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Thread: Eupedia Ancient Ethnicities Checker: reliably compare your DNA to ancient populations

  1. #201
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    1 members found this post helpful.


    Here is the PCA with the individual samples included with Maciamo's sample sets, as well as HGDP and Dodecad K12b samples for modern populations. For the 3D PCA, it really projects well.

  2. #202
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    Quote Originally Posted by Jovialis View Post
    In regards to Southwest Asian as a component, I noticed that the Natufians are a significant amount of it. Which makes me suspect that it is indeed an Anatolian_N-like ancestry being subsumed. Because Lazaridis' 2018 pre-print models Natufian as 73% Dzudzurna-like ancestry, which is highly similar to Anatolian_N. Which is perhaps why Southwest Asian is being detected in Neolithic European populations. The non-Anatolian_N part that can be distinguished as Ancestral North African-related ancestry in Natufians is possibly being detected separately, by Northwest African, East African, etc., by Dodecad K12b:

    What is interesting to me as well in the PCA, is the disk that forms in the middle. I think this is formed by Dzudzuana-like ancestry being augmented by outside sources on the periphery.

  3. #203
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    To create the 3D PCA, download from the mediafire link, and copy the text in the note file. It contains all of the values I used; the individual ancient samples; the modern west Eurasian samples; Maciamo's Ancient Ethnicities Checker sample sets:

    https://www.mediafire.com/file/lesgc...10-21.txt/file

    Then go to the following website:

    https://vahaduo.github.io/custompca/

    Paste it in the source tab; then click on the Plot PCA tab. Click the PCA Run button; then Plot PCA; finally, the 3D button.

    Et voilà:


  4. #204
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    Quote Originally Posted by Jovialis View Post
    Here is my pie chart, compared to my best 2-way modeling pie charts:



    Here is a 3D and 2D PCA, with all of the available samples, highlighting my best 2 way modeling, as well as all of the Ancient Greek samples we have:




    2D projection:


  5. #205
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    3 members found this post helpful.
    Also, here are the values for the northern Greek samples from The genomic history of the Aegean palatial civilizations

    Here was the thread on it: The genomic history of the Aegean palatial civilizations. (eupedia.com)

    Code:
    Kou01,0.13,0,2.62,0,36.59,0.3,0,0,13.35,0.53,45.02,1.45
    Kou03,4.64,0,2.77,0,32.51,1.12,0,0,11.34,0.32,45.28,2.02
    Log02,2.02,0.51,1.68,0.46,32.46,23.57,0,0.25,7.97,0,30.09,1
    Log04,7.05,1.16,0.26,0,31.18,28.21,0,0.13,4.25,0.92,24.07,2.77
    Mik15,0,0,5.75,0.07,41.42,0.91,0,0.03,13.26,0.69,35.94,1.94
    Pta08,0,0,3.85,0.33,34.73,0.38,0.14,0.05,14.68,0.48,43.65,1.72
    Last edited by Jovialis; 29-04-21 at 22:00.

  6. #206
    Satyavrata Maciamo's Avatar
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    3 members found this post helpful.
    Quote Originally Posted by Jovialis View Post
    Also, here are the values for the northern Greek samples from The genomic history of the Aegean palatial civilizations

    Here was the thread on it: The genomic history of the Aegean palatial civilizations. (eupedia.com)
    Thanks. I have added the average for EMBA Greece to the coordinates. It is much closer to Mycenaean Greece (3.9) than Minoan Greece (11.8).
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  7. #207
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    Hey Maciamo, Iím looking into the ancestors of CHG, these coordinates look realistic but I was wondering if these are to your liking. :)

    Dodecad K12B

    Target: Epipaleolithic_Mesolithic_Caucasus_(CHG)_(n=2)
    Distance: 59.2634% / 59.26336003
    39.0 Mesolithic_Anatolia_(AHG)_(n=1)
    31.5 Mesolithic_Volga-Ural_(n=2)
    22.8 Epipaleolithic_Levant_(Natufians)_(n=6)
    6.7 Epipaleolithic_Magreb_(Iberomaurusians)_(n=5)



