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Thread: A clustering of the Europeans from Global 25

  1. #1
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    A clustering of the Europeans from Global 25

    Like many others I am curious about the possibility of clustering the post Bronze Age Europeans in Global 25.
    But not along the cultural population labels, which are the accidental results of a history of conquering, independence, dynastic and religious wars.
    Instead I prefer a clustering on exclusively the genetic properties (a.k.a. 'unsupervised classification').
    I found an acceptable result with 9 clusters. Only after I generated this genetical classification, I have compared it with the population labels of G25.
    In the next plot I have mapped the 9 genetic clusters on the PCA coordinates.
    plot_k3_G9_s1.jpg
    And here you can compare my genetic clusters with the population labels of G25.
    Import the content of the spoiler box into a spreadsheet, separator=','
     
    ,'1','2','3','4','5','6','7','8','9'
    Abkhasian,0,0,0,0,9,0,0,0,0
    Adygei,0,0,0,0,10,0,0,0,1
    Alan,0,0,0,0,5,0,0,0,0
    Albanian,0,0,5,0,0,2,0,0,0
    Anc_Finn,0,1,0,0,0,0,0,0,0
    Anc_Saami,0,0,0,1,0,0,0,0,1
    Armenian,0,0,0,0,10,0,0,0,0
    Ashkenazi_Jew,0,0,0,0,0,7,0,0,0
    Austrian,9,0,8,0,0,0,0,0,0
    Avar,0,0,0,0,3,0,0,0,0
    Avar_Hungary_Szolad,0,0,0,0,0,0,2,0,0
    Azeri,0,0,0,0,10,0,0,0,0
    Azeri_Dagestan,0,0,0,0,5,0,0,0,0
    Balkans_IA,0,0,0,0,0,1,0,0,0
    Balkar,0,0,0,0,3,0,0,0,0
    Baltic_IA,0,0,0,0,0,0,1,0,0
    Bashkir,0,0,0,0,0,0,0,0,10
    Basque_French,0,0,0,0,0,0,0,10,0
    Basque_Spanish,0,0,0,0,0,0,0,9,0
    Belarusian,0,0,0,2,0,0,13,0,0
    Belgian,26,1,0,0,0,0,0,0,0
    Bosnian,0,0,5,0,0,0,0,0,0
    Bulgarian,0,0,5,0,0,0,0,0,0
    Chechen,0,0,0,0,9,0,0,0,0
    Chuvash,0,0,0,1,0,0,0,0,9
    Cimmerian_Moldova,0,0,0,0,0,0,0,0,3
    Cossack_Kuban,0,0,0,1,0,0,0,0,0
    Cossack_Ukrainian,0,0,0,0,0,0,1,0,0
    Croatian,0,0,10,0,0,0,0,0,0
    Cypriot,0,0,0,0,0,8,0,0,0
    Czech,1,0,12,0,0,0,1,0,0
    Dutch,17,47,0,0,0,0,0,0,0
    England_Anglo-Saxon,0,3,0,0,0,0,0,0,0
    England_IA,2,1,0,0,0,0,0,0,0
    England_Roman,1,5,0,0,0,0,0,0,0
    England_Roman_o,0,0,0,0,0,1,0,0,0
    English,1,18,0,0,0,0,0,0,0
    English_Cornwall,0,13,0,0,0,0,0,0,0
    Estonian,0,0,1,7,0,0,4,0,0
    Finnish,0,0,9,8,0,0,0,0,0
    Finnish_East,0,0,0,10,0,0,0,0,0
    French,64,4,0,0,0,0,0,0,0
    French_East,10,0,0,0,0,0,0,0,0
    French_South,0,0,0,0,0,0,0,7,0
    Georgian_Imer,0,0,0,0,5,0,0,0,0
    Georgian_Jew,0,0,0,0,7,0,0,0,0
    Georgian_Laz,0,0,0,0,5,0,0,0,0
    Gepid_Serbia_ACD,1,0,0,0,0,0,0,0,0
    German,59,7,20,0,0,0,1,0,0
    Germany_Medieval,6,4,0,0,0,0,0,0,0
    Germany_Medieval_ACD,2,1,1,0,0,3,0,0,1
