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Thread: DMXX's Geno 2.0 Results

  1. #21
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    Based on your mixed Bengali/Iranian/Central Asian background, I'd assume most calculators will have northwest South Asian populations as your closest matches, despite you not having any recent ancestry from the region. Do you get the Bene Menashe Jews (also known as Bene Isreal Jews on some calculators, which I think is the correct designation) a lot? I'd imagine so, since they're a South Asian population with very substantial West Asian-Southwest Asian admixture, and they cluster with the HGDP Pakistani populations on PCA plots, rather than with neighboring Indian populations. Most calculators have the HGDP Pashtuns as my closest population, unless the Kalash are included, in which case they tend to be the closest. The Burusho, Baloch, Brahui, Punjabi Jatts, Sindhis, and Tajiks tend to follow, in that approximate order. Then I get various North Indian and West Asian populations. Just out of curiosity, which Dodecad calculator did you use?

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  3. #22
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    India Pakistan Bangladesh United States of America
    I get the following

    Dodecad K12b

    # Population (source) Distance
    1 Bnei_Menashe_Jews (Behar) 9.36
    2 Cochin_Jews (Behar) 17.61
    3 Pathan (HGDP) 19.01
    4 Burusho (HGDP) 20
    5 Brahmins_from_Uttar_Pradesh (Metspalu) 21.3
    6 Jatt (Dodecad) 21.61
    7 Brahmins_from_Tamil_Nadu (Metspalu) 23.35
    8 Kshatriya (Metspalu) 23.55
    9 Sindhi (HGDP) 23.82
    10 Indian (Dodecad) 24.4
    11 Iyer (Dodecad) 26.07
    12 Iyengar (Dodecad) 27.2
    13 Tajiks (Yunusbayev) 27.55
    14 Tharus (Metspalu) 27.78
    15 Turkmens (Yunusbayev) 28.22
    16 GIH30 (Dodecad) 29.01
    17 INS30 (SGVP) 29.41
    18 Dharkars (Metspalu) 29.83
    19 Muslim (Metspalu) 29.92
    20 Kanjars (Metspalu) 30.79
    Dodecad K7b

    # Population (source) Distance
    1 Bnei_Menashe_Jews (Behar) 10.17
    2 Burusho (HGDP) 13.41
    3 Pathan (HGDP) 14.27
    4 Sindhi (HGDP) 14.49
    5 Jatt (Dodecad) 15.12
    6 Cochin_Jews (Behar) 16.17
    7 Brahmins_from_Uttar_Pradesh (Metspalu) 18.1
    8 Kshatriya (Metspalu) 20.17
    9 Brahmins_from_Tamil_Nadu (Metspalu) 21.24
    10 Indian (Dodecad) 21.86
    11 Iyengar (Dodecad) 22.52
    12 Iyer (Dodecad) 22.7
    13 Balochi (HGDP) 25.21
    14 Tajiks (Yunusbayev) 25.72
    15 Brahui (HGDP) 26.04
    16 Muslim (Metspalu) 26.22
    17 GIH30 (Dodecad) 26.82
    18 INS30 (SGVP) 26.85
    19 Makrani (HGDP) 26.89
    20 Tharus (Metspalu) 27.14

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  5. #23
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    For comparison, my K12b results:

    Gedrosia=37.66%
    South_Asian=22.67%
    Caucasus=15.42%
    North_European=13.17%
    Southwest_Asian=4.77%
    East_Asian=3.64%
    Siberian=2.45%
    Northwest_African=0.19%
    Atlantic_Med=0.03%

