More analyses of the Mal’ta and Afontova Gora genomes

Below are the results of more analyses of the Mal’ta and Afontova Gora genomes. I’ve also included the results of the previous analyses to allow for easy comparison.

The new results shed a great deal of light on the origin of the West Asian, Caucasus, and Gedrosia components in Europe.

I have recently been arguing that the globe13 West Asian component in Europe is associated with Y haplogroup J2, and not with R1b or R1a. But the globe13 West Asian component is basically a combination of the K12b Caucasus and Gedrosia components, and in order to understand how these components got to Europe, it’s necessary to look at the two more highly resolved K12b components. The West Asian component does show a much stronger association with J2 than with R1b or R1a, but it’s really only the Caucasus component that J2 is associated with. The Gedrosia component, on the other hand, shows a strong association with R1b.

The MDLP World-22 Indo-Iranian component, which is basically just a Kalash component, shows a similarly strong association with R1b in Europe. The Kalash are 18.2% R1a, 6.8% R*, and 2.3% R1*, but they don’t have any R1b, so the genetic affinity between R1b Western Europeans and the Kalash cannot be due to gene flow mediated by R1b people. It must be due to common descent from the common ancestors of the R1b people in Western Europe and the R1a, R*, and R1* people in Pakistan. Those common ancestors were the original R* people.

R1b shows no association with the Caucasus component in Europe. Basques have one of the highest frequencies of R1b, and although they have 9.8% of the Gedrosia component, they don’t have any of the Caucasus component. The Caucasus component is present in large amounts throughout West Asia, so the R* people who imparted the Gedrosia component to the R1b people of Western Europe cannot have reached Europe by going west from Pakistan through West Asia. They instead must have gone north, through Central Asia.

Mal’ta 1 was one of these R* people. The K12b results below show that Mal’ta 1 had 24.73% of the Gedrosia component, and none of the Caucasus component. And the dv3 results below show that Mal’ta 1 was more closely related to Western Europeans than to Eastern Europeans. The results for Afontova Gora 2 show that he also had a large amount of the Gedrosia component, none of the Caucasus component, and was also more closely related to Western Europeans than to Eastern Europeans.

After moving north through Central Asia, the R* people would have entered the steppe-tundra region that stretched from the Atlantic to Lake Baikal. Once they had adapted to a lifestyle of hunting mammoths and other big game, they would have expanded east through Siberia, and west to Europe, where they would make their appearance as the Gravettians.

R1b Western Europeans preserve more of the original genetic makeup of the R* people than R1a Eastern Europeans do. The reason for this must be that the R1b people of Western Europe mixed less with the Y hg I Aurignacians than the R1a people of Eastern Europe did.

We can see this difference in the amount of Aurignacian admixture in the physical features of Europeans today. I believe that the leptomorphic type (having a long and narrow face) of Sungir 1 and Predmost 3 was the original physical type of Y hg R people, and that the eurymorphic type (having a short and wide face) of Cro-Magnon 1 was the original physical type of Y hg I people. A leptomorphic face is a feature of the Irano-Afghan type found today in Pakistan, and it is also a feature of the classic Nordic type found today in Northwestern Europe, where R1b predominates. A eurymorphic face, on the other hand, is a feature of the East Baltic type found today in Northeastern Europe, where R1a predominates.

Mal’ta 1


  • 57.69% European
  • 31.79% Amerindian
  • 7.16% Asian
  • 3.37% African


  • 37.79% Atlantic_Baltic
  • 21.36% Amerindian
  • 20.47% South_Asian
  • 14.54% West_Asian
  • 3.50% Siberian
  • 1.71% Neo_African
  • 0.62% Australasian
  • 0.01% Palaeo_African
  • 0.00% East_Asian
  • 0.00% Southern


  • 45.62% North_European
  • 16.52% South_Asian
  • 16.03% Amerindian
  • 10.82% West_Asian
  • 8.48% Arctic
  • 1.27% West_African
  • 0.67% Australasian
  • 0.60% East_African
  • 0.00% East_Asian
  • 0.00% Mediterranean
  • 0.00% Palaeo_African
  • 0.00% Siberian
  • 0.00% Southwest_Asian


  • 40.26% Atlantic_Baltic
  • 23.06% South_Asian
  • 20.86% West_Asian
  • 14.01% Siberian
  • 1.80% African
  • 0.00% East_Asian
  • 0.00% Southern


  • 50.42% Atlantic_Baltic
  • 20.72% South_Asian
  • 16.25% Siberian
  • 10.89% West_Asian
  • 1.71% Sub_Saharan
  • 0.01% Palaeoafrican
  • 0.00% East_Asian
  • 0.00% Mediterranean
  • 0.00% Red_Sea
  • 0.00% Southeast_Asian