    Germany_Medieval_o,0,0,0,0,0,1,0,0,0
    Germany_Roman,0,0,0,0,0,0,0,1,0
    Golden_Horde_European,0,0,0,0,0,0,1,0,0
    Greek,0,0,10,0,0,9,0,0,0
    Greek_Central_Anatolia,0,0,0,0,1,2,0,0,0
    Greek_Crete,0,0,0,0,0,3,0,0,0
    Greek_Trabzon,0,0,0,0,9,0,0,0,0
    Hallstatt_Bylany,2,0,0,0,0,0,0,0,0
    Hun-Sarmatian,0,0,0,0,1,0,0,0,1
    Hungarian,2,0,14,0,0,0,0,0,0
    Hungary_IA,0,0,0,0,0,0,0,0,1
    Hungary_Medieval,1,0,0,0,0,0,0,0,0
    Hungary_Medieval_Szolad_o1,0,0,0,0,0,1,0,0,0
    Hungary_Medieval_Szolad_o2,1,0,0,0,0,0,0,0,0
    Icelandic,0,14,0,0,0,0,0,0,0
    Ingrian,0,0,0,3,0,0,0,0,0
    Irish,1,63,0,0,0,0,0,0,0
    Italian_Abruzzo,0,0,0,0,0,11,0,0,0
    Italian_Bergamo,0,0,0,0,0,1,0,5,0
    Italian_Jew,0,0,0,0,0,10,0,0,0
    Italian_South,0,0,0,0,0,4,0,0,0
    Italian_Tuscan,0,0,0,0,0,5,0,0,0
    Italy_Medieval_Collegno_o1,0,0,0,0,0,3,0,0,0
    Kabardin,0,0,0,0,10,0,0,0,0
    Karelian,0,0,0,19,0,0,0,0,0
    Komi,0,0,0,9,0,0,0,0,1
    Latvian,0,0,0,0,0,0,5,0,0
    Lithuanian,0,0,0,1,0,0,4,0,0
    Longobard_North,14,15,0,0,0,0,0,0,0
    Longobard_South,7,0,0,0,0,7,0,2,0
    Macedonian,0,0,5,0,0,0,0,0,0
    Malak_Preslavets,0,0,0,0,0,3,0,0,0
    Maltese,0,0,0,0,0,8,0,0,0
    Moldovan,0,0,10,0,0,0,0,0,0
    Montenegrin,0,0,5,0,0,0,0,0,0
    Mordovian,0,0,0,23,0,0,0,0,0
    Nordic_IA,1,0,0,0,0,0,0,0,0
    North_Ossetian,0,0,0,0,4,0,0,0,0
    Norwegian,1,7,0,0,0,0,0,0,0
    Orcadian,0,12,0,0,0,0,0,0,0
    Ostrogothic_Crimea_ACD,0,0,0,0,1,0,0,0,0
    Polish,0,0,10,4,0,0,26,0,0
    Poprad_Medieval,1,0,0,0,0,0,0,0,0
    Portuguese,5,0,0,0,0,1,0,9,0
    Romanian,0,0,10,0,0,0,0,0,0
    Russian_Kostroma,0,0,0,6,0,0,0,0,0
    Russian_Kursk,0,0,0,2,0,0,2,0,0
    Russian_Orel,0,0,0,3,0,0,4,0,0
    Russian_Pinega,0,0,0,3,0,0,0,0,0
    Russian_Smolensk,0,0,0,2,0,0,6,0,0
    Russian_Tver,0,0,0,4,0,0,0,0,0
    Russian_Voronez,0,0,0,1,0,0,3,0,0
    Saami,0,0,0,4,0,0,0,0,0
    Sarmatian,0,0,0,0,0,0,0,0,3
    Sarmatian_Pokrovka,0,0,0,0,0,0,0,0,2
    Sarmatian_Urals,0,0,0,0,0,0,0,0,4
    Sarmatian_West,0,0,0,0,0,0,0,0,7
    Scottish,1,27,0,0,0,0,0,0,0
    Scythian_Hungary,1,0,3,0,0,1,0,0,0
    Scythian_Moldova,1,0,0,0,0,3,0,0,2
    Scythian_Samara,0,0,0,0,0,0,0,0,1
    Scythian_Ukraine,0,0,1,0,0,0,1,0,1
    Serbian,0,0,5,0,0,0,0,0,0
    Shetlandic,0,3,0,0,0,0,0,0,0
    Sicilian_East,0,0,0,0,0,3,0,0,0
    Sicilian_West,0,0,0,0,0,3,0,0,0
    Slavic_Bohemia,0,0,1,0,0,0,0,0,0
    Slovakian,0,0,1,0,0,0,4,0,0
    Slovenian,0,0,4,0,0,0,1,0,0
    Spanish,2,0,0,0,0,1,0,38,0
    Sweden_Viking_Age,0,2,1,1,0,0,0,0,0
    Swedish,17,5,0,0,0,0,0,0,0
    Tatar,0,0,0,0,0,0,0,0,10
    Tatar_Lipka,0,0,0,0,0,0,0,0,6
    Udmurt,0,0,0,0,0,0,0,0,8
    Ukrainian,0,0,0,4,0,0,19,0,0
    Vepsian,0,0,0,8,0,0,0,0,0
    Welsh,0,3,0,0,0,0,0,0,0