    1 Pathan (HGDP) 7.92
    2 Burusho (HGDP) 10.47
    3 Jatt (Dodecad) 15.18
    4 Tajiks (Yunusbayev) 17.63
    5 Sindhi (HGDP) 19.22
    6 Bnei_Menashe_Jews (Behar) 21.8
    7 Turkmens (Yunusbayev) 23.62
    8 Brahmins_from_Uttar_Pradesh (Metspalu) 23.99
    9 Cochin_Jews (Behar) 26.36
    10 Kshatriya (Metspalu) 27.68
    11 Brahmins_from_Tamil_Nadu (Metspalu) 28.65
    12 Indian (Dodecad) 29.25
    13 Makrani (HGDP) 29.51
    14 Iranians (Behar) 29.95
    15 Balochi (HGDP) 30.61
    16 Iyer (Dodecad) 31.08
    17 Iranian (Dodecad) 31.87
    18 Iyengar (Dodecad) 31.93
    19 Kurd (Dodecad) 33.8
    20 GIH30 (Dodecad) 34.66

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  7. #24
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    A quick update since the original post:

    - Some other mtDNA D4 profiles have been updated. All with known maternal ancestors seem to be either Japanese or Siberian. Not surprising given the great frequency and diversity of D4 in this part of Eurasia. Unfortunately none of these samples appear "close" to mine.

    - No updates on the R2a-M124 result. Will be transferring the raw data to R2 Project for more analysis.

    Quote Originally Posted by Imadaddin Nasimi View Post
    Your results look like to me. I am fully Azerbaijani Turk from Azerbaijan Republic.
    Xoş gəlmişsiniz Imaddin; yes, our results are quite similar. It doesn't look like a coincidence that your NE Asian scores is double mine when I'm half Azeri Iranian. Fairly good chance my father's value will be around yours, though inheritance isn't always a 50-50 affair.

    Quote Originally Posted by Sein
    am a Pashtun, so Afghanistan is basically it (although my family originates from the Pakistani side of the Durand line, but since Pashtuns are a single ethnic group, that isn't necessarily relevant. I have seen the results for two Afghan Pashtun friends, and one of them has results virtually identical to my own). My top population is North Caucasian (Daghestanis, Abkhazians, and other unspecified Caucasian populations), and my second closest population is West Indian (Gujarati). I guess if one averaged these two populations, but with a distinct bias towards the North Caucasian, my location on the map would probably be in Eastern-Central Iran...
    Welcome to the forum, Sein!

    What you've posted is in accordance with the results I've seen from other Pashtuns online; I recall one (Shenandoah?) posted their McDonald BGA, showing them to be on the Iranian-Turkmen border.

    The situation with Pashtuns isn't that dissimilar to the Kurds; despite the current distributions around the Durand Line in Af-Pak and Anatolia-N. Mesopotamia respectively, both genetically plot towards the Iranian plateau.

    Whether or not Pashtuns and Iranic-speaking Iranians display significant DNA segment sharing with each other's an open question. Having said this, one curious observation is the similarity between the two groups in component scores, especially if the Near-Eastern and South-Asian specific autosomal components are set aside. This was an observation Dienekes also made (will post link once located).

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  9. #25
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    Thank you DMXX!

    I have quite a few Iranian relatives at 23andMe. Interestingly, more Iranian matches than Pakistani matches. Perhaps this would apply to other Pashtuns as well? I'd love to see a fastIBD or ChromoPainter analysis of my raw-data, but I'm just too inept to try anything myself .

    I think you've hit the nail right on the head! From a cultural perspective, the Pashtun region is an eastern continuation of Greater Iran, so there might be some very strong and persistent genetic links at play. I think we could go so far as to say that Pashtuns and Iranic-speaking Iranians mutually share a very substantial proportion of their respective genetic ancestries. Although, being at the eastern edge of the Iranian plateau, we have quite a substantial South Asian affinity absent in currently sampled Iranian groups. And originating from the western portion of the plateau, most Iranians have quite a substantial Southwest Asian affinity. Still though, I find it very interesting that one of the factors differentiating Iranians from their western neighbors is a slightly heightened South Asian affinity.

