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Thread: Eurogenes Global 25 with Gradient Descent Optimization - Run Your Own Models!

  1. #651
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    Quote Originally Posted by lana6765 View Post
    On unscaled coordinates, 'Siberian' traces seem to pop everywhere (G25 scaled and unscaled, K13, K15, MDLP etc.), but they're especially extreme in G25 unscaled.

    This may be a silly question, but can't 'exotic' populations get exaggerated in unscaled?

    I've seen Irish people get 'Native American'. Is this 'Siberian' the same thing? Is this something about the Irish population left from ancient times?

    Examples (AncestryDNA coordinates used):

    Adam Quick - Unscaled Modern

    Distance: 0.7548827590640099%

    Icelandic: 43.4%
    Orcadian: 34.2%
    French_Paris: 22.3%
    Other: 0.1%

    (So far so normal!)

    Adam Thorough - Unscaled Modern

    Distance: 0.14496211938345233%

    Dutch: 45.6%
    Irish: 13.2%
    Orcadian: 11.5%
    Basque_French: 9.9%
    English: 7.0%
    Scottish: 6.5%
    Saami: 4.2%
    Belgian: 1.1%
    Norwegian: 0.8%
    Italian_Aosta_Valley: 0.2%
    Other: 0.0%

    Adam Thorough - Unscaled Modern Averages

    Distance: 0.779511521650911%

    Norwegian: 40.2%
    Shetlandic: 18.7%
    French_Pas-de-Calais: 18.7%
    Irish: 7.6%
    Basque_French: 5.8%
    Icelandic: 5.3%
    Japanese: 2.0%
    Mari: 1.0%

    Papuan: 0.5%
    Other: 0.1%
    The "Siberian" and "Native American" that you see are the same thing, most likely. If you see it on the good low K admixture tests, it probably is "something", but the question is what? I would guess, given proximity to Ireland, that it may be some Saami-like interaction maybe from Scandinavia contact in the past that is hanging around, but there could be other explanations. The Adam - Quick preset sets this minor stuff aside, which is useful. I don't get much exaggeration, meaning I get very similar percentages as I get on admixture tests, but maybe you are seeing more than usual. It is obviously an overfitting artifact on the Adam - Thorough models, because it is not likely that you have a Saami g-g-g grandparent. But, I have had success finding sources for minor admixture in my family using other tools. I like the G25 unscaled because it has dimensions that distinguish between Native American and Siberian, but if you scale the coordinates, those dimensions are rendered almost useless. You can look at my earlier post (I will add a link) where I used Adam - Slow and it correctly figures out that my father has Siberian and East Asian, but my mother has Amerind and South Asian admixture, for example. If I try to run with scaled values, my mother's results often become East Asian and my father's less precise, too.

    Edit: Adam - Slow results: https://anthrogenica.com/showthread....l=1#post725969
    Last edited by randwulf; 02-06-2021 at 09:47 PM.

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  3. #652
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    Quote Originally Posted by Mariusz95 View Post
    And it's better to use normal modern or averages populations?
    I like to try both. For my finished, custom models that you see I post here from time to time, I use unscaled, individuals. Here are my current working models for my family created this way:

    Me:

    Distance: 0.6839526673240739%

    French_Paris: 65.6%
    Welsh: 26.9%
    Ashkenazi_Germany: 3.2%
    Swiss_German: 2.1%
    Roma_Balkans: 1.4%
    Cree: 0.6%
    Biaka: 0.2%

    Dad:

    Distance: 0.8194644996054063%

    German: 85.5%
    Ashkenazi_Germany: 14.5%


    Mom:

    Distance: 0.8527504250255138%

    Welsh: 45.5%
    Swiss_German: 27.5%
    French_Paris: 21.5%
    Roma_Balkans: 3.5%
    Biaka: 1.2%
    Cree: 0.9%

    Wife:

    Distance: 0.3244452164918914%

    English_Cornwall: 44.9%
    English: 28.7%
    French_Alsace: 18.1%
    Ashkenazi_Ukraine: 8.2%

    Father in law:

    Distance: 0.7188033055507503%

    English_Cornwall: 50.1%
    English: 37.7%
    Ashkenazi_Ukraine: 5.4%
    French_Alsace: 5.1%
    Yoruba: 1.0%
    USA_Alaska_TrailCreek_9000BP: 0.7%
    Last edited by randwulf; 02-06-2021 at 10:02 PM.

