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Thread: 23andme says 99.8% South Asian, but Harappa only 65% (33% SI, 31% Baloch)

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    Question 23andme says 99.8% South Asian, but Harappa only 65% (33% SI, 31% Baloch)

    Hello, I'm new to this, so please bear with me. Any attempt to explain this is appreciated.

    My 23andme composition is 99.8% South Asian, 0.1% Korean, 0.1% Native American, and 0.1% Broadly NW European. It showed my Korean/Amerindian ancestry is from 1700-1800, which seems very interesting. No further explanation on the 0.1% NW European. I am Nepali brahmin from all my sides.

    When I try this with Harappa Genesis, it comes with just 65% South Asian, counting 33% South Indian and 31% North Indian. Also, in Harappa, my East Asian ancestry jumps significantly and so does the European. Is this normal? It looks like I match closest with my neighbor populations. Other calculators have me close to Burushos of all people.

    Harappa World
    Admix Results (sorted):

    # Population Percent
    1 S-Indian 33.71
    2 Baloch 31.67
    3 NE-Euro 13.78
    4 Caucasian 9.73
    5 NE-Asian 5.11
    6 Beringian 2.53
    7 Siberian 2.21
    8 American 1.07
    9 SW-Asian 0.17
    10 Mediterranean 0.03

    Single Population Sharing:

    # Population (source) Distance
    1 nepalese-a (xing) 7.18
    2 up-muslim (harappa) 7.66
    3 kashmiri (harappa) 9.28
    4 punjabi (harappa) 9.53
    5 kashmiri-pandit (reich) 9.55
    6 punjabi-brahmin (harappa) 9.63
    7 up-brahmin (harappa) 9.76
    8 singapore-indian-c (sgvp) 10.15
    9 punjabi-jatt-muslim (harappa) 10.21
    10 bengali-brahmin (harappa) 10.61
    11 punjabi-khatri (harappa) 10.68
    12 haryana-jatt (harappa) 10.75
    13 punjabi-jatt-sikh (harappa) 10.84
    14 kashmiri-pahari (harappa) 11.21
    15 brahmin-uttar-pradesh (metspalu) 11.26
    16 punjabi-ramgarhia (harappa) 11.33
    17 gujarati-muslim (harappa) 11.45
    18 bihari-muslim (harappa) 11.84
    19 sindhi (harappa) 12.99
    20 vaish (reich) 13.22


    -----


    puntDNAL K13 Oracle

    Admix Results (sorted):

    # Population Percent
    1 South_Asia 37.71
    2 West_Asia 30.37
    3 NE_Europe 15.92
    4 NE_Asia 4.85
    5 Siberia 3.98
    6 SW_Europe 3.29
    7 Americas 3.09
    8 SE_Asia 0.46
    9 Oceania 0.35

    Single Population Sharing:

    # Population (source) Distance
    1 Kashmir_Pandit 7.88
    2 Burusho 9.07
    3 Punjabi 11.98
    4 Sindhi 14.17
    5 Tamil_Nadu_Brahmin 15.36
    6 Bengali 15.76
    7 Pakistan_Pashtun 17.36
    8 Pathan 18.13
    9 Afghan_Pashtun 19.56
    10 Balochi 21.29
    11 Makrani 22.23
    12 Brahui 22.29
    13 UP_Muslim 22.85
    14 Velamas 23.07
    15 Tadjik 24.4
    16 Tamil_Nadu_Caste 24.61
    17 Afghan_Uzbeki 25.33
    18 Kurumba 25.56
    19 Piramalai_Kallars 25.91
    20 Chenchus 26.11

    ----

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    23andme only looks at recent ancestry in the last 500 years I believe. Gedmatch looks much deeper than that. Your scores aren't too different from other Nepali Brahmins from what I've seen. The Korean ancestry is highly doubtable. It's probably just standard Nepali Brahmin NE Asian ancestry from the Himalayas that 23andMe is mistaking for Korean.

    Any closeness to the Burusho on other calculators is probably because of somewhat similar admixture scores. Burusho tend to score 9-10% East Eurasian like ancestry (some Nepali Brahmins score less than you and the Burusho) along with somewhat similar NE Euro and Baloch/Gedrosia and/or West Eurasian like ancestry scores. However, they score less South Asian ancestry than Nepalis, which makes sense geographically.

