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Thread: Eurogenes Global 25 Full Moderns Spreadsheet Runs with Gradient Descent Algorithm

  1. #521
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    Quote Originally Posted by randwulf View Post
    @Yggdrasi full spreadsheet results:

    distance%: 0.71

    Pallan 22.83
    Kohistani 20.74
    Chamar 15.03
    Gujarati 11.48
    Khatri 8.42
    Maratha 7.22
    Paniya 5.81
    Chenchu 3.46
    Kadar 2.32
    Punjabi_Lahore 1.57
    Iyer 0.87
    Velamas 0.17
    Pulliyar 0.08

    Cheers and thanks!

    Could you please do a second run without the summing to group level like you did for 26284729292?

  2. #522
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    Quote Originally Posted by Censored View Post
    PJL is not representative of the main population of the area
    PJL is similar to a UP native. In the Punjabi context they are similar to backward castes.

    "sample": "Punjabi_Lahore:Average",
    "fit": 1.464,
    "Piramalai": 71.67,
    "RUS_Sintashta_MLBA": 12.5,
    "Simulated_AASI": 10,
    "IRN_Ganj_Dareh_N": 5.83,

    "sample": "Uttar_Pradesh:Average",
    "fit": 1.9042,
    "Piramalai": 78.33,
    "RUS_Sintashta_MLBA": 10.83,
    "Simulated_AASI": 10.83,
    "IRN_Ganj_Dareh_N": 0,

    "sample": "Chamar:Average",
    "fit": 1.3129,
    "Piramalai": 75,
    "Simulated_AASI": 17.5,
    "RUS_Sintashta_MLBA": 6.67,
    "IRN_Ganj_Dareh_N": 0.83,

    "sample": "Punjabi_Lahore:Average",
    "fit": 2.2311,
    "Velamas": 91.67,
    "Kalash": 8.33,

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  4. #523
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    Which PJL samples were selected for the average on G25? The entirety of the PJL samples span a wide range from near pashtun and other biraderi type, to like chamars.

    A very heterogenous group.
    Paternal; Y-DNA: R1a-L657> Y6> Y11> Y920*
    Paternal; mtDNA: M5b'c
    Maternal; Y-DNA: R1a-L657> Y6
    Maternal; mtDNA: M4b1

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  6. #524
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    Quote Originally Posted by randwulf View Post
    I picked all of the Greek, Turk, Iranian, and Punjabi references. None of the Iranian was picked, but it does model out pretty well:

    distance%: 0.87

    Punjabi_Lahore 40.91
    Greek 30.59
    Turkish_Trabzon 17.9
    Greek_Crete 10.6
    Thank you
    33% Greek_Thessaloniki + 33% IraqiJew + 33% Punjabi @ 4.835

    Modern:


     
    fit: 2.4426,

    Greek_Crete: 51.67
    Gujarati: 38.33
    Iranian_Persian: 7.5
    Lithuanian: 2.5


    Ancient:

     
    fit": 1.7643

    DRAVIDIAN_Saidu_Sharif_IA_o: 32.5
    GRECO-ROMAN_Italy_Medieval_Collegno_o1: 17.5
    ILLYRIAN-THRACIAN_Balkans_IA: 15
    SLAVIC_Avar_Hungary_Szolad: 11.67
    LEVANTINE_Levant_LBN_MA_NE: 10.83
    ANATOLIAN_Anatolia_IA: 7.5
    ARIAN_PAK_Swat_Butkara_IA: 5

  7. #525
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    Quote Originally Posted by Reza View Post
    Which PJL samples were selected for the average on G25? The entirety of the PJL samples span a wide range from near pashtun and other biraderi type, to like chamars.

    A very heterogenous group.
    https://anthrogenica.com/showthread....-and-ASI-Oh-My!

    This is a complicated topic.

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  9. #526
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    Quote Originally Posted by Reza View Post
    Which PJL samples were selected for the average on G25? The entirety of the PJL samples span a wide range from near pashtun and other biraderi type, to like chamars.

    A very heterogenous group.
    Do you know how many samples are on the G25? If I recall, the biorxiv and other papers have used 7-8 of mostly AASI shifted samples.

    https://www.biorxiv.org/content/10.1101/001552v1

    There were also some very AASI shifted "Punjabi UK" samples used by Reich in the 2018 paper and the coordinates in the paper suggested they were actually PJL samples.
    Last edited by Sapporo; 07-12-2019 at 01:58 PM.
    I4285 I4285 1873-1661 calBCE (343025 BP, PSUAMS-2536) BMAC Sappali_Tepe_BA Sappali Tepe Uzbekistan U7a3 L1a
    I5604 I5604 1880-1697 calBCE (346520 BP, PSUAMS-2774) BMAC Bustan_BA Bustan Uzbekistan K1a1 L1a
    I6667 I6667 1497-1413 calBCE (317020 BP, PSUAMS-2998) Parkhai_LBA_o Parkhai_LBA_o Parkhai II Turkmenistan HV2a
    I6669 I6669 3082-2909 calBCE (436525 BP, PSUAMS-2950) Parkhai_EN Parkhai_EN Parkhai II Turkmenistan HV2
    I4899 I4899 1600-1300 BCE BMAC Bustan_BA Bustan Uzbekistan R0 J

