Eurogenes EUtest 3D & 2D PCA

Quote:

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Originally Posted by LePrieur

Using 1 population approximation:
1 NL @ 5.360508
2 English @ 5.642265
3 DK @ 6.438132
4 Cornish @ 6.909125
5 West_&_Central_German @ 7.005866
6 Orcadian @ 7.982291
7 NO @ 8.247042
8 IE @ 8.595057
9 South_&_Central_Swedish @ 9.035830
10 Scottish @ 10.340495
11 FR @ 12.453335
12 North_Swedish @ 13.026841
13 AT @ 14.265373
14 HU @ 19.990417
15 PT @ 20.254925
16 ES @ 20.849253
17 South_Finnish @ 22.171810
18 Serbian @ 23.137617
19 North_Italian @ 25.388145
20 PL @ 25.592957

Using 2 populations approximation:
1 50% FR +50% NO @ 5.280873


Using 3 populations approximation:
1 50% DK +25% DK +25% FR @ 4.698812


Using 4 populations approximation:
+++++++++++++++++++++++++++++++++++++++
1 DK + English + FR + NO @ 4.690612
2 DK + DK + DK + FR @ 4.698812
3 DK + DK + FR + NO @ 4.709173
4 DK + English + FR + South_&_Central_Swedish @ 4.713714
5 English + FR + NO + NO @ 4.730468
6 DK + FR + NL + NO @ 4.745772
7 DK + DK + FR + South_&_Central_Swedish @ 4.764232
8 DK + ES + NO + NO @ 4.772079
9 DK + ES + NO + South_&_Central_Swedish @ 4.795853
10 English + FR + NO + South_&_Central_Swedish @ 4.802351
11 DK + NO + NO + PT @ 4.802359
12 ES + NO + NO + NO @ 4.805685
13 DK + DK + FR + NL @ 4.811207
14 DK + FR + NL + South_&_Central_Swedish @ 4.814058
15 DK + DK + English + FR @ 4.817941
16 FR + NL + NO + NO @ 4.845960
17 DK + NO + PT + South_&_Central_Swedish @ 4.869868
18 DK + ES + South_&_Central_Swedish + South_&_Central_Swedish @ 4.870558
19 NO + NO + NO + PT @ 4.871549
20 ES + NO + NO + South_&_Central_Swedish @ 4.877505

Code:

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#        Population        Percent
1        NORTH-CENTRAL_EURO        29.21
2        ATLANTIC        24.43
3        WEST_MED        13.7
4        SOUTH_BALTIC        12.46
5        EAST_EURO        11.36
6        SOUTH_ASIAN        3.37
7        EAST_MED        2.08
8        WEST_ASIAN        2.02
9        SIBERIAN        1.27
10        EAST_AFRICAN        0.09

Single Population Sharing:

#        Population (source)        Distance
1        NL        4.89
2        English        5.16
3        DK        5.89
4        Cornish        6.19
5        West_&_Central_German        6.28
6        Orcadian        7.2
7        NO        7.45
8        IE        7.68
9        South_&_Central_Swedish        8.2
10        Scottish        9.24
11        FR        10.96
12        North_Swedish        11.69
13        AT        12.46
14        HU        17.55
15        PT        17.83
16        ES        18.39
17        South_Finnish        19.91
18        Serbian        19.99
19        North_Italian        21.99
20        PL        22.81

Mixed Mode Population Sharing:

#                Primary Population (source)        Secondary Population (source)        Distance
1                91.4%        DK        +        8.6%        Sardinian        @        3.77
2                96.3%        English        +        3.7%        South_Indian        @        3.99
3                95.7%        English        +        4.3%        Bangladeshi        @        4.15
4                96%        English        +        4%        Gujarati        @        4.23
5                95.9%        English        +        4.1%        IN        @        4.26
6                88.7%        NO        +        11.3%        Sardinian        @        4.27
7                97.3%        NL        +        2.7%        South_Indian        @        4.28
8                71.4%        DK        +        28.6%        FR        @        4.3
9                62.4%        NO        +        37.6%        FR        @        4.32
10                74.8%        NO        +        25.2%        ES        @        4.4
11                82.1%        DK        +        17.9%        ES        @        4.43
12                81.7%        DK        +        18.3%        PT        @        4.45
13                97.2%        NL        +        2.8%        Bangladeshi        @        4.46
14                74.3%        NO        +        25.7%        PT        @        4.47
15                97.4%        NL        +        2.6%        Gujarati        @        4.52
16                97.4%        NL        +        2.6%        IN        @        4.55
17                95.8%        English        +        4.2%        Burusho        @        4.56
18                96.2%        English        +        3.8%        Sindhi        @        4.56
19                59.4%        South_&_Central_Swedish        +        40.6%        FR        @        4.59
20                96.9%        NL        +        3.1%        Sardinian        @        4.64

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the 3D version of PCA appears to be sensitive to your 3.37% south Asian and 1.27% Siberian score, and shifts you away from English. In 2D pca there are no South Asian populations, so that component score doesn't matter.

Quote:

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Originally Posted by Lemgrant

the 3D version of PCA appears to be sensitive to your 3.37% south Asian and 1.27% Siberian score, and shifts you away from English. In 2D pca there are no South Asian populations, so that component score doesn't matter.

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Do you mean the score of the 2D PCA? or the South Asian/Siberian? I have minor Amerindian 2-3% So this calc probably represents it as such.

Quote:

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Originally Posted by LePrieur

Do you mean the score of the 2D PCA? or the South Asian/Siberian? I have minor Amerindian 2-3% So this calc probably represents it as such.

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I mean that your South Asian/Siberian score doesn't affect your positioning on 2d pca, because there are no south Asian populations. But it does on 3d pca.
Yes, south Asian can be Amerindian proxy in this calculator it seems.

http://i.imgur.com/rmcQjCP.png

3d version:

http://i.imgur.com/Pwmij2Z.png

here is collection of gedmatch kits for you for plotting:

https://www.theapricity.com/forum/sh...=1#post6234136

https://www.theapricity.com/forum/sh...=1#post6233948

https://www.theapricity.com/forum/sh...=1#post6240836

https://www.theapricity.com/forum/sh...-GEDmatch-kits

GEDmatch, list of ancient samples with kit numbers
https://www.eupedia.com/forum/thread...th-kit-numbers

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https://i.postimg.cc/kGjzmxgn/image.png

https://i.imgur.com/3mmSU61.png

https://i.imgur.com/VLrWaaU.png