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Thread: Towards a better modelling of NorthWest Europeans in Global 25

  1. #21
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    Edit: Never mind, apologies, I think I misunderstood how to interpret the data, I don’t believe that I’m capable of doing so. Sorry for wasting your time!
    Last edited by BackToTheForests; 05-01-2019 at 12:57 PM.
    Y DNA E-V13>Z5018>S2979>Z16659>S2972* John Saunders unknown birthdate, died 1840 in Kings Bromley, Staffordshire, England.
    MtDNA U5a2c3a Betty Hallissy b.1801 Passage West, Cork, Ireland

  2. #22
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    Quote Originally Posted by Huijbregts View Post
    In my previous post I presented a three-way ADMIXTURE like partitioning of the NW-European populations in Global25.
    I used the modern populations and submodern populations from Iron Age to early Middle Ages.
    My goal was a robust common estimation of the NW-European populations, without using the labels.
    Now that I have estimated this model, I want to interpretate the three components that I found.
    For this interpretation I must return the labeled populations. But keep in mind that I estimated the model without the labels.

    Here I present a breakdown of the three-way scores by the labeled populations.
    The next spoiler box contains the average proportions for each population. Import them into a spreadsheet (separator ',').
     

    ,A,B,C
    Belgian,0.147,0.833,0.021
    Czech,0.003,0.003,0.995
    Dutch,0.740,0.148,0.112
    England_Anglo-Saxon,0.999,0.001,0.001
    England_IA,0.953,0.037,0.01
    England_Roman,0.993,0.004,0.002
    English,0.901,0.059,0.04
    English_Cornwall,0.926,0.074,0.001
    French,0.088,0.906,0.005
    French_East,0.047,0.838,0.115
    German,0.206,0.445,0.349
    German_East,0.001,0.011,0.988
    Germany_Medieval,0.618,0.122,0.259
    Hallstatt_Bylany_DA111,0.004,0.99,0.006
    IcelandNorw,0.994,0.001,0.005
    Irish,0.991,0.009,0
    Longobard_North,0.738,0.229,0.033
    Nordic_IA,0.886,0,0.114
    Orcadian,0.996,0.003,0.001
    Poprad_Medieval,0.626,0.356,0.018
    Scottish,0.967,0.031,0.002
    Shetlandic,0.995,0.005,0
    Slavic_Bohemia,0,0,1
    Swedish,0.746,0.012,0.242
    Welsh,0.995,0.003,0.002


    The above table shows the averages of the labeled populations, but tells us nothing about the internal variance.
    For the next table I have determined the dominant component for each sample, which is the component with the highest proportion.
    Next I counted for each labeled population the number of samples in each of the three components. This gives an impression of the internal variance.
    For instance, in the very homogeneous Irish population, each of the 64 samples 'A' is the dominant component.
    The Dutch are also rather homogeneous, with 49 of the 64 samples having 'A' dominant.
    The German samples are very heterogeneous with dominant components of 15 37 27.

     

    ,A,B,C
    Belgian,3,24,0
    Czech,0,0,14
    Dutch,49,7,8
    England_Anglo-Saxon,8,0,0
    England_IA,4,0,0
    England_Roman,6,0,0
    English,17,1,1
    English_Cornwall,13,0,0
    French,5,63,0
    French_East,0,9,1
    German,15,37,27
    German_East,0,0,8
    Germany_Medieval,7,1,2
    Hallstatt_Bylany_DA111,0,1,0
    IceLandNorw,22,0,0
    Irish,64,0,0
    Longobard_North,15,4,0
    Nordic_IA,1,0,0
    Orcadian,10,0,0
    Poprad_Medieval,1,0,0
    Scottish,27,1,0
    Shetlandic,3,0,0
    Slavic_Bohemia,0,0,1
    Swedish,16,0,6
    Welsh,3,0,0

    In my previous post I have already offered some remarks on the heterogeneity of the German samples.
    I think the best way to describe the German B phenomenon is:
    "Characteristic for NW-Europeans is the DNA component 'A'.
    South of the A-region we find another component 'B'. This starts in Belgium and Northern France and extends until deep in Germany."
    it is fascinating that there is no autosomal continuity throughout the Rhine. I would expect a gradation instead of a real shift.

