Saturday, January 8, 2011

ADMIXTURE analysis with Dodecad Populations (update #2)

Thanks to all the participants of the Project, the number of populations has increased, and so have sample sizes within pre-existing populations in the Project. There are now 17 populations with at least 5 individuals in the Project:
Assyrian, Scandinavian, Greek, Finnish, S_Italian_Sicilian, Ashkenazi, German, Indian, Portuguese, Armenian, Russian, Spanish, British, Irish, Turkish, N_Italian, Balkans
Below are the K=10 ADMIXTURE results with these populations:

Admixture proportions can be found in the spreadsheet.

The fact that the addition of 17 populations and 143 individuals to the core set of 36 populations and 692 individuals results in the same 10 ancestral components testifies to the stability of this solution. Hopefully, within 2011 I will develop an even better comparison set to work with.

Another test of the validity of the analysis is comparison of independent samples of the same populations:
Ashkenazi, Armenian, Spanish, Turkish, N_Italian
I have a sample of Dodecad Project members for each of the above, as well as a published population. A way to measure the concordance between the two is to calculate the correlation coefficient (rounded to the 3rd decimal point):
  • Ashkenazi Jews: 0.999
  • Armenians: 0.988
  • Spanish: 0.998
  • Turkish: 0.995
  • N_Italian: 0.996
The concordance is remarkable.

I have also made a RAR of "population portraits". It is important to do this to determine whether minor ancestral components represent population-wide phenomena or are limited to a few individuals.

For example, here are the Turks of the Dodecad project:
The sample is a bit more varied than the sample included in Behar et al:
This probably underscores the importance of broad coverage of large countries and ethnic groups, as I have discovered recently in my analysis of 9 different populations of Pakistan.

Another new population are the Irish, presenting a picture of remarkable homogeneity:
Here is the population portrait for the Balkans, which consists of non-Greek, non-Roma inhabitants of the Balkans:
This appears quite varied; hopefully more Balkan project participants will allow me to split this into additional sample populations.

Finally, here is a portrait of the Ashkenazi population, which appears quite similar to the Behar et al. one:
A very interesting thing about this population is the existence of small slices of "East Asian" and "Northeast Asian" components totalling about 1.5% in almost all individuals. In my opinion this testifies to some type of old minor absorption, as it is fairly evenly spread in the population.

If you haven't joined the project yet, feel free to submit your sample during this opportunity.

35 comments:

  1. I've quietly followed your work for quite some time and greatly appreciate how you've made so much available to the general public.

    As for my 23andMe results, I unfortunately have grandparents with different ancestries. I am looking forward to the day that you allow a general download, of those like me, to help reveal the variety of derivations of my DNA.

    Steven Colson

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  2. Can you also do this with ftdna info or does it have to be 23andme?

    Btw, I really appreciate what you are doing

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  3. The Dodecad Turks are clearly more compatible with the totality of Turks tested by 23andMe than the Behar et al. Turks are (there are many ethnic Turks with no Mongoloid component in 23andMe), so the Dodecad Turks are more representative of Turks than the Behar et al. Turks are. Ashraf once speculated that the Behar et al. Turks were completely chosen from the Anatolian Turkmens (a minority group among the Anatolian Turks; they are traditionally seen as the purest subset of Anatolian Turks in terms of genetic Turkicness). Maybe his speculation has some truth. I also wonder geographical differences among Turks BTW.

    As to the Dodecad Armenians, they are also more representative of Armenians than the Behar et al. Armenians are, as, unlike the Behar et al. Armenians, there are apparently no mixed Armenians among the Dodecad Armenians. There were at least three mixed (probably with Russians) Armenians among the Behar et al. Armenians. It seems that non-mixed Armenians have no or almost no North European component.

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  4. Thanks Mr.D

    I can see where I would slot into the group portrait of the South Italians_Sicilians even though I am not one of them. Nice to see some differences with the Ashkenazim Jews who always overlap with South Italians_Sicilians on MDS plots.