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  5. #653
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    Quote Originally Posted by randwulf View Post
    The "Siberian" and "Native American" that you see are the same thing, most likely. If you see it on the good low K admixture tests, it probably is "something", but the question is what? I would guess, given proximity to Ireland, that it may be some Saami-like interaction maybe from Scandinavia contact in the past that is hanging around, but there could be other explanations. The Adam - Quick preset sets this minor stuff aside, which is useful. I don't get much exaggeration, meaning I get very similar percentages as I get on admixture tests, but maybe you are seeing more than usual. It is obviously an overfitting artifact on the Adam - Thorough models, because it is not likely that you have a Saami g-g-g grandparent. But, I have had success finding sources for minor admixture in my family using other tools. I like the G25 unscaled because it has dimensions that distinguish between Native American and Siberian, but if you scale the coordinates, those dimensions are rendered almost useless. You can look at my earlier post (I will add a link) where I used Adam - Slow and it correctly figures out that my father has Siberian and East Asian, but my mother has Amerind and South Asian admixture, for example. If I try to run with scaled values, my mother's results often become East Asian and my father's less precise, too.

    Edit: Adam - Slow results: https://anthrogenica.com/showthread....l=1#post725969
    Thank you for this. It's interesting that one can separate Asian from Native American in unscaled. Native American would be unlikely! It would certainly be unlikely in my case! I think this is far more likely from somewhere within Europe where links are known to exist.

    I've read that Ireland interacted with Norway during the Viking age. I wonder if this is indeed the reason behind some Irish results that I have seen. In my case, I'm only 1/3 Irish, so the influence could be from another source. I also found information on Russians in London and Liverpool (I don't know how relevant that is) and England has it's own Viking influence, mainly from southern Scandinavia.
    Last edited by lana6765; 02-06-2021 at 11:39 PM.

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  7. #654
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    Quote Originally Posted by lana6765 View Post
    Thank you for this. It's interesting that one can separate Asian from Native American in unscaled. Native American would be unlikely! It would certainly be unlikely in my case! I think this is far more likely from somewhere within Europe where links are known to exist.

    I've read that Ireland interacted with Norway during the Viking age. I wonder if this is indeed the reason behind some Irish results that I have seen. In my case, I'm only 1/3 Irish, so the influence could be from another source. I also found information on Russians in London and Liverpool (I don't know how relevant that is) and England has it's own Viking influence, mainly from southern Scandinavia.
    On this thread, I examine the information that each dimension contains and plot my five family coordinates with the dimension in a PCA plot:
    https://anthrogenica.com/showthread....l=1#post566344

    As far as source research for unusual admixture, I use Gedmatch segment searches to search for matches on well organized sub segments of the admixture type that can be found with chromosome painting. Then, I can use those "cousins" to help figure out from whence the admixture came.

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  9. #655
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    The ancients spreadsheets have several updates since I last loaded them to the application, so I loaded them. Some "Adam - Quick Alts" runs for my family with the new spreadsheets:

    Me:

    Distance: 0.8347952706942804%

    VK2020_DNK_Jutland_VA: 59.0%
    VK2020_SWE_Karda_VA: 26.4%
    VK2020_England_Oxford_VA: 14.7%

    Dad:

    Distance: 0.8372000858040369%

    ITA_Sicily_EBA: 37.3%
    VK2020_EST_Saaremaa_EVA: 25.2%
    HUN_MA_Szolad: 20.9%
    VK2020_SWE_Skara_VA: 16.6%


    Mom:

    Distance: 0.8586209888038117%

    VK2020_SWE_Gotland_VA: 52.2%
    VK2020_DNK_Jutland_VA: 29.0%
    VK2020_SWE_Skara_VA: 18.2%
    SRB_Mokrin_EBA: 0.7%

    Wife:

    Distance: 0.6091924628562864%

    VK2020_SWE_Oland_VA: 49.1%
    VK2020_DNK_Sealand_VA: 46.8%
    ITA_Rome_MA: 4.1%

    Father in law:

    Distance: 0.8520084711489345%

    VK2020_GreenlandE_VA: 45.7%
    VK2020_England_Dorset_VA: 38.3%
    VK2020_Faroes_EM: 16.0%
    Last edited by randwulf; 02-10-2021 at 01:12 PM.

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  11. #656
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    Hi all! I have added the ability to "truncate" the PCA and your G25 coordinates through a property. The property always defaults to 25 when you change presets, but if you would like to see the impact of removing upper dimensions, you can pick the number to use. It will run the calculation and your nearest neighbors list using the number of dimensions from the lower part of the PCA coordinates that you pick. I permitted any integer from "9" through "25" to be entered. Just paste your personal G25 coordinates, as usual. You should not truncate them yourself, the tool will do it, as well as truncating the model internally when you press the "Calculate" button.