    Here is a summary of the main features of the 9 clusters:

    cluster 1
    Cluster 1 contains 64 of the 68 French samples, and 10/10 of the French_East samples, but not the French_South and Basque samples.
    Also 26/27 of the Belgian samples are in #1.
    59/87 German are in cluster1.
    Cluster 1 also has 17/22 of the Swedish and 1/1 Nordic IA.
    This cluster is the non-British NW cluster.

    cluster 2
    Irish 63/64, Scottish 27/28, English 18/19, Cornwall 13/13, Orcadian 12/12, Shetlandic 3/3, Welsh 3/3, England_Roman 5/6, England_Anglo-Saxon 3/3,
    Icelandic 14/14, Norwegian 7/8, Dutch 47/64.
    This is the Britisch cluster. It also includes Norwegian/Icelandic. And a majority of 47/74 of the Dutch.

    cluster 3
    Hungarian 14/16, Czech 12/14, Croatian 10/10, Moldovan 10/10, Romanian 10/10, German 20/87, Greek 10/19.
    This is a Central European cluster with a Slavic accent.

    cluster 4
    Mordovian 23/23, Karelian 19/19, Finnish_East 10/10, Komi 9/10, Vepsian 8/8, Russian_Kostroma 6/6, Saami 4/4.
    Finnish 8/17.
    This appears to be a Finnish_East/Uralic cluster.

    cluster 5
    These are the Caucasus populations.

    cluster 6
    Italian_Abruzzo 11/11, Italian_Jew 10/10, Ashkenazi_Jew 7/7, Cypriot 8/8, Maltese 8/8, Sicilian 6/6.
    Mainly Italian and some more Eastern.

    cluster 7
    Ukrainian 19/23, Belarusian 13/15, Polish 26/40, Russia_Smolensk 6/8
    Apparently a Slavic cluster.

    cluster 8
    Spanish 38/41, Basque 19/19, Portuguese 9/14, French_South 7/7, Italian_Bergamo 5/6.
    The Iberian cluster.

    cluster 9
    Bashkir 10/10, Tatar 16/16, Chuvash 9/10, Udmurt 8/8,
    Sarmatian 16/16, Cimmerian_Moldova 3/3.
    This is a rest cluster from central European Russia. It also has captured several samples from the Migration period.

    Look in table from the spoiler box to check all the details.

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  3. #2
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    Sooo...can you add us to it to see which cluster we're in?
    G25 Hidden Content and Hidden Content distances
    Hidden Content
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    DEIBABOR
    IGO
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    BOR

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  5. #3
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    Quote Originally Posted by Ruderico View Post
    Sooo...can you add us to it to see which cluster we're in?
    Sure, send me your unscaled G25 scores.
    Keep in mind though that these 9 clusters are not as detailed as the 'cultural labels'.
    So probably your location will not surprise you, unless you are totally ignorant about your ancestry.
    Another possibility is that you are in the overlap of two clusters. I find that an interesting feature of this plot.