    Although, at Harappa Ancestry Project, there is an Iranian Bandari participant with some very distinctive results, HRP0355. This individual's Oracle results:

    [1,] "pashtun_harappa_3" "12.0071"
    [2,] "turkmen_yunusbayev_11" "16.7545"
    [3,] "iranian_behar_19" "16.7703"
    [4,] "tajik_yunusbayev_15" "17.5877"
    [5,] "kalash_hgdp_23" "17.7843"
    [6,] "pathan_hgdp_23" "18.0283"
    [7,] "iranian_harappa_9" "18.0506"
    [8,] "kurd_harappa_11" "19.4245"
    [9,] "makrani_hgdp_25" "20.5878"
    [10,] "balochi_hgdp_24" "21.0834"
    [11,] "kurd_xing_24" "21.3623"
    [12,] "burusho_hgdp_25" "21.7433"
    [13,] "bhatia_harappa_2" "21.9036"
    [14,] "kurd_yunusbayev_6" "22.3804"
    [15,] "gujarati-muslim_harappa_3" "22.687"
    [16,] "kashmiri_harappa_2" "22.9621"
    [17,] "bene-israel-jew_behar_4" "23.1323"
    [18,] "iraqi-arab_harappa_4" "23.6119"
    [19,] "punjabi-jatt_harappa_8" "23.7947"
    [20,] "sindhi_hgdp_24" "24.4917"
    [21,] "kashmiri-pandit_reich_5" "24.6076"
    [22,] "brahui_hgdp_25" "24.7421"
    [23,] "haryana-jatt_harappa_5" "24.8739"
    [24,] "punjabi-arain_xing_25" "25.2478"
    [25,] "azeri_harappa_2" "25.3113"
    [26,] "punjabi_harappa_10" "25.8293"
    [27,] "turkish_harappa_4" "26"
    [28,] "uzbekistan-jew_behar_2" "26.3174"
    [29,] "punjabi-brahmin_harappa_2" "26.5994"
    [30,] "stalskoe_xing_5" "26.6031"

    [1,] "59.9% iranian_behar_19 + 40.1% sindhi_hgdp_24" "4.5994"
    [2,] "42.9% bhatia_harappa_2 + 57.1% iranian_behar_19" "4.7957"
    [3,] "57.4% bhatia_harappa_2 + 42.6% iraqi-mandaean_harappa_2" "5.004"
    [4,] "60.8% iranian_behar_19 + 39.2% punjabi-arain_xing_25" "5.1374"
    [5,] "52% iranian_behar_19 + 48% pathan_hgdp_23" "5.2039"
    [6,] "42.5% iraqi-arab_harappa_4 + 57.5% kalash_hgdp_23" "5.214"
    [7,] "58.8% bhatia_harappa_2 + 41.2% iranian-jew_behar_4" "5.2257"
    [8,] "59.3% iranian_behar_19 + 40.7% punjabi-jatt_harappa_8" "5.3218"
    [9,] "59.7% bhatia_harappa_2 + 40.3% iraq-jew_behar_10" "5.4172"
    [10,] "37.5% iraqi-mandaean_harappa_2 + 62.5% pathan_hgdp_23" "5.4624"
    [11,] "53.6% kurd_xing_24 + 46.4% sindhi_hgdp_24" "5.4981"
    [12,] "52% bhatia_harappa_2 + 48% iraqi-arab_harappa_4" "5.5121"
    [13,] "63.3% kalash_hgdp_23 + 36.7% palestinian_harappa_2" "5.6202"
    [14,] "61.5% iranian_behar_19 + 38.5% punjabi_harappa_10" "5.6241"
    [15,] "56.2% kurd_harappa_11 + 43.8% sindhi_hgdp_24" "5.6605"
    [16,] "62.5% iranian_behar_19 + 37.5% singapore-indian-c_sgvp_10" "5.728"
    [17,] "36.1% iranian-jew_behar_4 + 63.9% pathan_hgdp_23" "5.7675"
    [18,] "74.7% kalash_hgdp_23 + 25.3% yemen-jew_behar_15" "5.8169"
    [19,] "62.5% iranian_behar_19 + 37.5% kashmiri-pahari_harappa_2" "5.825"
    [20,] "63.5% iranian_behar_19 + 36.5% punjabi-ramgarhia_harappa_2" "5.8313"
    [21,] "54.9% bhatia_harappa_2 + 45.1% uzbekistan-jew_behar_2" "5.8358"
    [22,] "51.7% iranian_behar_19 + 48.3% kalash_hgdp_23" "5.843"
    [23,] "68.4% kalash_hgdp_23 + 31.6% palestinian_hgdp_46" "5.8619"
    [24,] "51.9% sindhi_hgdp_24 + 48.1% uzbekistan-jew_behar_2" "5.87"
    [25,] "64.5% kalash_hgdp_23 + 35.5% syrian_behar_16" "5.8705"
    [26,] "62.3% iranian_behar_19 + 37.7% punjabi-brahmin_harappa_2" "5.8776"
    [27,] "42.7% iraqi-arab_harappa_4 + 57.3% pathan_hgdp_23" "5.9153"
    [28,] "35.2% iraq-jew_behar_10 + 64.8% pathan_hgdp_23" "5.9264"
    [29,] "40% iranian_behar_19 + 60% pashtun_harappa_3" "5.9412"
    [30,] "33.1% jordanian_behar_20 + 66.9% kalash_hgdp_23" "5.9449"

