Analysing Eurasian & African autosomal DNA from Lazaridis et al. 2013

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I have reorganised a bit the K=20 autosomal admixtures from Lazaridis et al. 2013 and assigned geographical regions for each component.

Admixtures-Lazaridis.png


These admixtures bear an uncanny resemblance to those of the Dodecad Project, and one could wonder if that Iosif Lazaridis could indeed be the person hidden behind the pseudonym Dienekes Pontikos.

Here is a few things we can deduce from these admixtures.


1) Neolithic farmers in Europe probably came from the Levant through Anatolia and Greece. For this reason I will call this admixture "East Mediterranean". Their genes are now found throughout Europe, North Africa and the Middle East until western Iran. The modern population most closely related to East Mediterranean Neolithic farmers are the Sardinians, as we already knew. The Basques are almost exactly half Neolithic farmers and half Mesolithic European in descent. The Saami are the only European completely lacking Neolithic farmer admixture.

2) Modern Levantines and South Caucasians are essentially a three-way mix of East Mediterranean, Caucaso-Perso-Gedrosian and Southwest Asian admixture. Egyptians also have two additional admixtures: North African and East African, which are only found at trace frequencies among other Semitic speakers in the Middle East.

3) In the Middle East, substantial percentages of Mesolithic European admixture are only found among the Turks and the North Caucasians.

4) Jewish people all share the same basic three-way admixtures as modern Levantines, but with additional admixture from the region from where they have settled historically. Ashkenazi Jews have the highest percentages of European admixture, followed by Turkish and North African Jews, who migrated from southern Europe. Other Jews (Georgian, Iraqi, Iranian, Yemenite, Ethiopian) have no European admixture.

5) There is hardly any East Mediterranean admixture in South Asia, starting from eastern Iran (Balochistan). Therefore it is unlikely that agriculture spread from the the Levant to South Asia, but rather developed independently in the Indus Valley. Neolithic farmers most likely belonged to Y-haplogroups G2, E1b1b (V13 and M34) and perhaps also T, and these haplogroups are almost absent from South Asia (apart from G2a3b1 brought by the Indo-Europeans). The presence of Y-haplogroup J1 and J2 in Central Asia and South Asia should be attributed to other migrations than that of Neolithic farmers from the Levant. The most likely hypotheses is that J1 and J2 were brought instead by Neolithic goat and sheep herders from the Caucasus and Zagros. Copper and Bronze Age expansions from the Caucasus and Iran (Kura-Araxes, etc.) would have brought more J1 and J2 to western South Asia.

6) The Neolithic farmer sample from Stuttgart (LBK culture, c. 5000 BCE) had only a small amount of Mesolithic European DNA. This means that Near Eastern farmers did not intermix much with their hunting-gathering neighbours, at least during their initial advance across Europe. Intermingling might have progressively increased over the centuries, but what brought the two populations closer together was their conquest by the Indo-Europeans during the Bronze Age, some 2500 years after the arrival of Neolithic farmers in Germany.

7) When looking at the non-Mongolid and non-Indian admixture in Central and North Asia, it can be deducted that the Bronze Age Indo-Europeans possessed approximately 40% of Mesolithic European (light blue), 45% of Caucaso-Perso-Gedrosian (beige) and 10% of Near Eastern farmer (bright pink) admixture. They also had about 5% of "Kalash admixture" (see below). The Near Eastern beige and pink components were in all likelihood absorbed by R1b during the 5000+ years of the Neolithic period around modern Kurdistan and the Caucasus, before moving to the Pontic Steppe, and from absorbing Balkano-Carpathian farmers (G2a3b1, J2b2, T1a) in the steppes. This admixture would have come from such maternal lineages as H2a1, H5a, H7, H8, I, J1, K, T1, T2, W and X2 (=> see mtDNA haplogroups associated with R1b people).

