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Thread: Harappa Ancestry Project

  1. #1
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    Harappa Ancestry Project

    Creating a thread to discuss Zack Ajmal's Harappa Ancestry Project.

    Created a few basic analyses based on the most recent Harappa admix run, for some Near Eastern populations.

    Indo-Iranian Speaking Populations
    Iranian_Harappa IRN_IR
    Kurd_Harappa KRD_IR

    Jewish Populations
    Ashkenazi Jews ASHJ
    Iranian Jews IRNJ
    Iraqi Jews IRQJ
    Sephardic Jews SEPJ
    Yemen Jews YEMJ

    Arab Populations
    Bedouin BEDA
    Iraqi IRQA
    Jordanian JORA
    Palestinian PALA1
    Qatari QATA
    Saudi SAUA
    Syrian SYRA
    Yemeni YEMA

    Lebanese Populations
    Lebanese Christian LEBC
    Lebanese Druze LEBD
    Lebanese Muslim LEBM

    Other Populations
    Assyrian_Harappa ASY
    Iraqi Mandaean_Harappa MAN
    Samaritan SAM


    Cluster, Neighbor-joining, and MDS analyses respectively:









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    Does the frequency of the SW Asian component in the Levant explain the placement of certain groups?

    If we presume the SW Asian component here peaks in Arabian peninsular populations, and based on the neighbour-joining chart, it seems Jordanians, Palestinians and Samaritans have a stronger pull towards the Arabian peninsula than the Lebanese or Iraqi Arabs, with Syrians falling somewhere in-between the two para-Levantine groups.

    I'm also surprised to see the "Iraqi Arab" group clustering with Iranians and Kurds. The samples here presumably have some form of Iranian ancestry. If only more ethnically uniform Iraqi Arabs tested to give us a better idea of where they sit.

    Also, if Zack hasn't already carried this out, would it be possible to carry out similar analyses on individual Near-Easterners in Harappa? Zack's created neighbour-joining charts that cover all of South Asia in the past and they've been quite informative.

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    Quote Originally Posted by DMXX View Post
    Does the frequency of the SW Asian component in the Levant explain the placement of certain groups?

    If we presume the SW Asian component here peaks in Arabian peninsular populations, and based on the neighbour-joining chart, it seems Jordanians, Palestinians and Samaritans have a stronger pull towards the Arabian peninsula than the Lebanese or Iraqi Arabs, with Syrians falling somewhere in-between the two para-Levantine groups.

    I'm also surprised to see the "Iraqi Arab" group clustering with Iranians and Kurds. The samples here presumably have some form of Iranian ancestry. If only more ethnically uniform Iraqi Arabs tested to give us a better idea of where they sit.

    Also, if Zack hasn't already carried this out, would it be possible to carry out similar analyses on individual Near-Easterners in Harappa? Zack's created neighbour-joining charts that cover all of South Asia in the past and they've been quite informative.
    When I had reviewed the values a few weeks back, I referred to the differences (and similarities) in the "Caucasus," "South Indian," and the various "African" components. But, certainly, one should also consider the "SW Asian" component, as you have pointed out.

    With regard to your other query, I ran cluster, neighbor-joining, and MDS analyses on Harappa West Asian participants (after excluding a handful of individuals).

    Cluster





    Neighbor-joining





    MDS






    Code:
    HRP0010	Assyrian IRN
    HRP0018	Iranian
    HRP0020	Iranian
    HRP0030	Iranian
    HRP0034	Iranian Khorasani
    HRP0040	Iranian
    HRP0043	Iraqi Arab
    HRP0046	Iranian
    HRP0081	Assyrian
    HRP0082	Assyrian
    HRP0083	Azeri Turk
    HRP0094	Iraqi Mandaean
    HRP0105	Kurd (Iranian)
    HRP0128	Iranian
    HRP0141	Kurd (Turkish)
    HRP0143	Turkish
    HRP0144	Kurd (Iraqi)
    HRP0145	Kurd (Iraqi)
    HRP0146	Kurd (Iraqi)
    HRP0147	Assyrian
    HRP0156	Kurd (Iraqi)
    HRP0175	Georgian Svan
    HRP0177	Azeri
    HRP0186	Georgian
    HRP0193	Georgian
    HRP0207	Iraqi Mandaean
    HRP0216	Assyrian IRQ
    HRP0224	Assyrian
    HRP0242	North Ossetian
    HRP0243	Georgian
    HRP0246	Kurd Zaza Turkey
    HRP0247	Kurd Kurmanji Iraq
    HRP0248	Kurd Kurmanji Iraq
    HRP0249	Kurd Yezidi Iraq
    HRP0255	Turk
    HRP0258	Kurd (Feyli)
    HRP0260	Turkish Alevi
    HRP0264	Iranian
    HRP0277	Iraqi Arab
    HRP0279	Iraqi Arab
    HRP0280	Armenian
    HRP0285	Armenian
    HRP0309	Iranian
    HRP0324	Kurd from Turkey
    Last edited by Humanist; 08-18-2013 at 08:23 AM.

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    This is great, thanks! We haven't had much work done on Southwest and West Asians in a while.

    Very interesting... I (HRP0020) am part of the cluster that specifically covers the entire range to which NW Iranic speakers were known to have existed (or still do). The only difference between the Cluster and Neighbour-Joining maps is the placement of the Khorasani Iranian, but that doesn't take away from the inference. In fact, given Parthian was spoken around the Khorasan-Mazandaran-Turkmenistan zone...

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    I made a tree a few months ago using HarappaWorld reference populations.
    HarappaWorld tree 371 samples ref only2.jpg
    Attached Files Attached Files

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    I am HRP0143. Interesting that I am close to the Georgians.

