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Thread: Dienekes' Anthropology (Genetics) and Dodecad Project Thread

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    Dienekes' Anthropology (Genetics) and Dodecad Project Thread

    fastIBD analysis of several Jewish and non-Jewish groups

    Dienekes:
    fastIBD identifies segments of relatively recent origin that are shared by individuals. These results should not be construed as measures of overall genetic similarity or origins. Rather, they suggest which populations have exchanged genes in the relative recent past, say, the last two thousand years or so.
    A note from Dienekes, from a previous fastIBD run:

    Remember that the tree groups similar populations together, and for each row in the matrix, the red end of the spectrum indicates lots of IBD sharing, and the blue end low IBD sharing.
    My neck of the woods, with my group in red, below, with names of populations added (disregard the colors to the immediate right of the population names). The full heatmap can be found here, on Dienekes' site.


     
    Last edited by Humanist; 08-08-2012 at 07:28 PM.

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    I did a double-take initially at seeing the Iranian pairing with Syrians on the fastIBS heatmap.

    As we've discussed before elsewhere, the Behar Iranian cohort generally exhibits greater Southwest Asian ADMIXTURE component values than Dodecad or Eurogenes Iranians, as well as significant (>2%, greater than 10% in some samples) African admixture (refer to Zack Ajmal's Harappa Project coverage). These results are consistent with their origins somewhere further south, such as Khuzestan, Hormozgan and other Persian Gulf provinces in Iran.

    As Syrians also present values of that quality, it isn't actually too surprising to see the Behar Iranians pairing with them instead of Kurds, Anatolian Turks or even Armenians.

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    Dienekes has posted a slew of fastIBD analyses for his participants:



    As demonstrated in the second entry, the cM values in and of themselves are not particularly useful, given regional shared ancestries (i.e. West vs. East Eurasian) dictate the overall picture. Comparative analysis of the results, be it between individuals or population averages, will give us a much better indication of the demic processes that took place in each.

    For example, the Dodecad Iranians compared with the Yunusbayev et al. Kurds (Spoiler below) presents us with the following:

    1. The Yunusbayev Kurds are a textbook example of a bottleneck effect through their high intra-population IBD sharing, which matches the historical context to which they were forced into Central Asia by Persia's Qajar dynasty.
    2. Moreover, their ancestral connection to East Anatolia has been preserved by uniformly higher IBD sharing with Anatolian Turks compared with the Dodecad Iranian average.
    3. Additionally the Dodecad Iranians have slightly larger IBD sharing values with the Turkmen and Uzbeks, in line with geography.
    4. Intriguingly, both Dodecad Iranians and Kurds have equivalent IBD scores with North-Central Asian/Siberian populations (i.e. Selkup, Altai, Yukaghir) but the Dodecad Iranians match East Asian proper populations better (i.e. Chinese_D, Cambodians, Daur)
    5. Otherwise, both Kurds and Iranians are comparable with one another implying (at the very least) both populations stem from the same West Asian population that underwent similar demic phenomena over the millennia






     

    Code:
    		Iranian_D	Kurds_Y
    Altai		5		4.5
    Balkars_Y	17.9		18.5
    Belorussian	14.2		13.6
    Buryat		3.2		2.7
    Cambodians	1.7		1.1
    CDX30		0.7		0.9
    CHB30		0.8		0.7
    CHD30		0.7		0.6
    Chinese_D	1.1		0.9
    Chukchi_11	1.2		0.7
    Chuvashs	10.6		12.1
    Dai		0.9		0.7
    Daur		2.1		1.4
    Dolgan		3.7		4
    Evenk_15	2.3		2
    FIN30		11.8		12.3
    Finnish_D	11.5		12.5
    Han		0.8		0.7
    Hazara		8.4		9.7
    Hezhen		1.7		0.9
    Iranian_D	20.1		20.9
    Japanese	0.9		0.7
    Japanese_D	0.6		0.3
    JPT30		0.8		0.5
    KHV30		1.2		0.7
    Korean_D	0.7		0.7
    Koryak_15	0.8		1
    Kumyks_Y	17.2		19.4
    Kurds_Y		20.9		84.1
    Kyrgyz_Bishkek	5		5.1
    Miaozu		0.7		0.5
    Mongol		4		3.5
    Mongola		2		2.2
    Mordovians_Y	12.7		12.9
    Naxi		1.1		0.7
    Nganassan_12	2.1		1.3
    Nogais_Y	14		14.3
    Oroqen		1.3		1
    Russian		12.9		13.3
    Russian_D	13.3		13.9
    Selkup		4.7		5.1
    She		1.1		0.4
    Tu		2.1		1.6
    Tujia		1		0.6
    Turkish_Aydin	16		17.1
    Turkish_Cypriot	17.7		19.9
    Turkish_D	17.8		21.2
    Turkish_Istanbu	18.1		21.4
    Turkish_Kayseri	17.5		21.4
    Turkmens_Y	16.5		15.4
    Turks		17.8		20.9
    Tuva		3.5		2.9
    Ukrainian_D	14.7		13.8
    Ukranians_Y	14.4		14
    Uygur		8.9		8.6
    Uzbeks		10.4		9.5
    Xibo		2.4		2
    Yakut		2.5		2.4
    Yizu		0.9		0.6
    Yukagir		4.8		5.2