8) The Kalash admixture (dark green) is found at trace frequencies in among all regions settled by the Indo-Europeans, or in other words in all populations possessing haplogroups R1a or R1b. Since the Mal'ta boy (Y-DNA R*) possessed the highest level of this dark green admixture after the modern Kalash, this admixture was almost certainly a minor genetic component found in the original carriers of haplogroup R. This admixture is virtually absent from Africa, the Arabian peninsula, Sardinia, the Basques, the Saami, and non-Indo-European tribes of South Asia such as the Kharia and Kusunda. What's interesting is that the Kalash are one of the few people who still possess both Y-DNA R* and R1* (in addition to R1a, L and H) according to Firasat et al. (2007).

9) Some Bedouins have 100% of Southwest Asian admixture (khaki green). This admixture is found among all populations with substantial levels of Y-haplogroups J1 and J2, such as the Arabs, Levantines, Cypriots, Greeks, Sicilians, Maltese, North Africans, and East Africans.

10) Iberians have a small percentage of North African admixture, linked to the presence of Y-haplogroup E-M81 and mtDNA L. Iberians also have traces of East African and Southwest Asian admixture. All three admixtures could have come with the Moors during the Islamic period, although it is likely that there was already some North African admixture in Iberia (though probably in isolated populations) at least since the Neolithic period.

11) Despite being Uralic speakers, the Hungarians have only tiny amounts of Siberian admixture, just like their Y-DNA and mtDNA suggested.

12) The very low frequency of the Caucaso-Perso-Gedrosian admixture among the Basques hints that the autosomal genes of Y-haplogroup R1b got heavily diluted. The dilution could have started already before R1b entered the Basque population. But if a very small number of R1b men came and married Basque women, and their children only married pure Basque women, their autosomal DNA would have become more and more diluted at each generation until hardly any genes from the original R1b patriarchs remained. This would confirm my theory of how did the Basques became R1b and how they did not become Indo-European speakers. A high level of Caucaso-Perso-Gedrosian admixture would have been problematic to explain why the Basques were not speakers of an IE language.

UPDATE:

13) The Caucaso-Perso-Gedrosian admixture might be a composite of the West Asian branch of macro-haplogroup K, comprising mostly the original autosomal genes of carriers of Y-haplogroups L and T. Over time, L and T appear to have been replaced by the paternal lineages of successive invaders, like J1 and J2 during the Neolithic and Chalcolithic, R1a and R1b during the Bronze and Iron Ages, and East Asian lineages (C, N, O, Q) during the Turkic and Mongolian invasions.

14) The Thai and Cambodians have about a quarter of South Asian admixture, unlike the Chinese, Japanese and Koreans who have none of it. The migration of South Indians to Southeast Asia is historically attested and is linked to the diffusion of Buddhism and Hinduism to the region. It also explains why Cambodians in particular have such dark skin, in sharp contrast with their Vietnamese neighbours.

15) Northern Han Chinese have about 10% of Northeast Asian admixture, like the Koreans and Japanese, while Han Chinese in central and southern China, as well as ethnic minorities in southern China lack that Northeast Asian admixture.

16) Altaians have considerable levels of Indo-European admixture (light blue + beige), which probably came from the EBA Afanasevo culture (c. 3600-2400 BCE). Other Northeast Asian people farther east known to carry small percentages of R1a or R1b, like Yakuts, Mongolians, Tuvinians and Xibo, all have traces of Indo-European admixture.

17) Traces of Northeast Asian ancestry are found among all Levantine people, including European and North African Jews, but also among Armenians, Bulgarians, Albanians, Greeks and Sicilians. This is corroborated by the presence of Y-haplogroup Q among these populations.

18) Tuscans have practically the same admixtures as the Albanians and the Greeks, or even the Turks once their Northeast Asian admixture has been removed. This reinforces the theory of a Greco-Anatolian origin of the Etruscans.
 
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I have reorganised a bit the K=20 autosomal admixtures from Lazaridis et al. 2013 and assigned geographical regions for each component.

Admixtures-Lazaridis.png


Here is a few things we can learn from these admixtures.


1) Neolithic farmers in Europe probably came from the Levant through Anatolia and Greece. For this reason I will call this admixture "East Mediterranean". Their genes are now found throughout Europe, North Africa and the Middle East until western Iran. The modern population most closely related to East Mediterranean Neolithic farmers are the Sardinians, as we already knew. The Basques are almost exactly half Neolithic farmers and half Mesolithic European in descent. The Saami are the only European completely lacking Neolithic farmer admixture.