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  11. #527
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    Quote Originally Posted by randwulf View Post
    I agree with Ruderico on not putting too much weight on the phenotype. You do seem to have a possible affinity with some North African and maybe there could be Sephardic, too. So, just for kicks, I added one of the North African references and Sephardic to your prior custom model. They both get picked for the model:

    distance%: 0.88

    Spanish_Castilla_La_Mancha 53.11
    Basque_Spanish 14.96
    Spanish_Extremadura 10.89
    Moroccan_South 10.14
    Spanish_Baleares 4.82
    Sephardic_Jew 4.09
    Spanish_Cantabria 1.99

    It is an interesting result. The fit improves quite a bit. I wouldn't say this kind of thing proves anything definite, but it does seem possible.
    The Sephardic might also be the other way around, as in the local Jewish community having picked up a bit of native Belmote ancestry (which is what he is). It's something pretty small, so I agree it's hard to say with any certainty if it's really anything or not.


    Edit: Just remembered. On the other hand, in 'ancient' models made for the Portuguese section, he did score relatively high Roman_Levant (highest amongst the tested Portuguese) so it could be something real. In fact people from Castelo Branco district scored the highest, but his was top. However it caused his Roman_proxy score to drop aswell.
    Last edited by Ruderico; 07-12-2019 at 08:48 AM.
    YDNA - E-Y31991>PF4428>E-Y134097>E-Y168273 (probably Scythian-Sarmatian). Domingos Rodrigues, b. circa 1680 Hidden Content , Viana do Castelo, Portugal
    mtDNA - H20. Maria Josefa de Almeida, b. circa 1750 Hidden Content , Porto, Portugal

    Global25 PCA West Eurasia dataset Hidden Content
    Hidden Content


    [1] "distance%=1.7726"

    Ruderico

    Celtiberian,77.6
    Roman_Imperial_proxy,13.6
    Guanche,8.8

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  13. #528
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    Quote Originally Posted by Sapporo View Post
    Do you know how many samples are on the G25? If I recall, the biorxiv and other papers have used 7-8 of the most AASI shifted samples.

    https://www.biorxiv.org/content/10.1101/001552v1

    There were also some very AASI shifted "Punjabi UK" samples used by Reich in the 2018 paper and the coordinates in the paper suggested they were actually PJL samples.
    Looking through the most uptodate G25 PCA datasheet, the following 8 PJL samples are used:

    HG02491, HG02600, HG02601, HG02687, HG02688, HG02724, HG02783, HG02790.

    So the same selection of samples as from that biorvix 2013 paper by Laziridis.

    Anyone have a link to khana's old excel which broke the PJL samples down? Would be interesting to see what the breakdown of the above individuals are. I can see why they have been selected (based on the academic paper), but if anyone had time, might be worth suggesting other PJL samples to provide a more representative average across the scale.

    Personally, I dislike the labelliing of PJL samples as inherently non-representative of Punjabis. They're just representative of segments of the Punjabi population which are AASI shifted - Dalit like. Which contrasts massively to biraderi types, or brahmin/upper caste Hindus.

    Someone mentioned before that generic ethnic terms such as Punjabi or Gujarati are probably unhelpful given the populations are so hetereogenous for the same geographical area, as well as autosomally stratified on a social level. These metaethnic groups are larger than most European countries. I'm sure the same concept applies to other South Asian ethnicities though less well sampled.
    Paternal; Y-DNA: R1a-L657> Y6> Y11> Y920*
    Paternal; mtDNA: M5b'c
    Maternal; Y-DNA: R1a-L657> Y6
    Maternal; mtDNA: M4b1

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  15. #529
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    Quote Originally Posted by Reza View Post
    Looking through the most uptodate G25 PCA datasheet, the following 8 PJL samples are used:

    HG02491, HG02600, HG02601, HG02687, HG02688, HG02724, HG02783, HG02790.

    So the same selection of samples as from that biorvix 2013 paper by Laziridis.

    Anyone have a link to khana's old excel which broke the PJL samples down? Would be interesting to see what the breakdown of the above individuals are. I can see why they have been selected (based on the academic paper), but if anyone had time, might be worth suggesting other PJL samples to provide a more representative average across the scale.

    Personally, I dislike the labelliing of PJL samples as inherently non-representative of Punjabis. They're just representative of segments of the Punjabi population which are AASI shifted - Dalit like. Which contrasts massively to biraderi types, or brahmin/upper caste Hindus.