    Here are my coordinates run with the "Modern within 5 pct Avg" spreadsheet and the "Adam - Quick" preset starting with the full 25 and removing one each time. For me, the "it would be amazing if it figured this out" results would be around 75%-78% French/German and 22%-25% Isles (well, 25 dims does that pretty well, already):

    Distance: 0.693% (25 dims)

    French_Paris: 49.6%
    Irish: 25.7%
    Swiss_French: 24.6%

    Distance: 0.398% (24 dims)

    Swiss_French: 20.5%
    French_Auvergne: 17.4%
    English: 12.4%
    Basque_Spanish: 10.0%
    French_Alsace: 9.7%
    Norwegian: 9.3%
    French_Brittany: 8.5%
    German: 8.4%
    Dutch: 3.5%
    Spanish_Galicia: 0.3%

    Distance: 0.509% (23 dims)

    French_Alsace: 39.0%
    Irish: 25.2%
    German: 14.1%
    Spanish_Catalunya_Central: 10.0%
    Basque_Spanish: 9.8%
    Dutch: 1.9%

    Distance: 0.565% (22 dims)

    French_Brittany: 33.2%
    Swiss_French: 29.8%
    French_Occitanie: 22.1%
    French_Alsace: 11.5%
    Dutch: 2.9%
    Spanish_Catalunya_Central: 0.4%

    Distance: 0.655% (21 dims)

    French_Paris: 48.1%
    French_Alsace: 29.6%
    French_Auvergne: 21.7%
    Spanish_Catalunya_Central: 0.7%

    Distance: 0.243% (20 dims)

    Dutch: 23.0%
    Belgian: 18.0%
    French_South: 17.4%
    Spanish_Eivissa: 15.2%
    Irish: 14.6%
    German: 6.9%
    Spanish_Lleida: 3.8%
    Yakut: 0.7%
    French_Occitanie: 0.4%

    Distance: 0.387% (19 dims)

    French_Paris: 34.0%
    French_Occitanie: 29.5%
    French_Alsace: 19.5%
    Dutch: 17.0%

    Distance: 0.224% (18 dims)

    French_Auvergne: 28.1%
    German: 27.3%
    French_Pas-de-Calais: 16.4%
    French_Seine-Maritime: 14.3%
    Irish: 7.4%
    Basque_French: 5.7%
    Spanish_Aragon: 0.8%

    Distance: 0.551% (17 dims)

    French_Pas-de-Calais: 62.5%
    French_Alsace: 20.7%
    German: 15.3%
    Danish: 1.5%

    Distance: 0.452% (16 dims)

    French_Paris: 45.4%
    German: 33.4%
    Irish: 15.6%
    French_Nord: 5.0%
    Spanish_Mallorca: 0.6%

    Distance: 0.429% (15 dims)

    French_Paris: 47.7%
    French_Alsace: 31.3%
    Belgian: 21.0%

    Distance: 0.283% (14 dims)

    Belgian: 56.8%
    French_Occitanie: 43.2%

    Distance: 0.121% (13 dims)

    French_Brittany: 52.4%
    French_South: 12.9%
    French_Nord: 10.5%
    French_Alsace: 8.7%
    Spanish_Lleida: 6.2%
    French_Occitanie: 5.5%
    Spanish_Catalunya_Central: 1.8%
    Basque_Spanish: 1.1%
    Spanish_Galicia: 0.4%
    Belgian: 0.3%

    Distance: 0.154% (12 dims)

    French_Auvergne: 43.4%
    Belgian: 36.6%
    Spanish_Barcelones: 7.8%
    German: 7.4%
    French_Paris: 3.6%
    French_Brittany: 0.4%
    Spanish_Camp_de_Tarragona: 0.4%
    French_Nord: 0.2%

    Distance: 0.284% (11 dims)

    French_Paris: 34.0%
    French_Auvergne: 28.9%
    Dutch: 22.4%
    Irish: 7.8%
    French_Nord: 6.6%
    French_Pas-de-Calais: 0.2%

    Distance: 0.514% (10 dims)

    Swiss_French: 67.1%
    French_Pas-de-Calais: 31.4%
    Belgian: 1.5%

    Distance: 0.106% (9 dims)

    Belgian: 32.2%
    French_Pas-de-Calais: 31.3%
    Irish: 25.2%
    French_Brittany: 11.2%
    Dutch: 0.2%

    Enjoy!
    Last edited by randwulf; 03-05-2021 at 09:21 AM.

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  13. #657
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    Cool stuff. Quick play around using Unscaled with Adam Thorough.