  • 44.27% North_European
  • 24.73% Gedrosia
  • 15.50% South_Asian
  • 13.76% Siberian
  • 1.73% Sub_Saharan
  • 0.01% East_African
  • 0.00% Atlantic_Med
  • 0.00% Caucasus
  • 0.00% East_Asian
  • 0.00% Northwest_African
  • 0.00% Southeast_Asian
  • 0.00% Southwest_Asian


  • 34.62% West_European
  • 27.30% South_Asian
  • 20.22% East_European
  • 15.36% Northeast_Asian
  • 1.40% Neo_African
  • 1.02% Palaeo_African
  • 0.06% Mediterranean
  • 0.01% West_Asian
  • 0.00% East_African
  • 0.00% Northwest_African
  • 0.00% Southeast_Asian
  • 0.00% Southwest_Asian

MDLP World-22

  • 31.00% North-East-European
  • 14.44% Samoedic
  • 12.62% Indian
  • 12.40% North-Amerind
  • 8.99% Indo-Iranian
  • 7.21% Mesoamerican
  • 4.75% West-Asian
  • 3.96% North-European-Mesolithic
  • 1.96% Sub-Saharian
  • 1.57% South-America_Amerind
  • 1.03% Arctic-Amerind
  • 0.07% Austronesian
  • 0.00% Atlantic_Mediterranean_Neolithic
  • 0.00% East-Siberean
  • 0.00% East-South-Asian
  • 0.00% Indo-Tibetan
  • 0.00% Melanesian
  • 0.00% Near_East
  • 0.00% North-Siberean
  • 0.00% Paleo-Siberian
  • 0.00% Pygmy
  • 0.00% South-African

Old World 26

  • 27.95% Finnish
  • 25.40% Burusho
  • 12.62% Gujarati
  • 8.58% Kalash
  • 5.16% Yakut
  • 4.36% Brahui
  • 4.02% Basque
  • 2.20% Archaic
  • 1.47% Dai
  • 1.14% Yoruba
  • 1.08% Papuan
  • 1.03% Sardinian
  • 0.74% Naxi
  • 0.72% San
  • 0.65% Melanesian
  • 0.55% Mbuti-Pygmy
  • 0.47% Kenya-Bantu
  • 0.42% Biaka-Pygmy
  • 0.38% Lahu
  • 0.36% Mandenka
  • 0.32% Palestinian
  • 0.19% She
  • 0.18% Japanese
  • 0.00% Bedouin
  • 0.00% Druze
  • 0.00% Mozabite

Afontova Gora 2


  • 70.95% European
  • 28.11% Amerindian
  • 0.91% African
  • 0.03% Asian


  • 58.93% Atlantic_Baltic
  • 16.37% Amerindian
  • 11.32% West_Asian
  • 9.86% South_Asian
  • 2.93% Siberian
  • 0.56% Neo_African
  • 0.02% Australasian
  • 0.00% East_Asian
  • 0.00% Palaeo_African
  • 0.00% Southern


  • 62.62% North_European
  • 11.87% Amerindian
  • 10.70% West_Asian
  • 7.45% South_Asian
  • 6.54% Arctic
  • 0.61% West_African
  • 0.13% Australasian
  • 0.07% East_African
  • 0.00% East_Asian
  • 0.00% Mediterranean
  • 0.00% Palaeo_African
  • 0.00% Siberian
  • 0.00% Southwest_Asian


  • 58.81% Atlantic_Baltic
  • 18.53% West_Asian
  • 11.74% Siberian
  • 10.20% South_Asian
  • 0.73% African
  • 0.00% East_Asian
  • 0.00% Southern


  • 66.13% Atlantic_Baltic
  • 13.40% Siberian
  • 10.74% West_Asian
  • 8.98% South_Asian
  • 0.75% Sub_Saharan
  • 0.00% East_Asian
  • 0.00% Mediterranean
  • 0.00% Palaeoafrican
  • 0.00% Red_Sea
  • 0.00% Southeast_Asian


  • 61.18% North_European
  • 20.28% Gedrosia
  • 11.36% Siberian
  • 6.12% South_Asian
  • 0.84% Sub_Saharan
  • 0.22% Atlantic_Med
  • 0.00% Caucasus
  • 0.00% East_African
  • 0.00% East_Asian
  • 0.00% Northwest_African
  • 0.00% Southeast_Asian
  • 0.00% Southwest_Asian


  • 45.00% West_European
  • 27.61% East_European
  • 12.96% South_Asian
  • 12.59% Northeast_Asian
  • 0.94% Neo_African
  • 0.60% Mediterranean
  • 0.22% East_African
  • 0.07% West_Asian
  • 0.00% Northwest_African
  • 0.00% Palaeo_African
  • 0.00% Southeast_Asian
  • 0.00% Southwest_Asian