    The mixed Oracle results are very suggestive. I wonder if this individual is an outlier for their part of Iran, or representative? Based on your prior knowledge, should we expect Iranians from this individual's region to be strongly South Asian shifted?
    Last edited by Sein; 12-20-2013 at 05:31 AM.

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  11. #26
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    Quote Originally Posted by Sein View Post
    Thank you DMXX!

    I have quite a few Iranian relatives at 23andMe. Interestingly, more Iranian matches than Pakistani matches. Perhaps this would apply to other Pashtuns as well? I'd love to see a fastIBD or ChromoPainter analysis of my raw-data, but I'm just too inept to try anything myself .
    Despite being from the far northwest and north of Iran ancestrally, my Oracle combinations regularly include Pashtuns and Tajiks. I don't think any of this is a coincidence. Given the great diversity in family histories across the region it probably isn't appropriate to extend the common pattern in both our results to any great degree, but it'd be safe to say quite a few other Pashtuns and Iranians will be similar.

    For what it's worth, please find below the ChromoPainter population chunk data for the HGDP Pathans from the Harappa Project, together with Zack's comments. It appears that, outside of South-Central and South Asia, it is the Kurds and Iranians who have "contributed" the most to the Pashtun genepool.



    Quote Originally Posted by Zack @ Harappa
    ...Interestingly, the number of chunks donated to Pathans from Balochi, Brahui and Sindhi seems to be a bit more than from Punjabis. Again, Tajiks are the closest non South Asian group at #55 and #59, followed by Kurds at #62 and Iranians/Kurds cluster (Pop172) at #63.
    I think you've hit the nail right on the head! From a cultural perspective, the Pashtun region is an eastern continuation of Greater Iran, so there might be some very strong and persistent genetic links at play. I think we could go so far as to say that Pashtuns and Iranic-speaking Iranians mutually share a very substantial proportion of their respective genetic ancestries. Although, being at the eastern edge of the Iranian plateau, we have quite a substantial South Asian affinity absent in currently sampled Iranian groups. And originating from the western portion of the plateau, most Iranians have quite a substantial Southwest Asian affinity. Still though, I find it very interesting that one of the factors differentiating Iranians from their western neighbors is a slightly heightened South Asian affinity.
    I agree with your assessment. Generally speaking, it appears that component values frequently observed in the Near-East are as high in Iranians as those South Asian-specific ones among Pashtuns.

    The slightly elevated South Asian component among Iranians is definitely something which separates "us" from other West Asian populations. I have previously demonstrated this using the ACD tool; you will note the Iranians and Kurds were more South Asian ("S Indian", "Baloch") than Armenians and Assyrians.

