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Thread: Eurogenes Northern_Europe PCA

  1. #571
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    Quote Originally Posted by anglesqueville View Post
    Aga, did you use actually the medianes? The euclidean distances are microscopic! Anyway, my mom is obviously more continental than her sister with this north-euro:
    Orcadian Danish Belgian German Austrian Dutch Scottish English
    1.542854 1.661542 1.713111 1.720756 1.756986 1.772315 1.774542 1.785385

    edit: OK, understood, you blend distances in % and raw distances.
    In the most recent version of nMonte both calculated distance and distance to nearest neighbors are in percentage format.
    In previous versions the distance to nearest neighbors is in decimal format and should be multiplied by 100 to be comparable with the calculated distances.

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  3. #572
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    First, with PC2

    1] "distance%=1.4148"

    Helgi

    French,56.5
    England_Anglo-Saxon,30.5
    Austrian,13

    Now without

    [1] "distance%=1.4033"

    Helgi

    French,55.6
    Austrian,22.8
    England_Anglo-Saxon,21.6

    The second version increases my Austrian, never got before.
    I don't know where's the truth, but by comparing with all I've already seen, the first version seems to me more logical.
    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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  5. #573
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    Quote Originally Posted by Helgenes50 View Post
    First, with PC2

    1] "distance%=1.4148"

    Helgi

    French,56.5
    England_Anglo-Saxon,30.5
    Austrian,13

    Now without

    [1] "distance%=1.4033"

    Helgi

    French,55.6
    Austrian,22.8
    England_Anglo-Saxon,21.6

    The second version increases my Austrian, never got before.
    I don't know where's the truth, but by comparing with all I've already seen, the first version seems to me more logical.
    The populations in the North European dataset are so closely related that they share large overlaps. This makes it hard to estimate them. It even makes a considerable difference whether you use averages or medians. So you just cannot expect that you always get a 'plausible' result.
    One more thing to keep in mind: England_Anglo-Saxon is the median of only three samples, that probably is not very accurate.
    That said, I see something that I do not quite understand. You get a high admixture of Anglo-Saxon (30%), which is relatively high on PC2. But French, Austrian and your mother are low on PC2. Which would make your father very high on PC2.
    My suggestion is:
    1. check whether you yourself are high on PC2
    2. drop Anglo-Saxon from the reference set and see what happens.

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  7. #574
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    nMonte median-all

    [1] "distance%=0.9221"

    Icelandic,46.4
    Dutch,29
    Scottish,15.8
    Norwegian,4.6
    Finnish,4.2



    NMonte-median first 5

    [1] "distance%=0.4644"

    Irish,47.7
    English,39.2

    Finnish,11.2
    Lithuanian,1.9

    nMonte median minus PC2

    [1] "distance%=0.8855"

    Icelandic,48.4
    Dutch,47.8
    Swedish,2.5
    Finnish,1.3

    Bolded=paper ancestry. Maybe these are all trying to tell me the same thing in different ways.
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  9. #575
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    Quote Originally Posted by randwulf View Post
    All 10 Principal Components:

    [1] "1. CLOSEST SINGLE ITEM DISTANCE%"
    English Scottish Dutch Belgian Irish Orcadian French Danish
    1.246315 1.307517 1.473669 1.518470 1.565854 1.576039 1.658885 1.908053

    [1] "distance%=1.0097"

    Scottish,53.1
    French,39.4
    Irish,7.3
    Latvian,0.2

    Without the second Principal Component:

    [1] "1. CLOSEST SINGLE ITEM DISTANCE%"
    Scottish English Irish Dutch Belgian French Orcadian Danish
    1.056740 1.240524 1.400678 1.461369 1.500950 1.526237 1.554445 1.766177

    [1] "distance%=0.9669"

    Scottish,73.5
    French,26.5
    Would you please do the same for me as you did for Garimund?

    sktibo,0.0232,0.0033,-0.0036,0.0072,0.0012,0.007,0.0056,0.0008,-0.0017,0.0055

    Thank you kindly
    Paper trail ancestry to the best of my knowledge:
    English 28.12%, East German or Eastern European 25%, Scottish 17.96%, Scotch-Irish 12.5%, French 8.2%, Welsh 3.125%, 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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  11. #576
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  12. #577
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    Quote Originally Posted by sktibo View Post
    Would you please do the same for me as you did for Garimund?

    sktibo,0.0232,0.0033,-0.0036,0.0072,0.0012,0.007,0.0056,0.0008,-0.0017,0.0055

    Thank you kindly
    Medians, all 10 PCs, moderns only:

    [1] "1. CLOSEST SINGLE ITEM DISTANCE%"
    Dutch English Orcadian Belgian French Scottish German Danish
    1.503729 1.610962 1.654086 1.656759 1.694816 1.851189 1.906856 1.924813

    [1] "distance%=1.1513"

    French,54.1
    Irish,30.6
    Komi,8
    Slovenian,7.3

    Medians, No PC 2, moderns only:

    [1] "1. CLOSEST SINGLE ITEM DISTANCE%"
    Dutch English Scottish Orcadian French Belgian Danish Austrian
    1.503596 1.584645 1.594773 1.597216 1.625423 1.655672 1.705650 1.779691

    [1] "distance%=1.138"

    French,55.4
    Irish,33.9
    Komi,10.7

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  14. #578
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    The medians table can not only be used for calculating admixture percentages with nMonte, it can also be used for constructing a very acceptable dendrogram of the populations.
    In the next graph I have plotted this dendrogram against the ten dimensions.
    heatmap.jpg
    The dendrogram suggests that Belgium is not intermediate between French and Dutch (as I expected), but closer to French.
    The nMonte results are:
    Belgium
    nearest neighbors: Dutch:0.9317457, French:0.9511835
    modelled distance: 0.4796
    admixtures:
    French,55.2
    England_Anglo-Saxon,20.9
    Dutch,8.9
    Austrian,7.8
    England_IA,7.2
    So in terms of raw distances Belgian is intermediate between Dutch and French as I expected.
    But in terms of admixture French comes first, with Dutch even trailing behind Anglo-Saxon.

    The heatmap also contains information about the 10 dimensions.
    In previous posts I have suggested that PC2 is an East-European dimension that maybe should be dropped from nMonte runs on Western populations.
    The heatmap shows that the situation is more complicated. True, the most positive values of PC2 are found in Karelian, Finnish, Vepsian and Komi; moderate negative values are Lithuanian, Polish and Belarusian.
    In West/Central Europe slightly negative values on PC2 are found in Czech, Slovakian, Slovenian and Hungarian.
    In West and North Europe slightly positive values on PC2 are found in the Northern populations Icelandic, Norwegian, Danish, Nordic_IA and also in the British populations England_Anglo_Saxon, Irish, Scottish.
    So the idea that PC2 is irrelevant to West European is incorrect. PC2 should be include in nMonte runs on West Europe.

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  16. #579
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    Quote Originally Posted by Huijbregts View Post
    The medians table can not only be used for calculating admixture percentages with nMonte, it can also be used for constructing a very acceptable dendrogram of the populations.
    In the next graph I have plotted this dendrogram against the ten dimensions.
    heatmap.jpg
    The dendrogram suggests that Belgium is not intermediate between French and Dutch (as I expected), but closer to French.
    The nMonte results are:
    Belgium
    nearest neighbors: Dutch:0.9317457, French:0.9511835
    modelled distance: 0.4796
    admixtures:
    French,55.2
    England_Anglo-Saxon,20.9
    Dutch,8.9
    Austrian,7.8
    England_IA,7.2
    So in terms of raw distances Belgian is intermediate between Dutch and French as I expected.
    But in terms of admixture French comes first, with Dutch even trailing behind Anglo-Saxon.

    The heatmap also contains information about the 10 dimensions.
    In previous posts I have suggested that PC2 is an East-European dimension that maybe should be dropped from nMonte runs on Western populations.
    The heatmap shows that the situation is more complicated. True, the most positive values of PC2 are found in Karelian, Finnish, Vepsian and Komi; moderate negative values are Lithuanian, Polish and Belarusian.
    In West/Central Europe slightly negative values on PC2 are found in Czech, Slovakian, Slovenian and Hungarian.
    In West and North Europe slightly positive values on PC2 are found in the Northern populations Icelandic, Norwegian, Danish, Nordic_IA and also in the British populations England_Anglo_Saxon, Irish, Scottish.
    So the idea that PC2 is irrelevant to West European is incorrect. PC2 should be include in nMonte runs on West Europe.
    Regarding your Belgian samples, what percentage was Flemish and what percentage was Walloon?

  17. #580
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    I think the dendrogram and admixture percentages from my simple model are really satisfactory, but they remain results of a model, not reality itself.
    Another model might have returned 'Belgian = 50.01% Dutch + 49.99% French' or 'The difference between Belgian and Dutch is too close to call'.
    To answer your question: I don't know the percentage Flemish and Walloon.
    I think these percentages of the present population are genetically not very relevant, because a few centuries ago the language border was much farther to the South; this development has been cultural, not a migration. So many French speakers have mainly Flemish ancestors.
    Last edited by Huijbregts; 12-04-2017 at 04:06 PM.

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