2) Modern Levantines and South Caucasians are essentially a three-way mix of East Mediterranean, Caucaso-Perso-Gedrosian and Southwest Asian admixture. Egyptians also have two additional admixtures: North African and East African, which are only found at trace frequencies among other Semitic speakers in the Middle East.

3) In the Middle East, substantial percentages of Mesolithic European admixture are only found among the Turks and the North Caucasians.

4) Jewish people all share the same basic three-way admixtures as modern Levantines, but with additional admixture from the region from where they have settled historically. Ashkenazi Jews have the highest percentages of European admixture, followed by Turkish and North African Jews, who migrated from southern Europe. Other Jews (Georgian, Iraqi, Iranian, Yemenite, Ethiopian) have no European admixture.

5) There is hardly any East Mediterranean admixture in South Asia, starting from eastern Iran (Balochistan). Therefore it is unlikely that agriculture spread from the the Levant to South Asia, but rather developed independently in the Indus Valley. Neolithic farmers most likely belonged to Y-haplogroups G2, E1b1b (V13 and M34) and perhaps also T, and these haplogroups are almost absent from South Asia (apart from G2a3b1 brought by the Indo-Europeans). The presence of Y-haplogroup J1 and J2 in Central Asia and South Asia should be attributed to other migrations than that of Neolithic farmers from the Levant. The most likely hypotheses is that J1 and J2 were brought instead by Neolithic goat and sheep herders from the Caucasus and Zagros. Copper and Bronze Age expansions from the Caucasus and Iran (Kura-Araxes, etc.) would have brought more J1 and J2 to western South Asia.

6) The Neolithic farmer sample from Stuttgart (LBK culture, c. 5000 BCE) had only a small amount of Mesolithic European DNA. This means that Near Eastern farmers did not intermix much with their hunting-gathering neighbours, at least during their initial advance across Europe. Intermingling might have progressively increased over the centuries, but what brought the two populations closer together was their conquest by the Indo-Europeans during the Bronze Age, some 2500 years after the arrival of Neolithic farmers in Germany.

7) When looking at the non-Mongolid and non-Indian admixture in Central and North Asia, it can be deducted that the Bronze Age Indo-Europeans possessed approximately 40% of Mesolithic European (light blue), 45% of Caucaso-Perso-Gedrosian (beige) and 10% of Near Eastern farmer (bright pink) admixture. They also had about 5% of "Kalash admixture" (see below). The Near Eastern beige and pink components were in all likelihood absorbed by R1b during the 5000+ years of the Neolithic period around modern Kurdistan and the Caucasus, before moving to the Pontic Steppe, and from absorbing Balkano-Carpathian farmers (G2a3b1, J2b2, T1a) in the steppes. This admixture would have come from such maternal lineages as H2a1, H5a, H7, H8, I, J1, K, T1, T2, W and X2 (=> see mtDNA haplogroups associated with R1b people).

8) The Kalash admixture (dark green) is found at trace frequencies in among all regions settled by the Indo-Europeans, or in other words in all populations possessing haplogroups R1a or R1b. Since the Mal'ta boy (Y-DNA R*) possessed the highest level of this dark green admixture after the modern Kalash, this admixture was almost certainly a minor genetic component found in the original carriers of haplogroup R. This admixture is virtually absent from Africa, the Arabian peninsula, Sardinia, the Basques, the Saami, and non-Indo-European tribes of South Asia such as the Kharia and Kusunda. What's interesting is that the Kalash are one of the few people who still possess both Y-DNA R* and R1* (in addition to R1a, L and H) according to Firasat et al. (2007).

9) Some Bedouins have 100% of Southwest Asian admixture (khaki green). This admixture is found among all populations with substantial levels of Y-haplogroups J1 and J2, such as the Arabs, Levantines, Cypriots, Greeks, Sicilians, Maltese, North Africans, and East Africans.

