ancestral population, while "Caucasus" is largely derived from this and may include some ancient Anatolian/ Near Eastern elements.

shenandoah said...

No 'Amerindian' (either Northern or Southern), indicates the major flaws and blatant bias in your theory. You can't force Native American DNA's definition to match "Siberian" or whatever. You can't call that "science". You can't allow some flimsy excuses for devaluing the testimony of Native Americans, compared with other ethnic groups -- that's discrimination, and it's just wrong.

Just an example of how data is being manipulated by geneticists; notice the list of "alochtonous" haplogroups reported in this study... One of which happens to be my own, W1e(at least tentatively, until further testing or classification proves otherwise). For years now, geneticists studying Native American DNA have been dismissing all data which doesn't fit their extremely narrow and prejudiced definition of the term. More often than not however, there is little or no mention of what is really going on behind the scenes. This paper is somewhat more revealing:

(Table 1)

pconroy said...

shenandoah,

I see you are mtDNA W1e and your profile says your maternal ancestral name was "Bird".

My Father has 9 mtDNA W as follows:
W1 x 4 - 2 Dutch and 2 Unknown
W1c x 5 - 3 German and 2 Irish

My Mother has 11 mtDNA W as follows:
W1 x 8 - 1 Polish, 1 Scottish, 4 Irish, 2 Unknown
W1c x 3 - 2 Irish and 1 Unknown

So the mtDNA haplogroup is mostly Irish, German or Dutch.

Here is the distribution of the name "Bird" in Ireland:
http://www.irishtimes.com/ancestor/surname/index.cfm?fuseaction=Go.&Surname=Bird&UserID=

In some parts of the country it is of English descent, but in most of the country it is simply an Anglicization of the Irish name "Mac An Aen" (Literally "Son of the Bird"), which is sometimes listed today as:
MacEneany
Heaney
Bird

So I'd say your maternal Cherokee ancestry goes back to Ireland.

shenandoah said...

pconroy, very generous of you to offer your interesting opinion about my personal ancestry, although that wasn't the main point of my comment. I'd already gathered that there's probably a relationship between some Cherokee and some Irish or other indigenous types of Europeans, which I believe was pre-Columbian in origin.

By the way, the Cherokee surname, "Bird", is yet another Anglicization: of the Cherokee matrilineal Bird Clan, "Anitsiskwa". While it's unlikely that gg-grandmother was herself from that clan, her family somehow ended up with that surname anyway, as an adaptation to the Patriarchal system of family relationships. (It's more likely that she or one of her female ancestors was ~married to a man from that particular clan, at the time the surname was adopted.)

"Bird" is a very, very common Cherokee surname, one of the Anglicized ones. I've traced many branches of my family tree as far back as the 12th century; but that one is extremely difficult. I can't get past my gg-grandmother's and her husband's (also Cherokee) generation, on that one. All of the politics and racism surrounding Native Ancestry, both now and then, is a large part of the problem.

Kurti said...

@Slumberry

"Gedrosia seems to be almost entirely a subset of West Asian"

I think Dienekes did mention several times that Gedrosia is almost fully West Asian with some (~10%) of it being West Asian related "South Asian"/ANI like.

You have to take into account that Gedrosia peaks in current day Baluch People. And it is believed that more people in Pakistan especially Punjab region are of Baloch descend but just linguistically Punjabi. And as we all should know Balochi people ultimately originated somewhere in Northern Syria according themselves and also their language is Northwest Iranian and most related to Kurdish. I believe that the Gedrosia component ultimately originated somewhere in Northern Mesopotamia/Western Iran.

Slumbery said...

Kurti

"...according themselves..."

You talk about an origin Myth that shows them as the descendants of Mohamed's uncle and states a Medieval Syrian origin. Even if this was somehow true, it would be still irrelevant for the case of Gedrosia/West Asian presence here 7000 years earlier.

"Northwest Iranian and most related to Kurdish"

For this to even matter it should be proven that current Kurds (and their language) are indigenous in that area for a several thousands of years.

SimonW said...

Now that's very odd! How are we now to explain the Gedrosia component in Basques?? I would have guessed that Gedrosia also participates in Atlantic-Baltic (or Southern), because of the Basques who are almost exclusively made up of these two K7b components and yet do have nontrivial amounts of Gedrosia.

If Gedrosia really just is West Asian + South Asian how can the Basques possibly have ~9-10% Gedrosia, when they've got neither of these in K7b?

The Caucasus component in Sardinians is perfectly well explained by its being part of the K7b Southern component. Ötzi already did have some of this Southern, non-West Asian Caucasus, so it's something historically real. But the Gedrosia in Basques is completely at odds with their apparent lack of West and South Asian. It's contradictory and perplexing.