MDLP World-22

  • 46.23% North-East-European
  • 10.32% Samoedic
  • 9.18% West-Asian
  • 7.95% North-European-Mesolithic
  • 5.58% South-America_Amerind
  • 4.73% Indo-Iranian
  • 4.47% Arctic-Amerind
  • 4.43% North-Amerind
  • 3.88% Mesoamerican
  • 2.73% Indian
  • 0.47% Sub-Saharian
  • 0.02% Paleo-Siberian
  • 0.01% Atlantic_Mediterranean_Neolithic
  • 0.00% Austronesian
  • 0.00% East-Siberean
  • 0.00% East-South-Asian
  • 0.00% Indo-Tibetan
  • 0.00% Melanesian
  • 0.00% Near_East
  • 0.00% North-Siberean
  • 0.00% Pygmy
  • 0.00% South-African

Old World 26

  • 40.57% Finnish
  • 17.29% Basque
  • 12.49% Burusho
  • 6.41% Gujarati
  • 4.56% Kalash
  • 3.91% Yakut
  • 3.31% Brahui
  • 2.46% Sardinian
  • 1.95% Archaic
  • 1.18% Naxi
  • 0.95% Yoruba
  • 0.91% Kenya-Bantu
  • 0.90% Dai
  • 0.77% Palestinian
  • 0.59% Papuan
  • 0.57% Melanesian
  • 0.41% San
  • 0.35% Biaka-Pygmy
  • 0.30% Mbuti-Pygmy
  • 0.08% She
  • 0.03% Lahu
  • 0.00% Bedouin
  • 0.00% Druze
  • 0.00% Japanese
  • 0.00% Mandenka
  • 0.00% Mozabite
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5 comments on “More analyses of the Mal’ta and Afontova Gora genomes
  1. […] analyses showed that Afontova Gora 2, like Mal’ta 1, had a large amount of the Gedrosia autosomal […]

  2. Great analysis.
    However, I do have some critical remarks. The idea that R1a Eastern Europeans differ from R1b Western Europeans because of stronger admixture from I people in the former is just an attempt to explain, not a very convincing one IMHO. According to Andreas Vonderach (Anthropologie Europas) the eastern European hunter-gatherers were more leptomorphic than the western European ones. See this Mesolithic hunter-gatherer from Latvia, for instance:
    It was also mentioned by Carleton Coon that Bronze Age Estonians were very long faced, with a nose of great height, while at the same time also having wide (UP-like) absolute lateral measurements. The upper facial index of Coon’s sample was 54.5, the facial index 92.2, so definitely leptomorphic. Although the bizygomatic diameter was 140.2 mm, very robust.
    Already the Boat Axe people of Estonia had a similarly high upper facial index of 54.7.
    But the pattern cannot be generalized, since more to the South, in the North Pontic region, the hunter-gatherers of the Dnepr-Donets culture were eurymorphic, while the later Yamnaya culture there attained mesomorphic means, likely because of West Asian and Early Farmer admixture. And more to the northeast, the Comb Ceramic hunter-gatherers also had low facial indices. So at least we can say that the Baltic region was a nucleus of leptomorphic hunter-gatherers, and clearly not because of R1b-people.
    Furthermore you have to take into account that Western Europeans also have a stronger Mediterranean/Early Farmer admixture than Eastern Europeans. This indubitably increased their leptomorphy in Neolithic times.

  3. Well, thinking about it, my above reasoning doesn’t contradict your idea that R1a people have more autosomal admixture from I people. It only contradicts your suggestion that leptomorphic Nordids were originally R1b, while I people were always eurymorphic. Definitely, this isn’t true.
    But R1a may have originated in the West Asian highlands. Now you’ll surely object that R1a people are only mildly West Asian/Caucasus admixed, and much more strongly North European. True, but this doesn’t rule out a West Asian origin of R1a. Because, consider this: Haplogroup N1c clearly has a North Siberian/Mongoloid origin, but this original autosomal profile is strongly diluted in Finns and Baltic people, although N1c is very common in them. Lithuanians are 42% N, and only 1.3% Siberian in Dodecad K7b. Finns are 61.5% N, and only 8.8% Siberian in Dodecad K7b. In the Globe13 analysis the respective Siberian component is even lower. And there is no reason why a similarly strong autosomal dilution shouldn’t have happened in the spread of R1a. So, the North European component in Eastern Europe may originally stem entirely from I people. N1c people brought Finno-Ugrian languages and Siberian admixture. R1a people brought Indo-European languages and West Asian/Caucasus admixture.

  4. I’ve had some fresh thoughts regarding the Gedrosia component. I think it isn’t correct to treat it like something completely independent from the Caucasus component. As the table of Fst divergences shows, the Caucasus component is the closest relative of the Gedrosia component:

    And accordingly, if we had to replace the Gedrosia component with other K12b components, the result would be almost entirely Caucasus:

    In that same diagram we also see that the Caucasus component is similar to a mixture consisting mostly of Atlantic_Med + Gedrosia.