    Myself

    Distance: 0.170% (25 dims)

    French_Nord: 33.9%
    Dutch: 18.4%
    German: 9.5%
    Czech: 8.8%
    French_Brittany: 8.7%
    Scottish: 6.9%
    Belgian: 6.4%
    Irish: 2.9%
    Danish: 1.8%
    Swiss_French: 1.2%
    Papuan: 1.0%
    Mari: 0.5%
    Other: 0.0%

    Father

    Distance: 0.166% (25 dims)

    French_Alsace: 18.8%
    Scottish: 17.8%
    Polish: 17.4%
    French_Occitanie: 10.6%
    Basque_Spanish: 6.4%
    Dutch: 6.4%
    Darginian: 5.7%
    Mari: 4.2%
    Danish: 3.8%
    German: 3.5%
    Yemenite_Mahra: 2.4%
    Swiss_German: 1.1%
    Lithuanian_PZ: 1.1%
    Mbuti: 0.6%
    Other: 0.0%

    Grandfather

    Distance: 0.569% (25 dims)

    Irish: 35.3%
    Scottish: 19.8%
    Dutch: 8.6%
    English: 8.4%
    German: 6.2%
    French_Auvergne: 5.9%
    Belgian: 4.9%
    Danish: 3.7%
    Basque_French: 3.0%
    Khanty: 1.9%
    Somali_Kenya: 1.8%
    Brahmin_Uttar_Pradesh: 0.4%

    Grandmother

    Distance: 0.357% (25 dims)

    Irish: 50.2%
    German: 22.9%
    Basque_French: 9.1%
    English: 6.9%
    Belgian: 5.6%
    Khanty: 2.3%
    Kalash: 1.5%
    Papuan: 0.8%
    Dinka: 0.6%
    Other: 0.0%
    Ancestry on paper: English, Scottish, Irish, Welsh, Croatian, Ashkenazi, Polish and Māori.

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  15. #658
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    Unscaled:

    Ancient
    Distance: 1.009%

    IND_Roopkund_B: 35.1%
    IRN_Tepe_Hissar_C: 28.1%
    KAZ_Kipchak: 19.2%
    TKM_Sumbar_LBA: 4.8%
    UZB_Sappali_Tepe_BA: 4.6%
    Levant_Megiddo_MLBA: 2.5%
    MNG_TUK001: 2.3%
    TUR_Alalakh_MLBA: 2.0%
    Levant_LBN_MA: 0.5%
    TKM_Parkhai_LBA: 0.4%
    Levant_Beirut_ERoman: 0.3%

    Modern
    Distance: 1.047%

    Iranian: 45.2%
    Lak: 25.5%
    Iranian_Fars: 17.7%
    Lebanese_Sunni_Muslim: 10.0%
    Kurdish: 1.6%
    Other: 0.0%

    Scaled:

    Ancient
    Distance: 3.309%

    IRN_Hasanlu_IA: 100.0%
    Other: 0.0%

    Modern
    Distance: 1.958%

    Iranian: 100.0%
    Other: 0.0%


    What ist MNG_TUK001?

  16. #659
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    Quote Originally Posted by AureliusDNA View Post
    Unscaled:

    Ancient
    Distance: 1.009%

    IND_Roopkund_B: 35.1%
    IRN_Tepe_Hissar_C: 28.1%
    KAZ_Kipchak: 19.2%
    TKM_Sumbar_LBA: 4.8%
    UZB_Sappali_Tepe_BA: 4.6%
    Levant_Megiddo_MLBA: 2.5%
    MNG_TUK001: 2.3%
    TUR_Alalakh_MLBA: 2.0%
    Levant_LBN_MA: 0.5%
    TKM_Parkhai_LBA: 0.4%
    Levant_Beirut_ERoman: 0.3%

    Modern
    Distance: 1.047%

    Iranian: 45.2%
    Lak: 25.5%
    Iranian_Fars: 17.7%
    Lebanese_Sunni_Muslim: 10.0%
    Kurdish: 1.6%
    Other: 0.0%

    Scaled:

    Ancient
    Distance: 3.309%

    IRN_Hasanlu_IA: 100.0%
    Other: 0.0%

    Modern
    Distance: 1.958%

    Iranian: 100.0%
    Other: 0.0%


    What ist MNG_TUK001?
    Go go this page and scan for "TUK001":

    https://www.sciencedirect.com/scienc...92867420313210

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    I decided to try out the dimension truncation change that I made to the Ancestry calculator on the classic "ancients" model for Europeans and the unscaled coordinates. I tried reducing to 23 dimensions, removing PC24 and PC25. The change was significant. There are four results for each person 1) Scaled results 2) Unscaled 25 dimensions 3) Unscaled 23 dimensions 4) Unscaled 23 dimensions and only Steppe-Farner-WHG references included.