    This is, however, in the context of overall ethnic/national ancestry and individual results must be considered. My own values (greater matching of Ukrainians, Kurds, Turkmen, Uzbeks specifically) match features of my background that seem to differentiate me from the average Iranian.
    Last edited by DMXX; 08-17-2012 at 03:52 PM. Reason: Thread merge

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    Dienekes may have picked up the ancient ''Amerindian'' component in ADMIXTURE at K=4 that Patterson et al. (2012) recently found in modern Europeans.

    http://dodecad.blogspot.ca/2012/10/g...alculator.html

    http://dienekes.blogspot.ca/2012/10/...ment-with.html


    Here are my own results from the 'globe4' calculator.

    90.08% European
    1.13% Asian
    0.22% African
    8.57% Amerindian

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    Quote Originally Posted by J Man View Post
    Dienekes may have picked up the ancient ''Amerindian'' component in ADMIXTURE at K=4 that Patterson et al. (2012) recently found in modern Europeans.

    http://dodecad.blogspot.ca/2012/10/g...alculator.html

    http://dienekes.blogspot.ca/2012/10/...ment-with.html


    Here are my own results from the 'globe4' calculator.

    90.08% European
    1.13% Asian
    0.22% African
    8.57% Amerindian
    Strangely I end up more European than you (though also more Asian and African). Perhaps this Amerindian in part reflects your Finnish heritage?

    92.46% European
    1.56% Asian
    0.63% African
    5.36% Amerindian

    In any case, my guess is globe4 is probably not the best measure for Near Eastern ancestry.
     

    Hidden Content
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    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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    New results from Dienekes' globe10 calculator, which is an extension of globe4 and designed to pick up the Amerindian-type subset of Europeans.

    My results, shown in conjunction with relevant related populations:

    Code:
    		Humata	Irn_D	Irn(S?)	Kurd_D	Kurds_Y
    Amerindian	0.2	0.4	0.6	0.8	0.6
    West Asian	52.2	55	55.5	56.3	56.3
    Australasian	0.5	0.2	0.3	0.3	0.3
    Paleo-African	0	0	0.2	0.1	0.1
    Neo-African	0.4	0.3	1.1	0	0
    Siberian	2.9	2.4	0.8	1	0.5
    Southern	22.4	24.1	25.2	26.8	25.7
    East Asian	1.7	0.7	0.4	0.4	0.4
    Atlantic-Baltic	12.2	10.1	7.6	9.4	11
    South Asian	7.6	6.9	8.4	5	5
    Same trends as usual; less SW/Asian and W Asian, more South Asian, Siberian+East Asian and Atlantic-Baltic/N Euro than the average Iranian cohort.

    One interesting observation is that, component wise in this run, I'd be almost parallel with the Pathans of Pakistan if the Southern and S Asian values were swapped round. Reminds me of Dienekes' old post concerning the Indo-Iranian impact in that broader region.

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    Mine:

    0.52 Amerindian
    15.96 West Asian
    0.02 Australasian
    0.00 Palaeo-African
    0.27 Neo-African
    1.57 Siberian
    23.35 Southern
    0.04 East Asian
    56.90 Atlantic-Baltic
    1.36 South Asian

    Most similar to Bulgarians, North Italians, Tuscans.
     

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    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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    Is the Siberian signal one you've noticed before, AJL?

    It seems West Eurasians generally have Siberian > East Asian. Likely due to continuous interactions between West Eurasia<->Siberia.

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    Quote Originally Posted by Humata View Post
    Is the Siberian signal one you've noticed before, AJL?

    It seems West Eurasians generally have Siberian > East Asian. Likely due to continuous interactions between West Eurasia<->Siberia.
    Yes, in my case it seems to be coming from both my paternal and maternal sides, though more so from my father. I have an 8-cM segment with a Kazakh guy from my father's mother's side, probably attached to her grandfather's line from Syria.

    On my mother's side, my HLA factors are most common among Swedish Saami, and she has a little Asian in her Ancestry Painting that probably reflects this northern component. I can't entirely rule out some remote Native American ancestry for her from before 1800, but she is still within normal ranges for someone with ancestry from Northern Europe.
     

    Hidden Content
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    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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  16. #10
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    Quote Originally Posted by AJL View Post
    Strangely I end up more European than you (though also more Asian and African). Perhaps this Amerindian in part reflects your Finnish heritage?

    92.46% European
    1.56% Asian
    0.63% African
    5.36% Amerindian

    In any case, my guess is globe4 is probably not the best measure for Near Eastern ancestry.

    Yes my higher Amerindian comes from the fact that I have some recent Finnish ancestry I believe. Here are my 'globe10' scores below.

    1.59% Amerindian
    13.18% West_Asian
    0.61% Australasian
    0.16% Palaeo_African
    0.11% Neo_African
    2.55% Siberian
    12.86% Southern
    0.10% East_Asian
    68.13% Atlantic_Baltic
    0.73% South_Asian


    I wonder if the Amerindian score is noise?

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