10) Iberians have a small percentage of North African admixture, linked to the presence of Y-haplogroup E-M81 and mtDNA L. Iberians also have traces of East African and Southwest Asian admixture. All three admixtures could have come with the Moors during the Islamic period, although it is likely that there was already some North African admixture in Iberia (though probably in isolated populations) at least since the Neolithic period.

11) Despite being Uralic speakers, the Hungarians have only tiny amounts of Siberian admixture, just like their Y-DNA and mtDNA suggested.

12) The very low frequency of the Caucaso-Perso-Gedrosian admixture among the Basques hints that the autosomal genes of Y-haplogroup R1b got heavily diluted. The dilution could have started already before R1b entered the Basque population. But if a very small number of R1b men came and married Basque women, and their children only married pure Basque women, their autosomal DNA would have become more and more diluted at each generation until hardly any genes from the original R1b patriarchs remained. This would confirm my theory of how did the Basques became R1b and how they did not become Indo-European speakers. A high level of Caucaso-Perso-Gedrosian admixture would have been problematic to explain why the Basques were not speakers of an IE language.

Any reason you excluded Albanian, Greek and Tuscan as they do appear in your link ................and all basically all the same.
 
What if the Caucaso-Perso-Gedrosian, supposedly associated with IE, was not initially spread by a R1b population? That would explain why the Basques (high R1b) don't have it.
 
I don't believe it but some from other sites would claim that 'Mesolithic European & North Eurasian' is a better match with IE. And that R1b can be better associated with 'North Eurasian'.
 
Any reason you excluded Albanian, Greek and Tuscan as they do appear in your link ................and all basically all the same.

That was not intentional. I was just tired and pressed by time when I edited the image. It has now been fixed.
 
What if the Caucaso-Perso-Gedrosian, supposedly associated with IE, was not initially spread by a R1b population? That would explain why the Basques (high R1b) don't have it.

Thenwho would have spread it around Europe and Siberia ?
 
"Mesolithic European and North Eurasian" = Y DNA I and R?

Kind of fuzzy classification. Are we to infer that hg. R is now Mesolithic European?

I ask this tongue in cheek-- long time readers of this site will understand...
 
There may be a 15,000 year split between the ANE in a Motala individual and the ANE re-introduced into Europe in the Chalcolithic.
So what does it mean to say that Europeans descend from 15% ANE?
 
"Mesolithic European and North Eurasian" = Y DNA I and R?

Kind of fuzzy classification. Are we to infer that hg. R now Mesolithic European?

I ask this tongue in cheek-- long time readers of this site will understand...

I have always said that the main haplogroups of Meolithic Europeans were I and R1a.

In this case, it means that the light blue admixture was found in the Mesolithic European samples (Motala, hg I) and the Paleolithic Siberian sample (Mal'ta boy, hg R).
 
I have always said that the main haplogroups of Meolithic Europeans were I and R1a.

In this case, it means that the light blue admixture was found in the Mesolithic European samples (Motala, hg I) and the Paleolithic Siberian sample (Mal'ta boy, hg R).

Well this makes sense if we are including Siberia in the boundaries of Europe. I know Europe can be larger or smaller geographically speaking depending on who you ask.

I guess the next question is how long will it be before hg. R1b is included in Paleolithic Europe?
 
I would add R* to "Caucaso-Perso-Gedrosian" because it obviously stem from a common origin of it. Also J* makes more sense for CPG. So R*, J*, T* and L* makes sense.

By the way according to Davidskis results this "Kalash" component is basically the same as Caucasus-Gedrosia. In other words Caucaso-Perso-Gedrosia is like a slightly drifted (East Mediterranean admixed) version of Kalash.
 
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Well this makes sense if we are including Siberia in the boundaries of Europe. I know Europe can be larger or smaller geographically speaking depending on who you ask.

I guess the next question is how long will it be before hg. R1b is included in Paleolithic Europe?

R1b could have been in "Europe" during the Palaeolithic, but that would have been in Northeast Europe, mostly Russia. After all, both R1a and R1b were supposedly mammoth hunters, and these tribes roamed vast geographical areas. Some Palaeolithic R1a and R1b could even have ended up in isolated pockets of Western Europe. That would explain how 5% of Irish belong to the Palaeolithic R1b1* (P25) subclade, which has nothing to do with the Indo-European branch.