    Epipaleolithic_Levant_(Natufians)_(n=6),0.00,0.34, 20.28,1.24,14.41,0.20,1.19,4.56,43.91,0.39,13.48,0 .00
    Epipaleolithic_Magreb_(Iberomaurusians)_(n=5),0.00 ,1.08,65.59,1.69,0.04,0.06,1.11,18.93,5.54,0.05,0. 00,5.90
    Mesolithic_Anatolia_(AHG)_(n=1),0.00,0.00,3.77,0.1 1,57.42,0.42,0.00,0.00,11.78,0.00,26.51,0.00
    Mesolithic_West_Europeans_(WHG)_(n=21),0.00,0.57,0 .00,0.74,30.90,65.73,0.38,0.08,0.00,0.02,0.00,1.57
    Mesolithic_Balkans_HG_(n=43),0.01,0.37,0.02,0.35,2 4.46,72.81,0.08,0.02,0.09,0.07,0.03,1.71
    Mesolithic_Baltic_Scandinavia_(SHG)_(n=31),0.25,2. 72,0.00,0.22,15.89,79.14,0.50,0.12,0.00,0.02,0.00, 1.13
    Mesolithic_Ukraine_(n=7),0.92,4.54,0.00,0.62,9.05, 81.79,1.31,0.55,0.00,0.00,0.00,1.21
    Mesolithic_Volga-Ural_(n=2),11.27,8.18,0.00,0.00,0.00,77.53,2.39,0. 00,0.00,0.00,0.00,0.64
    Mesolithic_Northwest_Russia_(n=4),7.23,7.78,0.00,1 .37,1.40,81.04,0.09,0.00,0.00,0.00,0.00,1.09

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    I can't seem to figure out how to do this. Can you please show a specific example of what the text I copy into the table is supposed to look like? I've tried it using the app and added commas but it's not working. Sorry.

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    In Target, sorry.

  10. #210
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    Quote Originally Posted by WFG80 View Post
    I can't seem to figure out how to do this. Can you please show a specific example of what the text I copy into the table is supposed to look like? I've tried it using the app and added commas but it's not working. Sorry.
    You have to get your results from Gedmatch, or Admixture Studio, under the Dodecad K12b calculator:



    Then after you run the sample through the calcualtor, and it processes, on the Visualization tab, there is a sub-tab called results:



    Click on "Copy", and it will give you a set of values, with the example above, it gives these:

    I would recommend using excel:



    These are the values you need, in this specific order, starting with Gedrosia, and ending with Sub-Saharan African. Delete everything except the values for the regional components, and separate them by commas. The example above should look like this, just the name of the sample, and the values with no spaces in between:

    Code:
    Log02_wgs,2.02,0.51,1.68,0.46,32.46,23.57,0,0.25,7.97,0,30.09,1

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    My results are pretty much blank. All I get is Component and the % sign.

  12. #212
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    I sort of got it to work. I changed over to my 23andMe file. Thanks for your help.