    And in these diagrams, which analyse the K12b components in terms of K7b components and vice versa, we see that Gedrosia is almost entirely West_Asian. While Caucasus is a blend of predominantly West_Asian + Southern, perfectly in line with my above mentioned observations:

    So, it seems like Gedrosia is the purer, original West_Asian component, while the Caucasus component is a blend of an ancient Southern population layer with a Gedrosia-like population layer that arrived later. We have already seen in ancient DNA specimens displaying some Caucasus admixture but having 0% West_Asian admixture.

    The ADMIXTURE analysis in the recent Lazaridis et al. paper confirms my observations: The light green component that appears at K=15 corresponds to the general West_Asian component. It’s somewhat stronger in Pakistan than in the Caucasus, especially at higher Ks, like K=17 or 18. In the Caucasus it amounts only to about half of the autosomal composition, the other half being southern and northern West Eurasian. While in Pakistan it’s closer to the whole, especially in the Kalash. And finally, at K=20, a separate Kalash component appears, which corresponds to the MDLP World-22 Indo-Iranian component. And this is present in Europe at trace levels where the Gedrosia component is strong. I interpret that as a special Kalash-relatedness in addition to the already Kalash-like general West_Asian component.

    In any case, if the Caucasus component only became West_Asian because of Gedrosia-like admixture, it’s possible that the Gedrosia component entered Europe via Western Asia, without bearing any additional Caucasus admixture – if it did so at a sufficiently early date, when it still was the main West_Asian component in westernmost Asia.

    As for the associated R1b, that Eupedia map is also interesting, it shows the distribution of R1b-L23 down to L11*, including the related Z2103, the sister clade of L51:

    I can’t help thinking of a West Asian origin, looking at it.
    Perhaps really from the Iranian plateau, as Grugni et al. 2012 suggested, because of the high variance of the R1b-M269* chromosomes there.

    You said a West Asian origin is ruled out because of the Basques who have lots of R1b and no West_Asian admixture. But as I noted in another comment, the Basques are autosomally less like the original R1b people than the northwestern Europeans are. The Basques’ autosomal ancestry from R1b people has got more diluted. And northwestern Europeans do have some West Asian admixture. Moreover 0% of a component in ADMIXTURE doesn’t necessarily mean that the population in question doesn’t have any ancestry from that component. It just denotes a relative minimum, compared to the other populations. In fact, in the Lazaridis et al. ADMIXTURE analysis, the Basques do have some slight admixture from the light green component.

    Now, how and when did R1b, Gedrosia and the associated Indo-Europeans first enter Europe? I think the Baden culture of the 4th millennium BC is a likely candidate. According to the archeologist Alexander Häusler it had strong relationships with eastern Anatolia, which even make some immigration likely. And this is also confirmed by the craniometrical analysis by Zsuzsanna Zoffmann:
    „According to the Penrose analysis, a new, alien population
    arrived in the Carpathian Basin after the Middle Copper
    Age, which is in harmony with the archaeological data. The
    Late Copper Age population, the so-called Baden population
    (its related cultures were the Kostolac in the South and the
    Cotofeni in Transylvania) had strong southern/south-eastern
    components according to the Penrose contacts, which is
    again in harmony with archaeological theories. The animal
    breeding populational groups flooded the whole of the
    Carpathian Basin, while the cultivating (archaeologically
    latent?) autochtonous populations seem to have survived the

    R1b-L11 has an age of roughly 6000 years, so it may have been brought to Europe by the Baden people, and subsequent mutations occured in Europe itself.

    If we look for a local substrate of the eastern Bell Beaker people in Austria and Moravia, and knowingly exclude the Corded Ware, because it belonged to a different complex, we find, immediately preceding, the Jevisovice culture, also known as Mödling-Zöbing, and this was a blend of the local Funnel Beaker group and the Baden culture.
    Accordingly, on the map of the MDLP Indo-Iranian component, we can see a pocket of elevated presence of this component in Austria, the Czech republic, Slovakia, Slovenia and Hungary. I think it’s very likely that this is the relic of the staging point which the Indo-Iranian component had held before expanding to western Europe. As I said before, the cranial „type fossil“ of the eastern Bell Beaker people, and indeed of much of the Bell Beaker people, was Dinaroid. First of all this would fit with an (at least partly) West Asian origin, and secondly it’s interesting to note that Austria, the Czech republic, Slovakia, Slovenia and Hungary are still quite Dinarid (and light pigmented, Norid) today.

  5. […] associates give the name “Ancient North Eurasians” to Y haplogroup QR Caucasoids like Mal’ta 1 and Afontova Gora 2, which is idiotic. Y hg NO Mongoloids were also “Ancient North Eurasians”, but they […]

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