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Thread: UMAP of (sub)modern Europeans

  1. #101
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    Quote Originally Posted by Huijbregts View Post
    nearest neighbors of ITA_Collegno_MA:CL84 :
    [1] "English_Cornwall:HG00243" "English_Cornwall:HG00236" "MitchellSince1893"
    [4] "VK2020_England_Oxford_VA:VK173" "English_Cornwall:HG00255" "Welsh:WalesCHF13"
    [7] "VK2020_SWE_Skara_VA:VK40" "English:English5" "English_Cornwall:HG00160"
    Interesting. He looks very southwestern English. Cornwall coming in 1st, 2nd, 5th, 9th. Not sure how to interpret this result.
    37% English, 26% Scot/Ulster Scot, 14% Welsh, 14% German, 3% Ireland, 3% Nordic, 2% French/Dutch, 1% India
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  3. #102
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    Quote Originally Posted by MitchellSince1893 View Post
    Interesting. He looks very southwestern English. Cornwall coming in 1st, 2nd, 5th, 9th. Not sure how to interpret this result.
    At various times he’s been a reasonably close fit of mine (in scaled). Although, the Vikings have pushed him down to 7th. In the paper he was modeled as approximately 98% CEU&GBR & 2% Finnish.

    https://www.nature.com/articles/s414...24-4/figures/3
    Paper Trail: 42.25% English, 31.25% Scottish, 12.5% Irish, 6.25% German, 6.25% Italian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Italian & 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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  5. #103
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    Quote Originally Posted by Huijbregts View Post
    As you know I often did a project on the (sub)modern European samples. But usually I got stuck with a very dense scatter plot, where the partitioning in clusters was not really convincing.
    I started this UMAP project mainly in the hope that UMAP could do a better job in partitioning the data.
    And it does. It clearly partitions the data into 3 well separated clusters. But that is a starter.
    I am interested in the internal structure of the huge Western cluster.
    There is already a suggestion of structure, but I am not yet content with it.
    I hope that with some more tuning or some more samples the structure will more clear.
    It is a work in progress, which will probably take quite some time.
    And the outcome can also be that the populations are too much overlapping to partition them. That would also be a result.

    That said, the emerging structure that I see, is different from your suggestion.
    You have drawn ellipses round the Anthrogenica members.
    But you should have drawn ellipses around groups of grey points (=all the subEuropean samples).
    For instance I see a candidate cluster in the middle of your plot. Probably mainly French samples.
    But are there also German samples in it?
    And what are the samples to the West of the 'French' protocluster?
    And first of all: how many clusters can be reliably identified?
    TOTALLY agree....now it would be nice to fill in the...?

    Because:
    That said, the emerging structure that I see, is different from your suggestion.
    Be my guest what would be the different outline?

    And
    But you should have drawn ellipses around groups of grey points (=all the subEuropean samples).
    For instance I see a candidate cluster in the middle of your plot. Probably mainly French samples.
    But are there also German samples in it?
    And what are the samples to the West of the 'French' protocluster?
    And first of all: how many clusters can be reliably identified?
    I can't fill in because what I see is all misty GRAY....so I can't make a connection....
    except the drawn ellipses round the Anthrogenica members
    .
    Last edited by Finn; 10-16-2020 at 08:03 AM.

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  7. #104
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    It looks like on this plot the Irish Dutch and Scandinavians share roughly the same space. We've seen on other plots that these groups are sometimes separate; why might they be in the same space here? and why does this vary from plot to plot? I'd love to hear what Huijbregts thinks about this but all input is welcome
    Paper trail ancestry to the best of my knowledge:
    English (possibly containing some Welsh ancestry) 31.25%, Scottish 17.96%, Scotch-Irish 12.5%, Eastern German 12.5%, Eastern European (Likely Polish possibly including Romanian) 12.5%, French 7.81%, Native American (Saulteaux and Assiniboine) 2.34%, and Colonial American, 3.125%, which cannot be traced with certainty. With certainty, there is Dutch (at least 1.36%) and some English.

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  9. #105
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    Quote Originally Posted by JMcB View Post
    At various times he’s been a reasonably close fit of mine (in scaled). Although, the Vikings have pushed him down to 7th. In the paper he was modeled as approximately 98% CEU&GBR & 2% Finnish.

    https://www.nature.com/articles/s414...24-4/figures/3
    That is very useful information.
    I will mark the stray Italian inn my next plot.

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  11. #106
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    Quote Originally Posted by Finn View Post
    TOTALLY agree....now it would be nice to fill in the...?

    Because:

    Be my guest what would be the different outline?

    And


    I can't fill in because what I see is all misty GRAY....so I can't make connection.....
    You know the Dutch proverb " Cologne and Aachen were not built in a day".

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  13. #107
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    Quote Originally Posted by sktibo View Post
    It looks like on this plot the Irish Dutch and Scandinavians share roughly the same space. We've seen on other plots that these groups are sometimes separate; why might they be in the same space here? and why does this vary from plot to plot? I'd love to hear what Huijbregts thinks about this but all input is welcome
    In the first place Irish and Dutch are overrepresented in Global25. Therefore I randomly reduced the number of both populations from 64 to 40.
    The several plots vary from each other for at least two reasons:
    1. In each new plot I have added at least one sample. That will cause subtle changes.
    2. The UMAP algorithm adds the data in a random starting sequence, which will cause slightly different outputs.I might freeze this by specifying a random seed, but I prefer to see the effect of these different starting conditions.

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  15. #108
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    Quote Originally Posted by sktibo View Post
    It looks like on this plot the Irish Dutch and Scandinavians share roughly the same space. We've seen on other plots that these groups are sometimes separate; why might they be in the same space here? and why does this vary from plot to plot? I'd love to hear what Huijbregts thinks about this but all input is welcome
    Yes I would love to hear what Huijbregts has to say but the only plot where I plot a bit different is the Celtic vs Germanic plot. All other plots I'm part way between Ireland and Norway. Even on the G25 I plot in the Icelandic portion so this plot is actually more similar to other plots for me.

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  17. #109
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    Quote Originally Posted by Huijbregts View Post
    You know the Dutch proverb " Cologne and Aachen were not built in a day".
    hahahah

    Frankish attitude

    I say:

  18. #110
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    Can I be added?

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