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    Distance to: William
    0.88891263 35.20% EMBA_Greece_(n=6) + 64.80% EBA_Unetice_culture_(n=18)
    1.02622244 65.60% EBA_Unetice_culture_(n=18) + 34.40% Mycenaean_Greece_(n=4)
    1.48185649 29.60% Minoan_Greece_(n=10) + 70.40% EBA_Unetice_culture_(n=18)
    1.64644077 16.80% Chalcolithic_North_Levant_(n=6) + 83.20% Bell_Beaker_Czechia_(n=15)
    1.67025567 34.80% Eastern_Corded_Ware_(n=8) + 65.20% Villanovans_(n=2)
    1.86794894 33.00% EMBA_Greece_(n=6) + 67.00% Swedish_Vikings_(n=23)
    1.92164818 77.00% Bell_Beaker_Czechia_(n=15) + 23.00% Italian_Greeks_(n=2)
    1.94911843 29.80% Early_Neolithic_Anatolia_(n=7) + 70.20% EBA_Unetice_culture_(n=18)
    1.99836690 32.20% Mycenaean_Greece_(n=4) + 67.80% Swedish_Vikings_(n=23)
    2.18769754 27.60% Minoan_Greece_(n=10) + 72.40% Swedish_Vikings_(n=23)
    2.22130807 82.00% Bell_Beaker_Czechia_(n=15) + 18.00% Middle_Bronze_Age_Anatolia_(n=2)
    2.25617662 61.00% Nordic_Bronze_Age_(n=14) + 39.00% Italian_Greeks_(n=2)
    2.36035551 29.00% Chalcolithic_Anatolia_(n=35) + 71.00% Nordic_Bronze_Age_(n=14)
    2.36537424 77.60% Bell_Beaker_Czechia_(n=15) + 22.40% EMBA_Greece_(n=6)
    2.38537267 41.80% Western_Corded_Ware_(n=17) + 58.20% Villanovans_(n=2)
    2.41692361 67.40% Bronze_Age_Illyrians + 32.60% Medieval_Estonia_(n=7)
    2.50104134 26.80% Italian_Greeks_(n=2) + 73.20% Lombards_(n=28)
    2.52841636 19.60% Chalcolithic_North_Levant_(n=6) + 80.40% Lombards_(n=28)
    2.55825951 44.60% EBA_Unetice_culture_(n=18) + 55.40% Bronze_Age_Illyrians
    2.56821853 16.00% Chalcolithic_Anatolia_(n=35) + 84.00% Bell_Beaker_Czechia_(n=15)
    2.57730148 32.20% Eastern_Corded_Ware_(n=8) + 67.80% Bronze_Age_Illyrians
    2.61303721 24.20% EMBA_Greece_(n=6) + 75.80% Chernyakhiv_culture_Goths_(n=3)
    2.63074083 29.80% Early_Neolithic_Greece_(n=3) + 70.20% EBA_Unetice_culture_(n=18)
    2.67616037 21.00% Middle_Bronze_Age_Anatolia_(n=2) + 79.00% Lombards_(n=28)
    2.70314805 48.20% Etruscans_(n=3) + 51.80% Avars_(n=2)

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    Trouble with calculation

    Hello, I was having trouble using the vahaduo spreadsheet. I followed the directions below. However, I get the following "WARNING! Number of white-space characters removed in TABTARGET data: 3782. ERROR! Data load error in TABTARGET."
    Do you have suggestions for trouble shooting?
    Thank you


    1. Go to Go to Vahaduo Dodecad K12b, delete the source coordinates (Ctrll+A to select, then backspace) and replace it by these coordinates (copy and paste the text highlighted in 'Code').
    2. In target, paste your Dodecad K12b coordinates (from step 1), with your name in front separated by a comma (just like in the coordinates you just copied and pasted in the previous step). Click on Distance, then Run to see the closest match with an entire ancient population. You may obtain better results in Single or 2Way to see the potential mix of your ancestral populations.

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    Quote Originally Posted by WFG80 View Post
    My results are pretty much blank. All I get is Component and the % sign.
    How did you get your results to work? I'm getting a blank Results tab with just Component and the % sign as well. Thanks

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    1 members found this post helpful.
    Quote Originally Posted by LFscience View Post
    How did you get your results to work? I'm getting a blank Results tab with just Component and the % sign as well. Thanks
    I did the copy values only thing then removed spaces, percentage symbols, added commas and placed a name in front, per
    Jovialis recommendation. I believe it worked for me this time because my 23andMe raw data matched me with 12 components whereas my Ancestry raw data only matched me with 10.


    Basically, I went from this:


    %
    6.08%
    0.65%
    1.66%
    0.37%
    32.55%
    37.84%
    0.53%
    0.02%
    3.76%
    0.19%
    16.18%
    0.18%


    To this:


    William,6.08,0.65,1.66,0.37,32.55,37.84,0.53,0.02, 3.76,0.19,16.18,0.18

    You, presumably, will have different numbers.


