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

  1. #11
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    Quote Originally Posted by Huijbregts View Post
    With the term 'label' I refer to the name that the samples get in the Global 25 PCA.
    For modern samples that name is derived from the self-reported genealogy. I suppose the label is usually correct, at least in a genealogical sense.
    My assertion is that these labels are not very helpful in a genetical sense; the Germans are a frightening example.
    This is worrying me, because software like nMonte use the labels to genetically classify the samples and assume that the labels are genetically 1:1 with the DNA.
    I assume that this also applies to qpAdm.
    You wrote "there is obvious continuity overlapping current boundaries(labels)". If you are saying that the present labels are too fine-grained, I quite agree.
    My self-imposed limitation was to develop a common DNA-only classification for the NW-Europeans.
    This limited the number of overlappings of German. Moreover my common model appeared not to be reliable with K=4 or higher. Therefore I ended up with only three components.
    I agree. The drawback is that you also have to label the new groups. How do you call a statistically homogenous group that includes some French from Alsace and some German from Rhineland or Baden-Wurttemberg? Even if you stick with statistics, you have to make an editorial decision. We have seen it with the K15, K13 PCAs. At the end of the day, and it certainly is the case with how France and Germany have historically been merged, there will be some level of diversity. The best example are the Dutch, such a diverse group on a PCA, and an unassuming historical pivot in so many migrations. We may be looking at a homogeneity that simply doesn't exist. Best example is the POBI study. What do you call the UK regions in the context of other autosomal intake? Are they still English?
    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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  3. #12
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    Quote Originally Posted by timberwolf View Post
    Are you going to do this analysis for more people?
    You can post your unscaled Global 25 coordinates.
    It remains your responsibility to decide whether a NW-European classification is sensible in your case.

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  5. #13
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    Quote Originally Posted by xenus View Post
    I've got a lot of programming experience but not in R and not working on population genetics so you can take this with a grain of salt but my advice would be to check the available resources online
    you could try to incorporate some other tools. There are tons of R libraries on for R on https://rdrr.io/ or you could try https://bio.tools for useful software.

    You can probably find a package with a much better than naive or at least a hw-accelerated brute force comparison type clustering based on shared snps in some software package. I'm assuming that cluster significance comes from either more SNPs matched or a smaller number if a group is shared among a larger number of samples to the exclusion of the rest but again i don't have experience working with these algorithms.
    I am not as inexperienced as you think.
    What I did was based on Gaussian mixture modeling which is more or less the de facto standard on clustering.

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  7. #14
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    I want to see please if my father and I come out as 100% NW European.

    Tim_G,0.0114,0.0129,0.0172,0.0146,0.0141,0.0069,0. 0011,0.0013,0.0034,-0.0003,-0.0016,0.0034,-0.007,-0.0081,0.0205,0.0048,-0.0163,0.0046,0.0015,0.0014,0.0035,0.0015,-0.0018,0.0071,-0.0026

    Tim_G_father,0.0121,0.0137,0.016,0.0122,0.0143,0.0 062,0.0022,0.005,0.0038,-0.0007,-0.0018,0.0031,-0.0068,-0.0029,0.022,0.0013,-0.0162,0.0043,0.002,0.0056,0.0074,0.0031,-0.0033,0.0065,-0.0014
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  8. #15
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    Quote Originally Posted by Huijbregts View Post
    In my next post I will more systematically explore the relation between labeled populations and the DNA components within NW-Europe.
    I'm very curios looking forward to it Huijbregts!

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  10. #16
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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.
    ,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
    Timberwolf,0.0117,0.0136,0.0163,0.0123,0.0159,0.00 69,0.0042,0.0044,0.0036,0.0032,-0.0052,0.0066,-0.0124,-0.0073,0.0183,0.0014,-0.0107,0.0009,-0.0003,-0.0028,0.0051,0.0043,-0.0034,0.0087,-0.0014


    Thanks.

  11. #17
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    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."

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  13. #18
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    A B C
    Timberwolf 0.976 0.024 0
    Tim_G 0.999 0.001 0
    Tim_G_father 0.988 0.012 0

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  15. #19
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    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
    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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  17. #20
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    It makes sense.
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