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  13. #7
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    Why are there so few submissions from the interior of India on the map?

    http://maps.google.com/maps/ms?ie=UT...,79.013672&z=4

    Just found it curious. A lack of significant submissions from that entire middle region of India is what's preventing the creation of a useful online admixture tool for recent ancestry in South Asians. All we have to work with are ancestral components from other parts of the world or the extremes of India (North, South, East, and Pakistan).

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    Hi Palisto,

    Excellent work! I find it interesting that me and other Pashtun participants at HAP cluster in such an interesting spot. Rather unexpected. Is the "Baloch" component responsible for this?

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    My harappa results:

    Using 1 population approximation:
    1 lebanese-muslim @ 6.227
    2 palestinian @ 6.425
    3 syrian @ 6.584
    4 iraqi-arab @ 7.170
    5 uzbekistan-jew @ 7.252
    6 lebanese @ 7.716
    7 armenian @ 8.083
    8 iraq-jew @ 8.299
    9 iraqi-mandaean @ 8.747
    10 iranian-jew @ 9.272
    377 iterations.



    Using 2 populations approximation:
    1 50% armenian +50% syrian @ 2.471
    2 50% syrian +50% uzbekistan-jew @ 2.700
    3 50% azeri +50% palestinian @ 2.830
    4 50% lebanese +50% uzbekistan-jew @ 2.921
    5 50% armenian +50% palestinian @ 3.116
    6 50% iranian +50% samaritian @ 3.177
    7 50% azeri +50% jordanian @ 3.209
    8 50% kurd +50% palestinian @ 3.369
    9 50% iraqi-arab +50% lebanese-muslim @ 3.406
    10 50% iraqi-arab +50% lebanese-druze @ 3.406
    71253 iterations.



    Using 3 populations approximation:
    1 50% syrian +25% iranian +25% lebanese-druze @ 2.062
    2 50% syrian +25% turkish +25% uzbekistan-jew @ 2.155
    3 50% syrian +25% azeri +25% iraq-jew @ 2.181
    4 50% syrian +25% armenian +25% uzbekistan-jew @ 2.182
    5 50% palestinian +25% azeri +25% kurd @ 2.186
    6 50% syrian +25% iranian +25% lebanese-christian @ 2.211
    7 50% syrian +25% iraqi-mandaean +25% turkish @ 2.252
    8 50% syrian +25% kurd +25% lebanese-muslim @ 2.253
    9 50% syrian +25% kurd +25% lebanese-druze @ 2.259
    10 50% syrian +25% iranian-jew +25% turkish @ 2.277
    1011837 iterations.



    Using 4 populations approximation:
    1 azeri + palestinian + syrian + uzbekistan-jew @ 1.858
    2 azeri + jordanian + syrian + uzbekistan-jew @ 1.955
    3 azeri + iranian + jordanian + samaritian @ 1.990
    4 azeri + georgia-jew + iraqi-arab + palestinian @ 1.991
    5 azeri + iranian + palestinian + samaritian @ 2.001
    6 azeri + palestinian + palestinian + uzbekistan-jew @ 2.014
    7 azeri + iraqi-arab + lebanese-christian + syrian @ 2.034
    8 iranian + lebanese-druze + syrian + syrian @ 2.062
    9 azeri + jordanian + kurd + samaritian @ 2.079
    10 azeri + iranian + jordanian + samaritian @ 2.084
    11 armenian + azeri + palestinian + syrian @ 2.102
    12 georgia-jew + iraqi-arab + palestinian + turkish @ 2.103
    13 armenian + azeri + palestinian + palestinian @ 2.132
    14 azeri + iranian + samaritian + syrian @ 2.135
    15 iraqi-arab + palestinian + turk + uzbekistan-jew @ 2.153
    16 syrian + syrian + turkish + uzbekistan-jew @ 2.155
    17 iranian + samaritian + syrian + turkish @ 2.177
    18 azerbaijan-jew + iraqi-arab + palestinian + turkish @ 2.180
    19 azeri + iraq-jew + syrian + syrian @ 2.181
    20 armenian + syrian + syrian + uzbekistan-jew @ 2.182

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    My Harappa Admix and Oracle Results:

    Admix Results (sorted):

    # Population Percent
    1 Caucasian 49.61
    2 Baloch 20.88
    3 SW-Asian 18.59
    4 Mediterranean 8.12
    5 NE-Euro 1.2
    6 NE-Asian 0.55
    7 S-Indian 0.46
    8 Siberian 0.4
    9 American 0.1
    10 Papuan 0.09
    11 Beringian 0.01

    Eastern Mizrahim (Jewish) populations in red. Arabic-speaking populations in blue.

    Single Population Sharing:

    # Population (source) Distance
    1 assyrian (harappa) 2.46
    2 iranian-jew (behar) 3.94
    3 iraqi-mandaean (harappa) 4.22
    4 uzbekistan-jew (behar) 4.32
    5 azerbaijan-jew (behar) 5.07
    6 georgia-jew (behar) 5.38
    7 iraq-jew (behar) 5.86

    8 armenian (harappa) 6.53
    9 armenian (yunusbayev) 8.83
    10 kurd (yunusbayev) 9.56
    11 lebanese-druze (haber) 10.19
    12 kurd (xing) 10.23
    13 turkish (harappa) 10.74
    14 kurd (harappa) 10.96
    15 lebanese-muslim (haber) 10.96
    16 armenian (behar) 11.43
    17 lebanese-christian (haber) 11.53
    18 iraqi-arab (harappa) 11.87
    19 azeri (harappa) 11.93
    20 palestinian (harappa) 12.39

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