    If we look at the PCA 1 and 2 intrapolation posted by on another thread, they don't seem to support that fact. Maybe, I am just not understanding them.
    K8: French East/German South/Austrian 26%, French North East/Belgian/German West 25%, French North 25%, Irish/Scottish/Welsh 10%, French South/French Basque 9%, German East/Czech/Austrian 5%
    K36: French East/German South/Swiss German 33%, French North East/Belgian/German West 31%, French North Central 21%, Irish/Scottish/Welsh 9%, French South/ French Basque 6%
    K16: German 50%, French North West 19%, French North East 11%, Irish/English 11%, French South 9%

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  4. #23
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    Quote Originally Posted by Theconqueror View Post
    Good job, if you want to run on my family, please do so. My wife is mostly a north sea creature and I am more continental. Kids are in between.

    PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 PC14 PC15 PC16 PC17 PC18 PC19 PC20 PC21 PC22 PC23 PC24 PC25
    Conqueror 0.0111 0.014 0.0138 0.0052 0.0141 0.0026 -0.0002 0.001 0.0062 0.0077 -0.0073 0.0028 -0.0036 -0.0063 0.0098 -0.007 -0.0084 -0.0024 -0.0019 -0.0063 -0.0028 0.0014 -0.0039 0.0049 0.0055
    Conqueror wife 0.0113 0.013 0.017 0.0142 0.0114 0.0034 -0.0017 -0.0021 0.0011 0.0014 -0.0003 0.0062 -0.0083 -0.0056 0.0146 0.0018 -0.0101 0.0012 0.0001 -0.0015 0.002 0.0059 0.0007 0.0077 0.0046
    Conqueror son 0.0116 0.0134 0.0152 0.0102 0.0117 0.0023 -0.0011 -0.0016 0.0046 0.004 -0.0017 0.0044 -0.0021 -0.0035 0.0115 -0.0035 -0.0084 0.0023 0.0018 -0.0067 0.0029 0.0001 -0.0033 0.0058 0.0046
    Conqueror daughter1 0.0114 0.0134 0.0145 0.009 0.0118 0.0037 -0.0016 -0.0018 0.0028 0.0048 -0.003 0.0046 -0.0071 -0.0088 0.0138 -0.0005 -0.0068 -0.0031 -0.0012 -0.0019 -0.0018 0.004 0.0002 0.0067 0.0075
    Conqueror daughter2 0.0117 0.0128 0.0165 0.0095 0.0138 0.0033 -0.0014 -0.0005 0.0027 0.0036 -0.0049 0.0039 -0.0051 -0.0044 0.0102 -0.0015 -0.0028 0.0011 0 -0.0036 0.0009 0.0054 -0.0037 0.0073 0.0044
    A B C
    Conqueror 0.000 1.000 0.000
    Conqueror_wife 0.989 0.011 0.000
    Conqueror_son 0.220 0.775 0.005
    Conquero_daughter1 0.189 0.811 0.000
    Conqueror_daughter2 0.076 0.921 0.003

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  6. #24
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    So the only ones with B are Belgian, French, French East, German, Lombards, Hallstatt. As per you comment: South of the A-region we find another component 'B'. This starts in Belgium and Northern France and extends until deep in Germany."

    Would it make sense to look at Germany from the four quadrants: NW, NE, SW, SE? I believe there a rift North South worth investigating.

    Thanks for this work.
    K8: French East/German South/Austrian 26%, French North East/Belgian/German West 25%, French North 25%, Irish/Scottish/Welsh 10%, French South/French Basque 9%, German East/Czech/Austrian 5%
    K36: French East/German South/Swiss German 33%, French North East/Belgian/German West 31%, French North Central 21%, Irish/Scottish/Welsh 9%, French South/ French Basque 6%
    K16: German 50%, French North West 19%, French North East 11%, Irish/English 11%, French South 9%

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  8. #25
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    Quote Originally Posted by Huijbregts View Post
    You can post your unscaled Global 25 coordinates.
    It remains your responsibility to decide whether a NW-European classification is sensible in your case.
    Hello Huijbregts,

    Would you please run mine through, too? I’m curious to see how my mixture divides up. I would guess a fairly even mix of A & B, with perhaps a little C thrown in but I could be wrong.