    Another somewhat related autosomal feature pushing Iranians towards Pashtuns is the frequency of South-Central Asian specific components. Iranians score quite a bit more Gedrosian/W. Central Asian than their immediate neighbours do.

    Although, at Harappa Ancestry Project, there is an Iranian Bandari participant with some very distinctive results, HRP0355. This individual's Oracle results:

    ...

    The mixed Oracle results are very suggestive. I wonder if this individual is an outlier for their part of Iran, or representative? Based on your prior knowledge, should we expect Iranians from this individual's region to be strongly South Asian shifted?
    The shift towards South Asia should be expected given that, within Iran, the frequency of uniparental lines which are quintessentially South Asian (Y-DNA H, mtDNA M) increase the further east and south you travel. To what extent is another question. As the majority of Iranians are from further north of the Persian Gulf coastline, the ability to quantify how typical this individual's results are is non-existent.

    I would venture to say their Single Population Sharing results are expected when one considers their Oracle results. The majority of this individual's ancestry is from the Iranian plateau with the rest consistently coming from around the Indus valley. As discussed above, Iranic-speaking Pakistani Pashtuns have quite a bit of South Asian ancestry in them. The overall population match would therefore very roughly be with Pakistani Pashtuns. Please note the relatively large genetic distance (GD) of 12, indicating it isn't a very "strong" overall fit.

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  13. #27
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    Thank you, very fascinating chunkcount data! One interesting/odd touch though, pop24 is composed of individuals who have mixed Indus Valley-Northwest European backgrounds?

    The ACD tool is great! A really nice way to visualize population differences.

    I anxiously look forward to greater sampling across the Iranian plateau, so much of Iran and Afghanistan lacks representation in genetic data-sets. We might see some very interesting heterogeneity and clinal variation.

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  15. #28
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    On a related note, a good friend of mine was running some "supervised" Admixture experiments on my 23andMe raw-data. What they found validates Geno 2.0's closest reference population choices, at least as far as I can see. The algorithm construes me as 49% Georgian, 47% Gujarati, and 4% Siberian (I might be switching the Georgian and Gujarati %, I'll check later). This is nicely congruent with Geno 2.0 putting me in between northern Caucasians, and northern Indians (but closer to northern Caucasians), as my 4% Siberian admixture would make North Caucasians a better match than Georgians in a broader context.
    Last edited by Sein; 12-26-2013 at 03:18 AM.

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  17. #29
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    Quote Originally Posted by Sein View Post
    On a related note, a good friend of mine was running some "supervised" Admixture experiments on my 23andMe raw-data. What they found validates Geno 2.0's closest reference population choices, at least as far as I can see. The algorithm construes me as 49% Georgian, 47% Gujarati, and 4% Siberian (I might be switching the Georgian and Gujarati %, I'll check later). This is nicely congruent with Geno 2.0 putting me in between northern Caucasians, and northern Indians (but closer to northern Caucasians), as my 4% Siberian admixture would make North Caucasians a better match than Georgians in a broader context.
    Gujaratis have quite a bit of West Eurasian admixture themselves. If the ADMIXTURE run was carried out and a South Indian ethnic group was used as a "forced" component, you'd probably end up with something like 70-80% Georgian/West Asian. I say that based on Pashtuns having around 20-30% "South Asian" in assorted autosomal runs.

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  19. #30
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    You're quite on the mark here, when he tried a "three-continent" model, I turned out 81% West Eurasian. Subtracting the 4% Siberian admixture I have, that would put me at 15% ASI. Since my West Eurasian ancestry is likely entirely West Asian, I guess this is equivalent to saying that I'm 81% West Asian. Although, when Dr. McDonald tried a chromosome painting assuming three reference populations, I turned out 91% "European". Individuals at 23andMe who share my position on the global PCA used to be around 94% "European", back when 23andMe had a three-population model. But haploblock approaches aren't really comparable to Admixture runs.
    Last edited by Sein; 12-26-2013 at 07:51 AM.

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