    You can see the Nepali Brahmin Harappa admixture scores below vary somewhat from person to person. That's normal. For example, one individual might score lower Baloch like yourself but higher Caucasus to compensates for it and vice versa with other individuals. In addition, you have to consider that inheritance is random so even siblings wouldn't have admixture scores that 100% replicate one another.

    Stealing an old post from bored:

    http://www.anthrogenica.com/showthre...ll=1#post56125


    Nepali Brahmin #1

    Admix Results (sorted):

    # Population Percent
    1 Baloch 35.53
    2 S-Indian 34.74
    3 NE-Euro 12.98
    4 Caucasian 4.4
    5 Mediterranean 3.77
    6 NE-Asian 2.31
    7 Siberian 1.82
    8 Beringian 1.56
    9 American 1.25
    10 Papuan 0.97
    11 SE-Asian 0.34
    12 W-African 0.34

    Single Population Sharing:

    # Population (source) Distance
    1 nepalese-a (xing) 4
    2 up-brahmin (harappa) 5.92
    3 brahmin-uttar-pradesh (metspalu) 7.53
    4 up-muslim (harappa) 7.68
    5 singapore-indian-c (sgvp) 7.82
    6 bengali-brahmin (harappa) 7.92
    7 punjabi-ramgarhia (harappa) 8.03
    8 punjabi-brahmin (harappa) 8.09
    9 punjabi (harappa) 8.74
    10 kashmiri-pahari (harappa) 9.02
    11 kashmiri-pandit (reich) 9.45
    12 punjabi-jatt-sikh (harappa) 9.51
    13 vaish (reich) 9.65
    14 haryana-jatt (harappa) 10.02
    15 bihari-muslim (harappa) 10.14
    16 punjabi-jatt-muslim (harappa) 10.2
    17 up-kshatriya (metspalu) 10.85
    18 gujarati-b (hapmap) 11.16
    19 kashmiri (harappa) 11.16
    20 punjabi-arain (xing) 11.76


    Nepali Brahmin #2

    Admix Results (sorted):

    # Population Percent
    1 Baloch 35.53
    2 S-Indian 34.08
    3 NE-Euro 12.73
    4 Caucasian 9.37
    5 NE-Asian 4.37
    6 American 2.18
    7 Beringian 1.19
    8 SW-Asian 0.31
    9 SE-Asian 0.2
    10 Mediterranean 0.03

    Single Population Sharing:

    # Population (source) Distance
    1 nepalese-a (xing) 5.03
    2 punjabi-brahmin (harappa) 6.21
    3 up-muslim (harappa) 6.46
    4 singapore-indian-c (sgvp) 6.58
    5 punjabi (harappa) 6.72
    6 kashmiri-pandit (reich) 6.78
    7 kashmiri (harappa) 7.49
    8 up-brahmin (harappa) 7.71
    9 kashmiri-pahari (harappa) 7.72
    10 punjabi-ramgarhia (harappa) 8.08
    11 punjabi-jatt-muslim (harappa) 8.16
    12 punjabi-jatt-sikh (harappa) 8.56
    13 punjabi-khatri (harappa) 8.59
    14 brahmin-uttar-pradesh (metspalu) 9.57
    15 gujarati-muslim (harappa) 9.63
    16 haryana-jatt (harappa) 9.77
    17 bengali-brahmin (harappa) 9.84
    18 sindhi (harappa) 10.9
    19 punjabi-arain (xing) 10.91
    20 bihari-muslim (harappa) 11.15

    Nepali Brahmin # 3

    Admix Results (sorted):

    # Population Percent
    1 Baloch 34.62
    2 S-Indian 34.15
    3 NE-Euro 11.42
    4 Caucasian 8.58
    5 Mediterranean 2.62
    6 American 2.5
    7 NE-Asian 2.05
    8 Siberian 1.51
    9 SE-Asian 1.3
    10 Papuan 0.62
    11 Beringian 0.41
    12 SW-Asian 0.21

    Single Population Sharing:

    # Population (source) Distance
    1 up-muslim (harappa) 4.39
    2 nepalese-a (xing) 5.12
    3 punjabi-brahmin (harappa) 6.27
    4 punjabi (harappa) 6.36
    5 singapore-indian-c (sgvp) 6.44
    6 kashmiri-pandit (reich) 6.63
    7 up-brahmin (harappa) 6.8
    8 punjabi-ramgarhia (harappa) 7.27
    9 kashmiri-pahari (harappa) 7.6
    10 kashmiri (harappa) 7.61
    11 punjabi-jatt-muslim (harappa) 7.66
    12 punjabi-jatt-sikh (harappa) 8.2
    13 bengali-brahmin (harappa) 8.39
    14 brahmin-uttar-pradesh (metspalu) 8.55
    15 gujarati-muslim (harappa) 8.71
    16 punjabi-khatri (harappa) 8.92
    17 haryana-jatt (harappa) 9.58
    18 bihari-muslim (harappa) 9.8
    19 punjabi-arain (xing) 10.45
    20 vaish (reich) 10.66

    Nepali Brahim #4

    Admix Results (sorted):

    # Population Percent
    1 S-Indian 35.14
    2 Baloch 32.58
    3 NE-Euro 10.97
    4 Caucasian 8.3
    5 NE-Asian 6.01
    6 Mediterranean 3.06
    7 American 1.79
    8 Papuan 0.85
    9 SE-Asian 0.65
    10 Siberian 0.46
    11 Pygmy 0.13
    12 Beringian 0.04

    Single Population Sharing:

    # Population (source) Distance
    1 up-muslim (harappa) 6.22
    2 nepalese-a (xing) 6.54
    3 bengali-brahmin (harappa) 8.48
    4 up-brahmin (harappa) 8.65
    5 punjabi (harappa) 9.03
    6 singapore-indian-c (sgvp) 9.19
    7 punjabi-brahmin (harappa) 9.33
    8 kashmiri (harappa) 9.38
    9 kashmiri-pandit (reich) 9.47
    10 brahmin-uttar-pradesh (metspalu) 9.59
    11 bihari-muslim (harappa) 9.66
    12 kashmiri-pahari (harappa) 9.75
    13 punjabi-ramgarhia (harappa) 10
    14 gujarati-muslim (harappa) 10.18
    15 punjabi-jatt-muslim (harappa) 10.35
    16 vaish (reich) 11.02
    17 punjabi-jatt-sikh (harappa) 11.37
    18 punjabi-khatri (harappa) 11.71
    19 haryana-jatt (harappa) 12.15
    20 up-kshatriya (metspalu) 12.17

    Nepali Brahmin #5

    # Population Percent
    1 Baloch 34.08
    2 S-Indian 33.96
    3 NE-Euro 10.57
    4 Caucasian 8.81
    5 NE-Asian 5.55
    6 Mediterranean 2.06
    7 American 1.54
    8 Beringian 1.15
    9 Siberian 1.02
    10 Papuan 0.49
    11 SE-Asian 0.38
    12 SW-Asian 0.29
    13 E-African 0.1

    Single Population Sharing:

    # Population (source) Distance
    1 up-muslim (harappa) 5.2
    2 nepalese-a (xing) 5.42
    3 punjabi (harappa) 7.09
    4 singapore-indian-c (sgvp) 7.5
    5 kashmiri-pandit (reich) 7.51
    6 punjabi-brahmin (harappa) 7.55
    7 kashmiri (harappa) 7.57
    8 kashmiri-pahari (harappa) 8.07
    9 up-brahmin (harappa) 8.26
    10 punjabi-jatt-muslim (harappa) 8.39
    11 punjabi-ramgarhia (harappa) 8.44
    12 gujarati-muslim (harappa) 8.81
    13 bengali-brahmin (harappa) 9.13
    14 punjabi-jatt-sikh (harappa) 9.54
    15 punjabi-khatri (harappa) 9.82
    16 brahmin-uttar-pradesh (metspalu) 9.89
    17 bihari-muslim (harappa) 10.2
    18 haryana-jatt (harappa) 11.03
    19 punjabi-arain (xing) 11.39
    20 vaish (reich) 11.58

    Nepali Brahmin #6

    Admix Results (sorted):

    # Population Percent
    1 S-Indian 33.54
    2 Baloch 33.33
    3 NE-Euro 12.43
    4 Caucasian 11.68
    5 Siberian 3.82
    6 SE-Asian 2.21
    7 Mediterranean 1.23
    8 NE-Asian 1.18
    9 American 0.38
    10 Beringian 0.12
    11 Papuan 0.1

    Single Population Sharing:

    # Population (source) Distance
    1 up-muslim (harappa) 5.83
    2 kashmiri-pandit (reich) 7.12
    3 kashmiri (harappa) 7.44
    4 punjabi (harappa) 7.55
    5 nepalese-a (xing) 7.55
    6 punjabi-brahmin (harappa) 7.77
    7 punjabi-jatt-muslim (harappa) 8.12
    8 singapore-indian-c (sgvp) 8.34
    9 punjabi-khatri (harappa) 8.57
    10 punjabi-jatt-sikh (harappa) 8.93
    11 up-brahmin (harappa) 9.11
    12 punjabi-ramgarhia (harappa) 9.22
    13 gujarati-muslim (harappa) 9.38
    14 kashmiri-pahari (harappa) 9.54
    15 haryana-jatt (harappa) 10.02
    16 bengali-brahmin (harappa) 10.54
    17 brahmin-uttar-pradesh (metspalu) 10.89
    18 sindhi (harappa) 10.97
    19 bihari-muslim (harappa) 11.39
    20 punjabi-arain (xing) 12.05

    http://www.anthrogenica.com/member.php?8690-gyanwali

    Gyanwali is Nepali Brahmin as well. One of my friends on the forum (everest) is Nepali Brahmin too but is no longer active.
    Last edited by Sapporo; 09-19-2017 at 06:13 AM.

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    I agree that 23andme really does not go that deep, and I would wager that it really only covers up to the last 5 generations of ancestry; maybe 2 to 300 years tops, and that 500 years, which the company claims, is a bit of a stretch. I am also always a little skeptical of those 0.1 estimates which appear frequently in their results even though these segments can supposedly be shown in their ancestry paintings. In your case, you received estimates of 0.I Korean, 0.1 NW European and .01 Native American added to a an estimate of 99.8% South Asian. I am just saying that if they are so precise and can detect ancestry to a level of .01 percent, they should have been better able to break down the 99.8% South Asian estimate. I am sorry if I am not wording this the way I would like.
    Last edited by tomz; 09-20-2017 at 12:48 AM.

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    23andme so far as what I have seen does a pretty bad job particularly for South and Central Asians. And they use some propriety formula for "phasing" the sequence without having parental sequences. My guess is it's population based, so if they don't have good data for your population they won't get it phased well. Or if you have a small admixture from another distant population it can get hidden it seems. That happened for me; they reported ~99% European with about 0.3% North Asian thrown in, and were way off on the European mix as well. Long story short, they missed the ~3% North Indian I have. So, yes, not very good for South Asian ancestry and I would be suspicious of anything less than 1%... maybe even higher than that!

    BTW, why are the population distances so large on the Nepali examples from GEDmatch?

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    Thanks Sapporo for those samples. They do look similar to mine.

    Therrien.joel - you raised a very interesting point. Are Nepali samples distances so large because of isolation or inbreeding? I want to see how much inbred I am. Culturally and religiously, Nepali Brahmins must not be inbred, so they must follow strict exogamy within paternal and maternal immediate relatives. But isolation might make that impractical.

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    Quote Originally Posted by poi View Post
    Thanks Sapporo for those samples. They do look similar to mine.

    Therrien.joel - you raised a very interesting point. Are Nepali samples distances so large because of isolation or inbreeding? I want to see how much inbred I am. Culturally and religiously, Nepali Brahmins must not be inbred, so they must follow strict exogamy within paternal and maternal immediate relatives. But isolation might make that impractical.
    Did you try the parental relatedness tests? 23andme and GEDmatch have them. That would be the place to start.

    But the higher distance is probably a result of poor sampling. If there are not enough Nepali that have been tested and were included in the samples used to create the populations the "standard" population percentages for that group can be skewed from what the mean values should be. That can result in a poor fit for the majority of people from that group that use the oracles. What did your non-single population results show?

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    Do you know what the good GEDMatch calculators are? I don't want to run outdated ones or those that are that good.