  17. #217
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    1 members found this post helpful.
    ... Neolithic_Lithuania_Narva_culture and Italian_Greeks :



  18. #218
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    4 members found this post helpful.
    I have added:

    - Late Antiquity Latium : most similar to modern Marche (1.4), Lazio (2.2) and Romagna (4.3).
    - Early Medieval Latium : most similar to modern Romagna (2.8), Marche (3.3) and Lazio (4.1).
    - Late Medieval Latium : most similar to modern Romagna (4.3), Tuscany (4.5) and Emilia (4.8).

    Using the 2WAY percentages with the Iron Age populations as sources, we get:

    - Late Antiquity Latium : 69.00% Italian_Greeks_(n=2) + 31.00% Gauls_Belgae_(n=16) => distance = 1.75
    - Early Medieval Latium : 63.00% Italian_Greeks_(n=2) + 37.00% Gauls_Belgae_(n=16) => distance = 3.5
    - Late Medieval Latium: 51.60% Italian_Greeks_(n=2) + 48.40% Gauls_Belgae_(n=16) => distance = 1.27

    So the Latium got more Celtic-like and less Greek-like over time between 300 and 1500 CE.
    Last edited by Maciamo; 23-04-21 at 09:25.

  19. #219
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    This makes sense considering the increase in the CHG/IN-cline the further south you go in the Italian peninsula.


  20. #220
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    From last updates :)

    Distance to: Dodecadk12bStuvanè
    1.21333868 86.80% Early_Medieval_Latium_(n=5) + 13.20% Avars_(n=2)
    1.31544663 8.00% Neolithic_Lithuania_Narva_culture_(n=4) + 92.00% Early_Medieval_Latium_(n=5)
    1.33787616 89.60% Early_Medieval_Latium_(n=5) + 10.40% Early_Medieval_Czechs_(n=2)
    1.38828111 9.20% Iron_Age_Estonia_(n=8) + 90.80% Early_Medieval_Latium_(n=5)
    1.40308287 8.40% Baltic_Bronze_Age_(n=12) + 91.60% Early_Medieval_Latium_(n=5)
    1.41632842 7.80% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 92.20% Early_Medieval_Latium_(n=5)
    1.41891825 90.00% Early_Medieval_Latium_(n=5) + 10.00% Medieval_Estonia_(n=7)
    1.43379052 8.40% Bronze_Age_Estonia_(n=16) + 91.60% Early_Medieval_Latium_(n=5)
    1.46155456 8.60% Mesolithic_Balkans_HG_(n=43) + 91.40% Early_Medieval_Latium_(n=5)
    1.51060219 58.20% Italian_Greeks_(n=2) + 41.80% Hallstatt_Celts_(n=2)
    1.53056178 7.40% Neolithic_Ukraine_(n=12) + 92.60% Early_Medieval_Latium_(n=5)
    1.57977958 42.00% Middle-Late_Bronze_Age_Hungary_(n=12) + 58.00% Italian_Greeks_(n=2)
    1.61842251 7.20% Mesolithic_Ukraine_(n=7) + 92.80% Early_Medieval_Latium_(n=5)
    1.67295690 9.80% Eastern_Corded_Ware_(n=8) + 90.20% Early_Medieval_Latium_(n=5)
    1.69980595 12.60% EBA_Unetice_culture_(n=18) + 87.40% Early_Medieval_Latium_(n=5)
    1.71689479 11.60% Western_Corded_Ware_(n=17) + 88.40% Early_Medieval_Latium_(n=5)
    1.78727890 9.60% Mesolithic_West_Europeans_(WHG)_(n=21) + 90.40% Early_Medieval_Latium_(n=5)
    1.85385340 6.80% Mesolithic_Northwest_Russia_(n=4) + 93.20% Early_Medieval_Latium_(n=5)
    1.86953183 11.00% MBA_Sintashta_culture_(n=4) + 89.00% Early_Medieval_Latium_(n=5)
    1.87517081 87.00% Early_Medieval_Latium_(n=5) + 13.00% Swedish_Vikings_(n=23)
    1.91828818 10.20% MBA_Andronovo_culture_(n=3) + 89.80% Early_Medieval_Latium_(n=5)
    1.93041691 12.00% Battle-Axe_culture_(n=3) + 88.00% Early_Medieval_Latium_(n=5)
    1.97501229 84.80% Early_Medieval_Latium_(n=5) + 15.20% Chernyakhiv_culture_Goths_(n=3)
    2.00879919 11.80% EBA_Fatyanovo_culture_(n=18) + 88.20% Early_Medieval_Latium_(n=5)
    2.02340952 15.80% Bell_Beaker_Czechia_(n=15) + 84.20% Early_Medieval_Latium_(n=5)