There must have been many small hunter-gathering tribes comprising R1b-P25 lineages. At least one of them settled around eastern Turkey and Kurdistan at the end of the a last glaciation (circa 12,000 years ago) and, I believe, domesticated cattle there. They then dispersed in several branches, one of which (M269) migrated to the Caucasus and the Pontic Steppe and became the Indo-Europeans. You can read about this in more details in my updated R1b history.

The original R1b1* would have been autosomally similar to other Mesolithic Europeans (I or R1a) and would probably have belonged essentially to mtDNA U5 and V.
 
I would add R* to "Caucaso-Perso-Gedrosian" because it obviously stem from a common origin of it. So R*, T* and L* makes sense.

I thought about this too, but the Mal'ta boy didn't have any Caucaso-Perso-Gedrosian, so it can't be linked to R*.

By the way according to Davidskis results this "Kalash" component is basically the same as Caucasus-Gedrosia. In other words Caucaso-Perso-Gedrosia is like a slightly drifted (East Mediterranean admixed) version of Kalash.

I saw that in the K=19 and K=18 admixtures, but I don't believe it, for 2 reasons :

1) the Kalash admixture was found in the Mal'ta boy (contrarily to Caucaso-Perso-Gedrosia)

2) the Kalash admixture is found in all populations with substantial percentages of R1a or R1b, but not in other (non-IE) populations with high Caucaso-Perso-Gedrosia, like in the Arabian peninsula or the Georgians, who also have very little Mesolithic European admixture. So there seem to be a clear linked between the Mesolithic European admixture and the Kalash admixture, and both are found in R1a/R1b populations.
 
I thought about this too, but the Mal'ta boy didn't have any Caucaso-Perso-Gedrosian, so it can't be linked to R*.





I saw that in the K=19 and K=18 admixtures, but I don't believe it, for 2 reasons :

1) the Kalash admixture was found in the Mal'ta boy (contrarily to Caucaso-Perso-Gedrosia)

2) the Kalash admixture is found in all populations with substantial percentages of R1a or R1b, but not in other (non-IE) populations with high Caucaso-Perso-Gedrosia, like in the Arabian peninsula or the Georgians, who also have very little Mesolithic European admixture. So there seem to be a clear linked between the Mesolithic European admixture and the Kalash admixture, and both are found in R1a/R1b populations.


Mal'ta did carry it. And this is exactly what I meant with "Kalash" is basically Caucasian-Gedrosia. If we look at the Mal'ta paper. the dark green is far too strong in Western Asia but here this dark green component which was found among Mal'ta completely lacks in non Indo European West Asians. So some of the Caucasus-Gedrosia must have been eaten up by it. But here in Lazaridis paper this dark green is seen as Kalash. So it is very likely that in the lower K's even as you said already in K19 the Kalash and Caucasus_gedrosia were one and the same. So I believe that Caucaso-Perso-Gedrosia is basically a very recently and slightly "Eastern Med" admixed version of this Kalash component. This explains why even in K19 these two are virtually the same. This is why I believe R* was involved in spreading Caucaso-Perso-Gedrosia.

Another good indicator is that R* as well L* lineages are among the Haplogroups the Kalash are rich in.

Maciamo, this is exactly the chart I mean.


http://img43.imageshack.us/img43/2810/hhx4.png

See here, even in the Levant this dark green component, which is a major part of Mal'ta, is so strong while the Kalash component completely lacks. There is no other explanation to me than that Kalash and Caucaso-Perso-Gedrosia must be two parts of one component which was found in Mal'ta. And the "Kalash" version must be the pure one while the CPG is the slightly shifted and East Med admixed one.


And I forget but I disagree with the idea that the yDNA J* exclusively carried Southwest Asian component. I would even add to this Caucaso-Perso-Gedrosia component J1 as well J2. considering that these Haplogroups are also frequent in territories believed to have been (and still are) rich in T*, L* as well R1b* (Sumerians, Elamites etc.).