It seems, either they do not really have Gedrosia, or they do in fact have something West Asian (or South Asian).

The Basques actually fit well into the general geographical pattern of elevated levels of Gedrosia in Western-Northwestern Europe, so it seems natural to assume that it arrived there as part of the same population movement. Maybe it has something to do with Bell Beakers and R1b. None of the pre 5 kya samples so far displayed any Gedrosia, the mesolithic Iberians neither, so I doubt that it's something old in Western Europe.

Slumbery said...

SimonW

My guess is that an early wave of the east to west migration, that created the Caucasus component by mixing with Southern and created the West Asian component too, made trough the Levant with minimal admixture and quickly reached the Atlantic region before the Middle-Eastern admixture taken place and before the West Asian formed in its current form. Therefore the Gedrosia of the Basques is a relic of an "Old Gedrosia" that was not yet caracteristic West Asian.

Or we just do not have enough data and the oddity of the Basques is either a virtula artefact of the imperfect analysis or comes from a strange drift/selection in a small population, or both combined.

If we could decide that the British West Asian is connected to the Caucasus or connected to Gedrosia it would be telling. The Caucasus and the Gedrosia in the British do not add up to the West Asian.

SimonW said...

The Westasian in the British Isles seems almost entirely stemming from the Gedrosia there.
The Caucasian component is most of all found in the southern/southeastern part of Britain, i.e. England, where it reaches 3,6% in Kent.
This may be partly Southern/LBK derived and partly West Asian, like in Baltoslavic peoples, where only little of the Southern component is found.

But Ireland (0,2%) and Argyll (0,5%) have negligible amounts of Caucasus admixture, and it's even zero in Orcadians. It really seems like all of their West Asian comes from the Gedrosia component. Which is BTW only slightly stronger than their Westasian:

Argyll_1KG: 13,1 Gedrosia 0,5 Caucasus 10,8 Westasian
Orcadian: 12 Gedrosia 0 Caucasus 9,7 Westasian
Orkney_1KG: 11,8 Gedrosia 0 Caucasus 9,5 Westasian
Irish_D 11,9: Gedrosia 0,2 Caucasus 9,8 Westasian

SimonW said...

However, Dienekes' elucidation of the interrelationships between K12 and K7 components opens up yet another intriguing possibility: Namely, that the west European IE West Asian component is related to the North European component rather than to Gedrosia! (K7 West Asian is found in K12 Caucasus and Gedrosia, but also in Southwest Asian and in North European. If I'm interpreting the coloured bars correctly, North European could account for up to ~8,5% West Asian.) If so, then the Basque West Asian-free Gedrosia would no longer be an exception in Western Europe. Then we could easily unite everything under one simple explanation/population movement: R1b-M412, Bell Beakers, west European Gedrosia and Vaskonic languages! Basques still do have North European / mesolithic admixture, but it would differ from the surrounding IE North European, by not being West Asian admixed. This would mean that Celtic didn't arrive earlier than in the bronze age in Western Europe.

SimonW said...

Sorry for triple posting, but I checked my idea with a look at the Lithuanian sample:

West_Asian
Lithuanians 10,4%

Caucasus
Lithuanians 8%

Gedrosia
Lithuanians 0%

Southern
Lithuanians 0,4%

Thus, about 2,4% of their West_Asian seems to be associated with their North_European. Not quite a lot.

SimonW said...

I promise, this will be my last comment, unless someone provokes a further answer - but I've got an idea that seems hot.

If we take the parts of the British Isles, where Caucasus plays no role:

Argyll = 10,8% West_Asian / 13,1% Gedrosia

Orkney = 9,6% West_Asian / 11,9% Gedrosia

Ireland = 9,8% West_Asian / 11,9% Gedrosia

And if we assume that, like in Lithuanians, about 2,4% of their West_Asian is associated with North_European, we get:

Argyll = 8,4% West_Asiatic Gedrosia / 4,7% Basque Gedrosia

Orkney = 7,2% West_Asiatic Gedrosia / 4,7% Basque Gedrosia

Ireland = 7,4% West_Asiatic Gedrosia / 4,5% Basque Gedrosia

Where Basque Gedrosia is Gedrosia without accompanying West_Asian, of course.

So how could we explain this pattern?
IMHO: What got to western Europe with IEs was neither Caucasus nor Gedrosia, but West_Asian in the first place.
And before the arrival of IEs, Vaskonic people had already brought some pseudo-Gedrosia to Western Europe, i.e. something looking like Gedrosia, but without the West_Asian component. Now, when a real West_Asian influence arrived with IEs, this made the Gedrosia, that was already there, only more "real", so why should it change something in the amount of Gedrosia? It didn't; it was like when a hollow receptacle is being filled. On the other hand, that in eastern Europe, West_Asian appears as Caucasus is just natural - after all the Caucasus mountains are much nearer than Balochistan.