    Target: fil
    Distance: 6.0371% / 0.06037101
    47.4 Yamnaya_RUS_Samara
    38.8 TUR_Barcin_N
    13.0 WHG
    0.8 MAR_Taforalt

    Distance: 2.703%

    Yamnaya_RUS_Samara: 53.6%
    TUR_Barcin_N: 36.1%
    WHG: 6.2%
    Han_Sichuan: 2.6%
    MAR_Taforalt: 1.5%

    Distance: 2.160%

    Yamnaya_RUS_Samara: 47.3%
    TUR_Barcin_N: 36.0%
    WHG: 12.3%
    Han_Sichuan: 2.5%
    MAR_Taforalt: 1.8%

    Distance: 2.211%

    Yamnaya_RUS_Samara: 49.5%
    TUR_Barcin_N: 38.3%
    WHG: 12.2%

    Target: wife
    Distance: 4.2564% / 0.04256386
    44.6 Yamnaya_RUS_Samara
    42.8 TUR_Barcin_N
    12.6 WHG

    Distance: 1.948%

    Yamnaya_RUS_Samara: 51.7%
    TUR_Barcin_N: 36.3%
    WHG: 7.8%
    Han_Sichuan: 2.1%
    MAR_Taforalt: 1.1%
    Dinka: 1.0%

    Distance: 0.886%

    Yamnaya_RUS_Samara: 42.9%
    TUR_Barcin_N: 38.3%
    WHG: 16.0%
    Han_Sichuan: 1.4%
    MAR_Taforalt: 1.2%
    Dinka: 0.1%

    Distance: 0.933%

    Yamnaya_RUS_Samara: 44.4%
    TUR_Barcin_N: 39.8%
    WHG: 15.8%

    Target: mom
    Distance: 4.3477% / 0.04347653
    43.2 TUR_Barcin_N
    43.2 Yamnaya_RUS_Samara
    13.6 WHG

    Distance: 1.697%

    Yamnaya_RUS_Samara: 45.4%
    TUR_Barcin_N: 39.3%
    WHG: 8.9%
    Dinka: 3.7%
    Han_Sichuan: 2.8%

    Distance: 1.400%

    TUR_Barcin_N: 40.9%
    Yamnaya_RUS_Samara: 39.7%
    WHG: 14.5%
    Han_Sichuan: 3.2%
    Dinka: 1.7%

    Distance: 1.440%

    TUR_Barcin_N: 43.6%
    Yamnaya_RUS_Samara: 41.6%
    WHG: 14.8%

    Target: dad
    Distance: 3.9145% / 0.03914549
    44.0 TUR_Barcin_N
    42.8 Yamnaya_RUS_Samara
    11.8 WHG
    1.2 Han
    0.2 Nganassan

    Distance: 1.682%

    Yamnaya_RUS_Samara: 49.2%
    TUR_Barcin_N: 41.4%
    WHG: 5.9%
    MAR_Taforalt: 2.1%
    Nganassan: 1.0%
    Han_Sichuan: 0.4%

    Distance: 0.902%

    TUR_Barcin_N: 44.8%
    Yamnaya_RUS_Samara: 39.5%
    WHG: 13.1%
    MAR_Taforalt: 2.5%

    Distance: 0.998%

    TUR_Barcin_N: 45.3%
    Yamnaya_RUS_Samara: 40.6%
    WHG: 14.1%

    Target: me
    Distance: 4.2747% / 0.04274674
    46.0 TUR_Barcin_N
    40.2 Yamnaya_RUS_Samara
    13.4 WHG
    0.4 Han

    Distance: 1.909%

    Yamnaya_RUS_Samara: 44.7%
    TUR_Barcin_N: 42.2%
    WHG: 8.6%
    Han_Sichuan: 3.2%
    MAR_Taforalt: 0.9%
    Dinka: 0.3%

    Distance: 1.464%

    TUR_Barcin_N: 43.8%
    Yamnaya_RUS_Samara: 38.4%
    WHG: 14.1%
    Han_Sichuan: 2.8%
    MAR_Taforalt: 1.0%

    Distance: 1.500%

    TUR_Barcin_N: 45.9%
    Yamnaya_RUS_Samara: 39.9%
    WHG: 14.2%

  19. The Following 4 Users Say Thank You to randwulf For This Useful Post:

     AureliusDNA (03-07-2021),  BalkanKiwi (03-07-2021),  Justnotyou (03-13-2021),  Nino90 (03-07-2021)

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