    Someone mentioned before that generic ethnic terms such as Punjabi or Gujarati are probably unhelpful given the populations are so hetereogenous for the same geographical area, as well as autosomally stratified on a social level. These metaethnic groups are larger than most European countries. I'm sure the same concept applies to other South Asian ethnicities though less well sampled.
    The PJL breakdown is on my spreadsheet:

    https://docs.google.com/spreadsheets...t#gid=55701066

    Click/scroll all the way to the right to the last tab.

    A quick basic breakdown of the samples you listed above excluding HG02687, which I don't believe was on khana's original sheet either:

    HG02491
    South Indian: 41.81
    Baloch: 36.25
    Caucasian: 8.98
    Northern European: 7.91
    SE Asian: 0
    Siberian: 0
    NE Asian: 1.59
    Papuan: 0.56
    American: 0.15
    Beringian: 1.38
    Med: 0.43
    SW Asian: 0.93

    HG02600
    South Indian: 46.31
    Baloch: 36.03
    Caucasian: 1.76
    Northern European: 6.59
    SE Asian: 1.05
    Siberian: 1.3
    NE Asian: 0.01
    Papuan: 1.46
    American: 0.64
    Beringian: 0.57
    Med: 3.72
    SW Asian: 0.12

    HG02601
    South Indian: 45.96
    Baloch: 32.1
    Caucasian: 7.42
    Northern European: 6.42
    SE Asian: 1.64
    Siberian: 1.38
    NE Asian: 0.02
    Papuan: 1.63
    American: 0.08
    Beringian: 0.29
    Med: 3.05
    SW Asian: 0.01


    HG02688
    South Indian: 51.87
    Baloch: 28.82
    Caucasian: 5.27
    Northern European: 5.44
    SE Asian: 1.47
    Siberian: 0.46
    NE Asian: 3.05
    Papuan: 1.93
    American: 0
    Beringian: 0.51
    Med: 0.68
    SW Asian: 0.51

    HG02724
    South Indian: 54.89
    Baloch: 31.8
    Caucasian: 1.37
    Northern European: 5.46
    SE Asian: 3.57
    Siberian: 1.38
    NE Asian: 0.02
    Papuan: 0.16
    American: 0.22
    Beringian: 0
    Med: 0.08
    SW Asian: 1.07

    HG02783
    South Indian: 54.83
    Baloch: 31.15
    Caucasian: 3.66
    Northern European: 1.87
    SE Asian: 3.87
    Siberian: 0.26
    NE Asian: 0.03
    Papuan: 0.34
    American: 0.44
    Beringian: 0
    Med: 3.31
    SW Asian: 0.24

    HG02790
    South Indian: 53.69
    Baloch: 29.37
    Caucasian: 2.91
    Northern European: 5.35
    SE Asian: 2.99
    Siberian: 0.03
    NE Asian: 0
    Papuan: 1.87
    American: 1.25
    Beringian: 0.51
    Med: 0.38
    SW Asian: 1.64


    Both HG02724 HG02790 are peculiar ones. Very high Northern European for samples which appear to be a dalit/chura at first glance with notable SE Asian and low Baloch. Overall, the samples chosen for G25 and the biorvix 2013 paper by Laziridis seem to be individuals that match up against various Punjabi chamar to Punjabi dalit samples that MDL and myself have come across on GEDMatch. Not sure if it is relevant but most of them show a stronger AASI/tribal shift but still seem to retain Steppe admixture albeit at levels clearly lower than Indo-Aryan speaking Brahmins.
    Last edited by Sapporo; 07-12-2019 at 11:54 AM.
    I4285 I4285 1873-1661 calBCE (343025 BP, PSUAMS-2536) BMAC Sappali_Tepe_BA Sappali Tepe Uzbekistan U7a3 L1a
    I5604 I5604 1880-1697 calBCE (346520 BP, PSUAMS-2774) BMAC Bustan_BA Bustan Uzbekistan K1a1 L1a
    I6667 I6667 1497-1413 calBCE (317020 BP, PSUAMS-2998) Parkhai_LBA_o Parkhai_LBA_o Parkhai II Turkmenistan HV2a
    I6669 I6669 3082-2909 calBCE (436525 BP, PSUAMS-2950) Parkhai_EN Parkhai_EN Parkhai II Turkmenistan HV2
    I4899 I4899 1600-1300 BCE BMAC Bustan_BA Bustan Uzbekistan R0 J

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  17. #530
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    [

    Are they related samples? They score quite similar to Bihari, possibly West Bengali samples non Brahmin samples.

    Do any other Punjabi samples you've come across score SE Asian? I've seen it pop up in some of the South Indian samples, but somehow doesn't strike me as AASI/Onge like.

    Edit.... We have G25 coordinates rather than relying on an outdated admixture calculator. Anyone able to model the individual samples specifically?
    Last edited by Reza; 07-12-2019 at 11:49 AM.
    Paternal; Y-DNA: R1a-L657> Y6> Y11> Y920*
    Paternal; mtDNA: M5b'c
    Maternal; Y-DNA: R1a-L657> Y6
    Maternal; mtDNA: M4b1

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