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  7. #4
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    Ger,

    Once more, thanks for this work.
    But I don't understand why some Swedish and Nordic_IA are in the same cluster (1) as the French and the Belgians ?
    My results from David Wesolowski's Ancestry Detective Service:

    West British (Britonic?) 42.3%
    Continental Northern and Eastern European 36.6%
    Central French 21.1%

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  9. #5
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    Netherlands Belgium
    Here is a plot of the three Dutch Anthrogenica members
    FHR.jpg
    The table shows that the Dutch samples are 47/64 members the 'British' cluster 2.
    Each of the three Dutch samples is near the overlapping zone of the clusters 1 and 2. But Finn and Radboud seem to be inside cluster 2, while Huijbregts is just outside. Finn is known to be Northern. Huijbregts has many Belgian ancestors, which is in line with a location within cluster 1.

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  11. #6
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    Normandie Sweden France Bretagne
    Can I send you the data of 3 Norman samples with 4 gp of same origin ?
    My results from David Wesolowski's Ancestry Detective Service:

    West British (Britonic?) 42.3%
    Continental Northern and Eastern European 36.6%
    Central French 21.1%

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  13. #7
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    Quote Originally Posted by Huijbregts View Post
    Sure, send me your unscaled G25 scores.
    Keep in mind though that these 9 clusters are not as detailed as the 'cultural labels'.
    So probably your location will not surprise you, unless you are totally ignorant about your ancestry.
    Another possibility is that you are in the overlap of two clusters. I find that an interesting feature of this plot.
    Hello Huijbregts,

    I suspect that I’ll be in the overlapping regions of of 1 & 2. Would you mind running mine, too?
    Known Paper Trail: 45.3% English, 29.7% Scottish, 12.5% Irish, 6.25% German & 6.25% Italian. Or: 87.5% British Isles, 6.25% German & 6.25% Italian.
    LivingDNA: 88.1% British Isles (59.7% English, 27% Scottish & 1.3% Irish), 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%), 4.4% Europe NW (Scandinavia) & 1.6% Europe East, (Mordovia).
    FT Big Y: I1-Z140 branch I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 900 AD) >A13242/YSEQ (circa 1030 AD) >A13243/YSEQ (circa 1550 AD).

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    Quote Originally Posted by Helgenes50 View Post
    Ger,

    Once more, thanks for this work.
    But I don't understand why some Swedish and Nordic_IA are in the same cluster (1) as the French and the Belgians ?
    Good question.
    When in the speculation mode, I might answer: It appears that the British cluster gets it northern admixture from Norway, while cluster 1 gets is northern admixture from Sweden.
    When in the statistical mode, I might point to the fact the the Norwegian and Swedish samples have much lower sampling densities than French and Irish. If in reality Norwegian and Swedish have similar DNA, they could not make it to a common cluster because their numbers are too low.

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    Helgenes, JMcB
    Send your unscaled G25 scores.

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  19. #10
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    Quote Originally Posted by Huijbregts View Post
    Helgenes, JMcB
    Send your unscaled G25 scores.
    Thank you, Ger, I appreciate it!

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
    JMcB,0.0116,0.0138,0.0175,0.0124,0.0133,0.0055,0.0 025,0.0023,0.0048,0.0054,0.0001,0.0001,-0.0109,-0.0092,0.0099,0.0024,-0.0047,0.002,0.0052,0.0016,0.0077,0.0022,0.0009,0. 0051,-0.0004
    Known Paper Trail: 45.3% English, 29.7% Scottish, 12.5% Irish, 6.25% German & 6.25% Italian. Or: 87.5% British Isles, 6.25% German & 6.25% Italian.
    LivingDNA: 88.1% British Isles (59.7% English, 27% Scottish & 1.3% Irish), 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%), 4.4% Europe NW (Scandinavia) & 1.6% Europe East, (Mordovia).
    FT Big Y: I1-Z140 branch I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 900 AD) >A13242/YSEQ (circa 1030 AD) >A13243/YSEQ (circa 1550 AD).

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