    Steven, some ethnic groups like mine are not recently mixed, all my ancestors back more than 17 generations come from the same place and ethnic group but they are rather dna testing shy. So are most SE European ethnic groups which is why Dienekes has a composite Balkan group.

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  5. May I ask if the Balkan participants are DOD007, DOD009, DOD013, DOD025 and DOD079?
    No wonder they look diverse, you can't compare Slovenians with Bulgarians, although classified as South Slavs.
    According to me there must be the following main clusters on the Balkans -
    1. Slovenians, Croats, some Serbs and Romanians with Hungarian and/or German input.
    2. Bulgarians, Serbs and real Vlachs(who used to live South and East of the Carpathian mts)
    3. Macedonians, Albanians, some South Bulgarians and real Continental Greeks (not admixed with Anatolians)
    Here is to say the separation may not be distinct at state and even ethnic borders due to constant population movements and political divisions in recent history.

    Eastara

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  6. The Dodecad Turks are clearly more compatible with the totality of Turks tested by 23andMe than the Behar et al. Turks are (there are many ethnic Turks with no Mongoloid component in 23andMe), so the Dodecad Turks are more representative of Turks than the Behar et al. Turks are.

    I doubt that the Dodecad Project Turks are representative of anything at this point, due to the small sample size.

    As for the "no Mongoloid component", the two Turks in my project who have almost none of it are from a very specific area of Turkey.

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  7. I too have been following your work with interest for some months now. I hope this submission period remains open until 23andMe's V3 chip results are released. I'd probably be the first fully Cypriot Turk (or as close to fully as one is likely to get) to participate.

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  8. I too have been following your work with interest for some months now. I hope this submission period remains open until 23andMe's V3 chip results are released. I'd probably be the first fully Cypriot Turk (or as close to fully as one is likely to get) to participate.

    I don't know how long it will be kept open, but you can always contact me in the meantime to see if I can process your sample; time allowing I usually accept data from populations that might interest me and that are unknown in the literature.

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  9. I haven't tested my autosomal DNA before so unfortunately don't have any data to send at the moment. I'll make sure to contact you when my results come through (probably within the next few weeks) though.

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  10. Dieneke, are all the Dodecad Turks unadmixed (in the known past) Turks? I guess you didn't include admixed Turks like Basar (DOD049, who is half Laz) in this analysis.

    I doubt that the Dodecad Project Turks are representative of anything at this point, due to the small sample size.

    Yes, but the results of the Dodecad Turks are clearly more compatible with the results of the totality of Turks who have been tested by 23andMe. That is why I said that the Dodecad Turks are more representative of Turks than the Behar et al. Turks are, as there are many more Turks tested by 23andMe than the Behar et al. Turks, who are just 19 people.

    As for the "no Mongoloid component", the two Turks in my project who have almost none of it are from a very specific area of Turkey.

    Are the 0% Mongoloid Turks from the same area of Turkey with Basar (eastern Black Sea coast)? I ask this because Basar's Turkish side clearly has no Mongoloid component.

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  11. I don't comment on individual samples.
    Also, you are in no position of comparing my analysis with "all Turks who have been tested by 23andMe" both because (a) you don't know all Turks who have been tested by 23andMe, and (b) 23andMe's ancestry analysis is not the same as my own.

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  12. Thank you (and Paul C) SO much for including the Irish, it is a remarkable result and as I have suspected! Hope more sign up to beef up the sampling.
    (Next time you run your charts, could you group together the peoples most alike in genetic makeup? Likeness comparison side by side is interesting, too)
    mm

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  13. I don't comment on individual samples.

    Then let me ask you a less private question: do you always choose samples for your Dodecad populations from the reportedly unadmixed samples from the respective source population? If yes, for instance, you don't include Basar among the Dodecad Turks, as he is reportedly half Laz.

    Also, you are in no position of comparing my analysis with "all Turks who have been tested by 23andMe" both because (a) you don't know all Turks who have been tested by 23andMe, and (b) 23andMe's ancestry analysis is not the same as my own.

    (a) I was informed personally by a 23andMe participant who knows the results of many of the Turkish participants of 23andMe and is in a position to come to general conclusions about them.