Kurti said...

@Slumberry

Even if we assume that the Kurdish language is not native to Kurdistan for over 7000 we still know that most of their genetics is. And the Gedrosia component is obviously West Asian and it makes obviously no sense to assume that it was brought to Western Asia from somewhere far else.

Since the langauge of Balochi people is classified as Northwest Iranic they have to be more recent immigrantis (~1000 years) in modern day Balochistan. Since the linguistic shift which turned the Iranic languages in Northwest-Southwest-Northeast-Southeast accured roughly 3000 years ago, it is wrong to assume that the(Balochis) did not live in Western Iran or Mesopotamia 1000 b.c.

Kurti said...

However I admit it was wrong to connect all of Gedrosia in South Asia to Baloch expansion.

@SimonW
Gedrosia is not West Asian+South Asian.

Gedrosia is almost exclusively West Asian.
Something like 90% West Asian and 10% South Asian (ANI like).

Gedrosia is the purer part of K7bs "West Asian".

Onur said...

@Kurti

Both the K=7 and K=12 "South Asian" components are ASI-ANI mixes, ASI being the major element and ANI being the minor element, so your statement that the "South Asian" component of either K=7 or K=12 is ANI-like is certainly wrong. Therefore, the "Gedrosia" component, which is composed of close to 10% K=7 "South Asian" and the rest being composed of "K=7 "West Asian" (which is itself a "Gedrosia"-"Caucasus" mix), clearly has non-negligible ASI admixture. Also, the "Caucasus" component is a purer Caucasoid component than the "Gedrosia" component.

The below links demonstrate what I am saying in an easy to understand way:

http://3.bp.blogspot.com/-o3aBKiyqagc/TyfglQUIlPI/AAAAAAAAEdI/LQj6qi7LE8k/s1600/1_2.png

http://4.bp.blogspot.com/-cYC4bY-koB0/TybKBMtXRSI/AAAAAAAAEbs/zka5fg8fmRQ/s1600/nj.png

http://3.bp.blogspot.com/-2JplvwzgtOw/Tyew3hYgzMI/AAAAAAAAEcM/vIdqDVn-fpI/s1600/nj.png

As for the Balochi, they are genetically almost the same as their Dravidian-speaking neighbors, the Brahui, buttressing the thesis that their acquisition of NW Iranic speech occurred via an elite dominance process that had very little no effect on their genetics.

Kurti said...

@Onur

I think you missed something. No one was talking about the South Asian component in k12b per se. I was talking about the South Asian part in the Gedrosia component which is ANI like.

The South Asian component on K12b might be ASI/ANI mixed but the South Asian related part of Gedrosia is surely ANI like.

Kurti said...

@Onur something else. The Brahui and Balochi are by large (80%) West Asian like populations and you assume and are telling me that the reasony why Balochi and Brahui speak Northwest Iranic is due "elite dominance " of Iranic groups over Dravidians?

In contrary its more likely the other way around. Brahui are extremely Balochi admixed Dravidians who have simply preserved their Dravidian language.

Also it seems to me you are just showing maps which suit your believes. how about you just show us the fst distance table of k12b

The K12b Gedrosia component shares just slightly more relationship to the South Asian component as the North European does, and this is probably only because of the West Eurasian like part of the South Asian component.

but at the same time it is further away from the East African component compared to Southwest Asian. Or further away from the Southwest Asian component (which itself is close to East African) compared to Atlantic_Med.

And you are telling me that Gedrosia is "less Caucasoid" than the other components?

Onur said...

I think you missed something. No one was talking about the South Asian component in k12b per se. I was talking about the South Asian part in the Gedrosia component which is ANI like.

The South Asian component on K12b might be ASI/ANI mixed but the South Asian related part of Gedrosia is surely ANI like.

Nonsense. The "South Asian" components are ASI majority-ANI minority mixes and this is the same everywhere (e.g., as part of another component) they are found.

@Onur something else. The Brahui and Balochi are by large (80%) West Asian like populations and you assume and are telling me that the reasony why Balochi and Brahui speak Northwest Iranic is due "elite dominance " of Iranic groups over Dravidians?

In contrary its more likely the other way around. Brahui are extremely Balochi admixed Dravidians who have simply preserved their Dravidian language.

It is clear that the Balochi language is a new comer to the region (it is a NW Iranic language like Kurdish and the only NW Iranic language spoken that far south), and even you admit that. But it is far from clear when Dravidian languages arrived at that region; they may be very old there. This bolsters the thesis of the spread of the Balochi language via an elite dominance process in a Northern Dravidian-speaking region.

Also it seems to me you are just showing maps which suit your believes. how about you just show us the fst distance table of k12b