    ,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

    Many thanks!
    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 930 AD) >A13242/YSEQ (circa 1075 AD) >A13243/YSEQ (circa 1660 AD).

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  10. #26
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    I'm very interested in having this done for myself, if you could please...

    Code:
    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC12,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC22,PC23,PC24,PC25
    Sktibo,0.0119,0.0118,0.0172,0.013,0.0127,0.0044,0.0004,0,0.0026,0.0053,-0.0026,0.0078,-0.0102,-0.0014,0.0089,0.0024,-0.0022,0.0027,0.0043,0.005,0.0036,0.0091,-0.0021,0.0064,0.0027
    I'm thinking component B will be my largest component but I really want to see if "C" reflects my known ancestral percentages from Eastern Europe and Germany.
    Thank you
    Paper trail ancestry to the best of my knowledge:
    English (possibly containing some Welsh ancestry) 31.25%, Eastern European and Eastern German (Galicia, Poland) 25%, Scottish 17.96%, Scotch-Irish 12.5%, French 8.2%, Native American 1.95%, and Colonial American, 3.125%, which cannot be determined with complete certainty: there is Dutch (at least 1.36%) and some English. The rest could include Spanish, Norwegian, German, and French, but these percentages would be minuscule.

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  12. #27
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    Quote Originally Posted by Theconqueror View Post
    So the only ones with B are Belgian, French, French East, German, Lombards, Hallstatt. As per you comment: South of the A-region we find another component 'B'. This starts in Belgium and Northern France and extends until deep in Germany."

    Would it make sense to look at Germany from the four quadrants: NW, NE, SW, SE? I believe there a rift North South worth investigating.

    Thanks for this work.
    In the past I have noticed that nMonte has a tendency to underestimate German and to overestimate French. I think that is because nMonte interprets NW-German as Dutch or Swedish and interprets SW-German as French, etc.
    The problem is that the NW-European DNA is highly mixed and for a more fine-grained classification you need much more reference data samples than Global 25 can offer; maybe you even need the raw DNA instead of the PCA scores.
    And in a pessimistic mood I sometimes fear that the estimation problem may be mathematically undecidable.
    For these reasons I prefer a simple but robust classification above a richly detailed but unreliable classification.
    But I agree with your conclusion that 'German' is internally very heterogeneous.

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  14. #28
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    For sure, I tap into South Dutch and Dutch on many legacy models, especially by chromosome.
    K8: French East/German South/Austrian 26%, French North East/Belgian/German West 25%, French North 25%, Irish/Scottish/Welsh 10%, French South/French Basque 9%, German East/Czech/Austrian 5%
    K36: French East/German South/Swiss German 33%, French North East/Belgian/German West 31%, French North Central 21%, Irish/Scottish/Welsh 9%, French South/ French Basque 6%
    K16: German 50%, French North West 19%, French North East 11%, Irish/English 11%, French South 9%

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  16. #29
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    Is part of this effort to identify populations that should be included/avoided when performing analysis? e.g. Irish samples would be good to include, but German ones should be avoided as they are all over the place?
    Y-DNA R-Z49>Z142>Z12222>FGC12378>FGC12401>FGC12384
    Ancestry: 37% English, 26% Scot/Ulster Scot, 14% Welsh, 14% German 3% Ireland, 3% Nordic, 2% French & Dutch, 1% India

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  18. #30
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    Quote Originally Posted by sktibo View Post
    I'm very interested in having this done for myself, if you could please...

    Code:
    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC12,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC22,PC23,PC24,PC25
    Sktibo,0.0119,0.0118,0.0172,0.013,0.0127,0.0044,0.0004,0,0.0026,0.0053,-0.0026,0.0078,-0.0102,-0.0014,0.0089,0.0024,-0.0022,0.0027,0.0043,0.005,0.0036,0.0091,-0.0021,0.0064,0.0027
    I'm thinking component B will be my largest component but I really want to see if "C" reflects my known ancestral percentages from Eastern Europe and Germany.
    Thank you
    A B C
    Sktibo 0.569 0.404 0.027

    This does not look very good, but I notice that you have much ancestry from outside the NW-European horizon where I took the reference samples from.

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