    (b) In the 23andMe ancestry analysis the "South Asian" cluster of your analysis is consumed by the "European" and "Asian" clusters of 23andMe ancestry analysis, but this difference has almost no effect in the inferred quantity of Caucasoidness and Mongoloidness for Turks. So a Turk analyzed by both 23andMe and you gets the same or almost the same inferred quantity of Caucasoidness and Mongoloidness in your analysis as in the 23andMe ancestry analysis.

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  14. I was informed personally by a 23andMe participant

    That 23andMe participant is a Turk BTW.

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  15. Then let me ask you a less private question: do you always choose samples for your Dodecad populations from the reportedly unadmixed samples from the respective source population? If yes, for instance, you don't include Basar among the Dodecad Turks, as he is reportedly half Laz.

    "Turks" in the context of the Project refers to citizens of Turkey and/or Turkish-occupied Cyprus who do not profess that they are not Turks.

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  16. who do not profess that they are not Turks.

    At least partially, or only fully?

    BTW, I would also include Turks who are citizens of the Balkan countries, if there are any among your samples, in the Dodecad Turks for consistency, as there are many Balkan Turk descendants (partially or fully) among the citizens of Turkey.

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  17. BTW, I would also include Turks who are citizens of the Balkan countries, if there are any among your samples, in the Dodecad Turks for consistency, as there are many Balkan Turk descendants (partially or fully) among the citizens of Turkey.

    If any Turks from the Balkans join the Project, I will be happy to include them.

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  18. Dieneke, you didn't answer my question:

    "at least partially, or only fully?"

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  19. How to explain Armenians who spoke one of the most archaic IE languages do lack the north European component very present amongst European IE sepaking populations!?

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  20. There is good evidence that (linguistically at least) Armenians came from the Balkans. So, even if the Armenian-speaking minority admixed with a much larger native population, we would expect to see some of the "NE" component.

    Even Turks and Iranians have some of the "NE" component. So, its lack in Armenians is quite interesting and difficult to interpret.

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  21. Even Turks and Iranians have some of the "NE" component.

    In the case of Turks, most of the "North European" component should be from the natives of Asia Minor (Anatolian Greeks if not Armenians) and the Balkans, as Mongoloid components of Turks are small compared to the their "North European" component, unlike Central Asian Turkics. As to the people of Iran, I think the people of western Iran lack or almost lack the "North European" component like Arabs, Armenians, Assyrians and Cypriots, while those in the east of Iran have it in amounts intermediate between the people of Western Iran and Central Asian Iranics.

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  22. BTW, only 4 of the 20 Georgians of Behar et al. have the "North European" component and in unusually high amounts and together with unusual Mongoloid components. So, like the 4 Armenians of Behar et al. with the "North European" component, those 4 Georgians with the "North European" component are very probably Russian-admixed. Thus non-admixed Georgians too seem to lack the "North European" component.

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  23. I think the absence of north european component and its scarcity amongst anatolians (very probably by 2000 bc the north european component amongst anatolians was tiny if not 0) is a clue about the "western asian component" being an "autosomal marker" of proto indo-hittite/pre-proto indo-european.
    The Armenian language is according to Gamkrelidze&Ivanonv, native to eastern Anatolia, as its shown by hurric,luwian and hittite loanwords into ancient Armenian.
    http://rbedrosian.com/Classic/sciam1.htm
    http://armenianlanguage.org/etymology/etymology.html

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  24. Both historical evidence and linguistics links Armenian to Phrygian and Greek. THe Anatolian languages however are not particularly close to either Greek or Armenian. The simplest explanation for this is that the linguistic ancestors of the Armenians went east, just as the tradition holds.

    I don't see what is your argument about the loanwords, as one would expect precisely such loanwords to be found in a language that went from the Balkans to eastern Anatolia.

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  26. I think the "North European" component itself is relatively young and is connected with the relatively recent (probably post-agriculture) spread of intensive depigmentation now common in northern Europe. West Asia was densely populated since the Neolithic, so the "North European" component hasn't managed to spread in any notable degree beyond the mountain chains and rivers separating the Anatolian peninsula from the Armenian Highlands, Transcaucasia, Mesopotamia and Greater Syria, the deserts and mountain chains separating eastern Iran from western Iran and the mountain chains separating Transcaucasia from the rest of the Caucasus.

