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Thread: NW European samples on Voronoi tesselation

  1. #1
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    NW European samples on Voronoi tesselation

    I always have been curious about Voronoi tessellation. A good way to get a helicopter view of the data.
    No statistics, just plotting the data.
    voronoi.png
    The (PC15,PC4)coordinates of modern NW Europeans are represented by the little black dots.
    They are surrounded by a round colored area, unless these are compressed by neighboring samples.
    Look where your unscaled Global25 coordinates PC15,PC4 plot on the map.
    See your pet theory about the British Islands confirmed (or not).

    Of course this plot only displays the location on the PC15,PC4 coordinates, but for Europeans this is usually the best pair.

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  3. #2
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    Could you try doing a similar thing for SW Europe?
    YDNA E-Y31991>PF4428>Y134097>Y134104>Y168273>FT17866 (TMRCA ~1100AD) - Domingos Rodrigues, b. circa 1690 Hidden Content , Viana do Castelo, Portugal - Stonemason, miller.
    mtDNA H20 - Monica Vieira, b. circa 1700 Hidden Content , Porto, Portugal

    Hidden Content
    Global25 PCA West Eurasia dataset Hidden Content

    [1] "distance%=1.6007"

    Ruderico

    NW_Iberia_IA,80.4
    Berber_EMA,11
    Roman_Colonial,8.6

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  5. #3
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    Quote Originally Posted by Huijbregts View Post
    I always have been curious about Voronoi tessellation. A good way to get a helicopter view of the data.
    No statistics, just plotting the data.
    voronoi.png
    The (PC15,PC4)coordinates of modern NW Europeans are represented by the little black dots.
    They are surrounded by a round colored area, unless these are compressed by neighboring samples.
    Look where your unscaled Global25 coordinates PC15,PC4 plot on the map.
    See your pet theory about the British Islands confirmed (or not).

    Of course this plot only displays the location on the PC15,PC4 coordinates, but for Europeans this is usually the best pair.
    If I’m understanding you correctly than I should be about here.

    Attachment 34164

    PCA4 0.0124 & PCA15 0.0099

    I don’t have a computer, so I hand placed it on my iPhotos app.

    According to my unscaled fit check, Belgian is my closest fit.
    Paper Trail: 42.25% English, 31.25% Scottish, 12.5% Irish, 6.25% German, 6.25% Sicilian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Sicilian & 1.5% French.
    LDNA(c): 86.3% British Isles (48.6% English, 37.7% Scottish & Irish), 7.8% NW Germanic, 5.9% Europe South (Aegean 3.4%, Tuscany 1.3%, Sardinia 1.1%)
    BigY 700: I1-Z140 >I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 620 AD) >A13242/YSEQ (circa 765 AD) >FT80854 (circa 1650 AD).

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    Quote Originally Posted by Ruderico View Post
    Could you try doing a similar thing for SW Europe?
    The plot itself isn't that much work. But you will have to do some preparation yourself:
    1. Is PC15,PC4 the best pair of coordinates for SW?
    2. Which populations will you condense in 8 or less groups.

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    double post

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    Appears like I am located right in the middle of that chart.
    Last edited by jstephan; 10-25-2019 at 06:00 PM.

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    Quote Originally Posted by Huijbregts View Post
    The plot itself isn't that much work. But you will have to do some preparation yourself:
    1. Is PC15,PC4 the best pair of coordinates for SW?
    2. Which populations will you condense in 8 or less groups.
    How do you evaluate which pair works best?
    YDNA E-Y31991>PF4428>Y134097>Y134104>Y168273>FT17866 (TMRCA ~1100AD) - Domingos Rodrigues, b. circa 1690 Hidden Content , Viana do Castelo, Portugal - Stonemason, miller.
    mtDNA H20 - Monica Vieira, b. circa 1700 Hidden Content , Porto, Portugal

    Hidden Content
    Global25 PCA West Eurasia dataset Hidden Content

    [1] "distance%=1.6007"

    Ruderico

    NW_Iberia_IA,80.4
    Berber_EMA,11
    Roman_Colonial,8.6

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    Quote Originally Posted by Ruderico View Post
    How do you evaluate which pair works best?
    There are only 300 combinations.
    I was hoping you knew already.
    One shortcut is to calculate the variance the SW populations by PC. The two highest might be a good pair, unless they are correlated.
    I think PC4 is good guess for the vertical dimension. That leaves a choice of 25 (or the first 15) for the horizontal dimension.

    Edit: If you don't already, a could solution is doing a secondary PCA on the SW populations and using the first two dimensions of the secondary PCA.
    Last edited by Huijbregts; 10-25-2019 at 05:48 PM.

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    Quote Originally Posted by jstephan View Post
    Appears like I am located right in the middle of that chart, thanks for your work Huijbregts ! What do these 2 specific coordinates represent exactly, are they related to some specific admixtures ?
    My experience is that from NW to central Europe these are the dimensions that display the most structure.
    PC4 is the North-South direction in Western Europe. Eastern Europe has another NS direction which is the direction from Siberia to the Caucasus.
    PC15 is the East-West direction in Northern and Central Europe. South Europe might have its own EW dimension which is more in the direction of the Levant and the Caucasus.
    All of this in very broad lines.

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    Quote Originally Posted by Huijbregts View Post
    My experience is that from NW to central Europe these are the dimensions that display the most structure.
    PC4 is the North-South direction in Western Europe. Eastern Europe has another NS direction which is the direction from Siberia to the Caucasus.
    PC15 is the East-West direction in Northern and Central Europe. South Europe might have its own EW dimension which is more in the direction of the Levant and the Caucasus.
    All of this in very broad lines.
    Well here's what a secondary PCA with just SWE looks like. (edit: I excluded all French, although I suppose quite a few of them could have been included)
    The N-S cline is obvious, but I have no idea what its perpendicular direction hints at. There are always a few individuals (even ancient ones) which seem to plot in that direction, and those who do generally have closer distances to each other, and nMonte3 models seem to favour them. An example is the two Spanish_Pais_Vasco (green) samples, who have pretty good distances to me. Same with the Asturian. Why that is I have no idea.

    Last edited by Ruderico; 10-25-2019 at 06:26 PM.
    YDNA E-Y31991>PF4428>Y134097>Y134104>Y168273>FT17866 (TMRCA ~1100AD) - Domingos Rodrigues, b. circa 1690 Hidden Content , Viana do Castelo, Portugal - Stonemason, miller.
    mtDNA H20 - Monica Vieira, b. circa 1700 Hidden Content , Porto, Portugal

    Hidden Content
    Global25 PCA West Eurasia dataset Hidden Content

    [1] "distance%=1.6007"

    Ruderico

    NW_Iberia_IA,80.4
    Berber_EMA,11
    Roman_Colonial,8.6

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