However, overall the charts and labels make pretty much sense, though it would have been better to use the term "Caucaso-Irano-Gedrosian" instead (just personal taste here).
 
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There is hardly any East Mediterranean admixture in South Asia, starting from eastern Iran (Balochistan). Therefore it is unlikely that agriculture spread from the the Levant to South Asia, but rather developed independently in the Indus Valley

I'm assuming you mean East of Balochistan/Gedrosia. If you look at Mehrgahr in the PPN, you have Near Eastern emmer wheat, barley and cattle, so you should see Near Eastern haplogroups.

I think you see those in the Brahui people who have a respectable showing of the standard NNE haploset, described in other posts. [G, J, E1b + H, HV, T1a]

I think Mehrgahr phase II could be the initial expanse of R1a, R2 in the Indus Valley, potentially ushering in the Pottery Neolithic/Chalcolithc and the obvious choice for people suddenly addicted to Afghan Lapis Lazuilli. I would feel comfortable saying that the Near Eastern presence is there, it's just been swamped by native lineages and steppe migrations in most populations in the Indus Valley.
 
The pink component seems West-Med not East-Med since it peaks in Sardinians...and would be associated with I2...yes, it's a mesolithic haplogroup, but I believe this component entered in Europe already in Mesolithic, remember La Braña had decent amount of Mediterrnean, and also the that Sardinians or EEF have themselves a decent amount of hunter-gatherer ancestry.
 
The pink component seems West-Med not East-Med since it peaks in Sardinians...and would be associated with I2...yes, it's a mesolithic haplogroup, but I believe this component entered in Europe already in Mesolithic, remember La Braña had decent amount of Mediterrnean, and also the that Sardinians or EEF have themselves a decent amount of hunter-gatherer ancestry.

The associations I made above are based on the region of origin, not the region where it is most common now. Obviously Neolithic farmers didn't originated in the West Mediterranean and colonised the Near East !
 
Another indicator is the macro Haplogroup IJK. Considering that I* as well K* is connected to ANE and WHG, it is unlikely that only J is entirely different.
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Another indicator is the macro Haplogroup IJK. Considering that I* as well K* is connected to ANE and WHG, it is unlikely that only the close cousin J is entirely different.

I would rather assume that Southwest Asian was spread by E1b1b* and some subclade of J1*(J1c3d) since it is basically East Mediterranean with an East African shift.
 
Why do you associate L & T with Caucaso-Perso-Gedrosia?


Accordig to you graph, people in the Caucasus are heavily of Caucaso-Perso-Gedrosia component, but there ain’t much of L & T in Georgia? Georgia is mostly Caucaso-Perso-Gedrosia. And the only haplogorupos that dominate Georgia are G2a and J2a. Also it has been said that folks from the East (Leyla-Tepe (J2a and R1b?)) entered Georgia and other Maykop regions. I believe that those people left J2a (and maybe R1b) marker in the Caucasus. So the best association with Caucaso-Perso-Gedrosia component is J2a.

 
Why do you associate L & T with Caucaso-Perso-Gedrosia?


Accordig to you graph, people in the Caucasus are heavily of Caucaso-Perso-Gedrosia component, but there ain’t much of L & T in Georgia? Georgia is mostly Caucaso-Perso-Gedrosia. And the only haplogorupos that dominate Georgia are G2a and J2a. Also it has been said that folks from the East (Leyla-Tepe (J2a and R1b?)) entered Georgia and other Maykop regions. I believe that those people left J2a (and maybe R1b) marker in the Caucasus. So the best association with Caucaso-Perso-Gedrosia component is J2a.


What Haplogroups nowadays dominate is not always most important to what it was in the past. CPG is also strong in Balochistan and surrounding areas and L* + T* is very prominent there too. T and L are also very common throughout Mesopotamia and Iran as well in Georgia (L* in Laz is very prominent). G2a is definitely connected to East Med and as you see on the chart East Med is very strong in Georgians too (pink component).

But I agree on the point that J* as well R* very likely played also a role in distributing CPG.
 

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