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  27. When The Armenians were first attested the Anatolian languages were already extinct that's why the fact that Armenian has Hittite loanwords is very important.
    I think you may be not aware of Gamkrelidze&Ivanonv's book "indo-europeans and indo-european languages" in that book the authors propose(with proofs)an eastern anatolian origin for "proto Greco-Armeno-Indo-Iranian" based upon semitic and kartvelian loanwords peculiar to greek-armenia-aryan as well as many other arguments I could not post it here.

    "The separation of Proto-Anatolian from Proto-Indo-European was followed by
    the separation of the Greek-Armenian-Aryan dialect grouping, which subsequently
    divided into Greek, Armenian, and Indo-Iranian. The widespread migrations of the tribes making up this dialect community evidently began after
    its breakup and the creation of Greek, Proto-Armenian, and Indo-Iranian as individual Indo-European dialects. This breakup evidently began when the dialect grouping was still part of Proto-Indo-European, with the formation of a
    separate Aryan dialect area while Greek-Armenian dialect unity was still preserved."

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  28. PIE * phelekhu- 'poleaxe, axe' : Sem. *p-I-k ' split apart; axe ' : Akkad.pilaku 'axe', pulluku 'kill with an axe)', Syr. pelka 'axe ',
    Mand. pfna ' axe' , Arab. falaha ' split apart':
    (The word has an unusual root structure not typical of native IndoEuropean forms) The Semitic word entered the Greek-Armenian-Aryan
    dialect group and subsequently underwent regular development in these dialects,showing the characteristic satem reflex of palatal *kh in Indo-Iranian.
    PIE *Handh- 'edible plant' (Skt. andha- 'plant from which soma was made',Gk. anthos 'flower', anthinon 'vegetable food, lotus', Arm. and 'field ') :Sem. *Hint-(at-) 'wheat, grains' (): Ugar. /htt 'wheat', Akkad. (Babyl.)hetu 'barley grain', (Assyr.) uhutu
    'grain crops; grain', Arab. Hinta 'wheat', S.Arab. (Soqotri) /hinteh, (Mehri) 'wheat'
    The Indo-European word is restricted to the GreekArmenian-Aryan dialect area and testifies to contact between this dialect group and the Semitic linguistic world in some part of the Near East
    we can see the ancient presence of the Greeks in Miletus and Ahhiyawa as a relic of these early
    migrations. Support for this comes from links observed between the cultures of western Asia Minor and those of the Peloponnesus and the Aegean islands. Minyan gray ware pottery is found through northwest Asia Minor Beycesultan). It is the same type that becomes the dominant ware in mainland Greece about a century later (ca. 1 900 B.c.). A direct connection has been established between these cultures, and the direction of movement is assumed to have been from east to west (Mellaart Lloyd )
    The ethnic substratum of these cultures would have been the Proto-Hellenic Greeks (minus the Dorians),or possibly other groups of lndo-Europeans moving westward1 with the Greeks under pressure from the Anatolian tribes.
    The historical presence of the Greeks in Asia Minor after the breakup of Greek-Armenian-Aryan dialect unity is reflected in numerous lexical and culturehistorical connections between Greek and the linguistic world of Asia Minor.
    Traces of these connections can be seen in lexical loans and in shared mythological and ritual themes that arose at a time when Greek already existed as a separate language
    Phrygian and its relation to the Greek-Armenian-Aryan dialect community Phrygian is known to us from a few inscriptions of the first half of the first millennium B.c., found in Asia Minor. It shows structural traits that link it with the dialects of the Greek-Armenian-Aryan area....Balkan culture in the fifth to fourth millennia B.C. and its connection with Asia Minor (çatal Hüyük)A Near Eastern homeland for Proto-Indo-European requires relatively little
    movement of Proto-Armenian, which remained in Asia Minor where it could have come into contact with the Anatolian linguistic world. From there the Proto-Armenians spread to historical Armenia and overlaid a Hurrian-Urartean substratum (see Diakonoff).
    Contacts of Proto-Armenian with Hittite and Luwian are confirmed by a number of Armenian borrowings from the Anatolian languages.