    ---

    Harappa

    Mixed Mode Population Sharing:

    # Primary Population (source) Secondary Population (source) Distance
    1 81.6% up-brahmin (harappa) + 18.4% uyghur (hgdp) 4.09
    2 80.2% up-brahmin (harappa) + 19.8% uzbek (behar) 4.1
    3 80.4% brahmin-uttar-pradesh (metspalu) + 19.6% nogai (yunusbayev) 4.24
    4 77.5% brahmin-uttar-pradesh (metspalu) + 22.5% uzbek (behar) 4.28
    5 83.1% up-brahmin (harappa) + 16.9% nogai (yunusbayev) 4.46

    ---
    Eurasia K9 ASI Oracle

    Mixed Mode Population Sharing:

    # Primary Population (source) Secondary Population (source) Distance
    1 87.6% Punjabi + 12.4% Ulchi 5.66
    2 83.6% Punjabi + 16.4% Altaian 6.12
    3 82.3% Punjabi + 17.7% Kyrgyz 6.31
    4 75.4% Punjabi + 24.6% Hazara 6.53
    5 73.2% Punjabi + 26.8% Uzbek 6.7
    6 65.1% Punjabi + 34.9% Hazara_Afghan 6.76
    7 88.2% Pathan + 11.8% Ulchi 6.85
    8 77.4% Punjabi + 22.6% Uygur 6.9
    9 70.9% Punjabi + 29.1% Turkmen 7.08
    10 92% Burusho + 8% Great_Andamanese 7.26
    11 94.5% Burusho + 5.5% BedouinB 7.32
    12 72.2% Punjabi + 27.8% Turkmen_Afghan 7.34
    13 92.1% Burusho + 7.9% Saudi 7.38

    ---

    Eurogenes EUtest V2 K15
    Mixed Mode Population Sharing:

    # Primary Population (source) Secondary Population (source) Distance
    1 77.8% Kshatriya + 22.2% Nogay 3.9
    2 81.7% Brahmin_UP + 18.3% Nogay 4.02
    3 55% Brahmin_UP + 45% Burusho 4.04
    4 69.5% Kshatriya + 30.5% Tadjik 4.18
    5 74.5% Brahmin_UP + 25.5% Tadjik 4.35
    6 57.2% Kanjar + 42.8% Tadjik 4.43
    7 78.9% Gujarati + 21.1% Nogay 4.53
    8 75.2% Brahmin_UP + 24.8% Afghan_Tadjik 4.64
    9 74.9% Brahmin_UP + 25.1% Afghan_Uzbeki 4.74

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    Unfortunately, "good" is subjective. It's in theory whichever one gives you the best match.

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    You can try the following calculators:

    It's a mix of older admixture calculators and more recent ancient genome based calculators.

    MDLP World
    MDLP World 22
    MDLP K23B
    Eurogenes ANE K7
    Eurogenes K13
    Gedrosia Eurasia K9 ASI
    Gedrosia Near East Neolithic K13
    Gedrosia Ancient Eurasia K6
    puntDNAL K10 Ancient

    The ones you've done so far are fine as well. Harappa is useful for South Asians but heavily outdated because of the lack of updates. Kurd's New K12 Ancient Calculator on Geneplaza is interesting as well but cost $5 to use after you transfer your 23andMe raw data.
    Last edited by Sapporo; 09-21-2017 at 07:28 AM.

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    Hi Sapporo, I went through GenePlaza's calculators yesterday. K12 and Ancestry:

    Ancient K12

    STEPPE CULTURES 40.5%
    KARASUK-E SCYTHIAN (2000-3000 years) 25.0%
    ANDRONOVO-SRUBNAYA (3000-4000 years) 10.4%
    YAMNAYA-AFANASIEVO-POLTAVKA (4000-5000 years) 5.1%

    ANCIENT FARMERS 32.0%
    WEST EUROPEAN FARMERS (4000-5000 years) 0.0%
    LEVANT (4000-8000 years) 4.9%
    NEOLITHIC-CHALCOLITHIC IRAN-CHG (5000-12000 years) 17.5%
    EAST EUROPEAN FARMERS (5000-8000 years) 9.6%

    SOUTHEAST EURASIAN 23.5%

    EASTERN NON AFRICANS (modern) 4.0%
    AFRICAN 0.0%
    WESTERN EUROPEAN & SCANDINAVIAN HUNTER GATHERERS (4000-5000 years) 0.0%

    ----

    Ancestry

    West Eurasian67.4%
    --Ambiguous7.7%
    --South Asian53.1%
    --North Slavic6.5%

    Central Asian24.5%

    Ambiguous4.2%

    Central Chinese4.0%
    --Mongolic/Tungusic4.0%
    Last edited by poi; 09-21-2017 at 01:21 PM.

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