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  29. Ashraf,

    I think you are correct as far as linguistic affinity of Greek - Phrygian/Armenian - Indo-Aryan, however I think you are wrong as regards where they were located.
    The Indo-European homeland is most likely the area just North of the Caucasus, and Semitic influences spread North to that area probably via the Kura-Araxes Culture - together with Y-DNA J1, which swamped the local R1b lineages. The Greek language could have arrived with the Dorians from the North of modern Greece, followed later by the Phyrigian into the Balkans, and later still East to Armenia. The Indo-Aryans spread West, with at least one group heading due South into Eastern Anatolia, to become the Mitanni.
    Of course the Mitanni could just be a military elite which were once mercenaries - due to their horsemanship and/or knowledge of the war chariot - just like the Mamelukes were millennia later in Egypt, and coincidentally from the exact same area as the Mitanni probably were from.

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  30. BTW, I'm suggesting that if the Dorians brought Greek to Greece, it was a case of elite dominance - like that of Magyars in Hungary.

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  31. The Balkans should not be lumped together. scientifically it looks very shabby and lazy.

    We all know that the Balkans is a big genetic melting pot that is so diverse and heterogeneous.

    I can see that this has been commented on before but neither Dienekes or the Dodecad Project has responded.

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  32. Interesting to note that the Germans and British are essentially identical.

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  33. BTW, I'm suggesting that if the Dorians brought Greek to Greece, it was a case of elite dominance - like that of Magyars in Hungary.

    Dorians did not bring Greek to Greece, because (a) Dorian is a dialect of Greek, (b) there were definitely Greeks (=the Mycenaeans) in southern Greece before the Dorians, (c) there is no evidence whatsoever that the Dorians came to Greece.

    The Balkans should not be lumped together. scientifically it looks very shabby and lazy.

    They are lumped together because none of the Balkan sub-groups has reached the 5-person mark. It's better to lump them together than have a big hole on the European map with no data.

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  34. "The Indo-European homeland is most likely the area just North of the Caucasus"
    I agree, however the ancestral Indo-Hittite homeland is most likely situated in eastern Anatolia, as for why?Please read the 4 threads below (in a nutshell, pontic steppes were lowly populated after LGM and were populated by migrants from overcrowded agricultural and pastoral western asia+the absence of north european component amongst anatolians who descend from most archaic IE folks[anatolian branch]+the fact that north european component having,western asian component lacking Basques are not IE speaking+the fact that mythology+social norms of early IE's is similat to other western asian civilizations+egyptian and sumerian loans into PIH+Hurrian having a heavy IE element.

    pih homeland
    http://anthrocivitas.net/forum/showthread.php?p=86523#post86523

    toponomy of pie
    http://anthrocivitas.net/forum/showthread.php?t=10202&page=3

    social norms of pie speakers
    http://anthrocivitas.net/forum/showthread.php?t=10188


    ie elements in hurrian
    www.nostratic.ru/books/(432)bomhard-hurrian.pdf

    diffusion of ie's
    http://anthrocivitas.net/forum/showthread.php?p=105442

    About the mythological and cultural parallels between early IE's and other western asian myths and cultural elements you may read "indo-europeans and indo-european languages" book

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  35. I think you are correct as far as linguistic affinity of Greek - Phrygian/Armenian - Indo-Aryan, however I think you are wrong as regards where they were located.

    The Greek language could have arrived with the Dorians from the North of modern Greece, followed later by the Phyrigian into the Balkans, and later still East to Armenia.


    Conroy, you are writing as if Phrygian and Armenian are the same language, did I understand you right? They clearly are not the same language, but they may be from the same subgroup of languages within the Indo-European language family together with some other IE languages like Greek and Indo-Iranian.

    As to Dorians and the Greek language, I agree with Dienekes/Dodecad Project.

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