  21. #221
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    1 members found this post helpful.
    I have just added:

    - Imperial Age Rome & Latium : most similar to Greek islanders from Kos and Rhodes (both 3.0) and Italian Jews (5.0). That may be because ethnic Romans were cremated and therefore not part of the remains tested.

    I first separated the data from Rome and the rest of the Latium, but the difference between the two was negligible.

    - Imperial Age Marche : This time closest to modern Abruzzo (2.1), Campania (4.0) and Apulia (5.0), confirming that the samples from Latium were essentially immigrants.

    Using the 2Way with Iron Age samples in sources like above, we get:

    - Imperial Age Rome & Latium : 3.40% Iron_Age_Armenia + 96.60% Italian_Greeks => distance = 4.47 (not very good match)

    - Imperial Age Marche : 80.80% Italian_Greeks + 19.20% Gauls_Belgae => distance = 2.18
    Last edited by Maciamo; 23-04-21 at 09:26.

  22. #222
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    I get very close to Imperial Roman Marche in the distance tab.

  23. #223
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    Quote Originally Posted by Jovialis View Post


    I get very close to Imperial Roman Marche in the distance tab.
    Here is a 2D PCA with the new samples, along with the updated Italian samples for Dodecad K12b on vahaduo:

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    My Greek friend

    Distance to: Chris
    1.98602136 24.40% Chalcolithic_Northwest_Caucasus_(n=3) + 75.60% Early_Medieval_Latium_(n=5)
    3.00713292 19.80% Chalcolithic_Northwest_Caucasus_(n=3) + 80.20% Late_Antiquity_Latium_(n=24)
    3.14102633 29.80% EBA_Fatyanovo_culture_(n=18) + 70.20% Middle_Bronze_Age_Anatolia_(n=2)
    3.20949491 29.40% Western_Corded_Ware_(n=17) + 70.60% Middle_Bronze_Age_Anatolia_(n=2)
    3.26185440 71.00% Middle_Bronze_Age_Anatolia_(n=2) + 29.00% LBA_Srubna_culture_(n=27)
    3.26548650 72.60% Middle_Bronze_Age_Anatolia_(n=2) + 27.40% MBA_Andronovo_culture_(n=3)
    3.38915418 54.80% Middle_Bronze_Age_Anatolia_(n=2) + 45.20% Western_Scythians_(n=28)
    3.45450598 26.20% Eastern_Corded_Ware_(n=8) + 73.80% Middle_Bronze_Age_Anatolia_(n=2)
    3.61736499 36.80% Chalcolithic_Northwest_Caucasus_(n=3) + 63.20% Etruscans_(n=3)
    3.63725150 27.00% Kura-Araxes_culture_(n=8) + 73.00% Early_Medieval_Latium_(n=5)
    3.67024817 50.60% Middle-Late_Bronze_Age_Hittites_(n=2) + 49.40% Bronze_Age_Illyrians
    3.82507065 28.00% MBA_Sintashta_culture_(n=4) + 72.00% Middle_Bronze_Age_Anatolia_(n=2)
    3.98350176 11.60% Chalcolithic_Northwest_Caucasus_(n=3) + 88.40% Imperial_Roman_Marche_(n=2)
    3.99790440 81.80% Imperial_Roman_Marche_(n=2) + 18.20% Caucasian_Alans_(n=2)
    4.02926388 55.60% Chalcolithic_Anatolia_(n=35) + 44.40% Bell_Beaker_Poland_(n=6)
    4.03668999 55.80% Chalcolithic_Anatolia_(n=35) + 44.20% Middle_Bronze_Age_North_Alps_(n=7)
    4.05420188 59.60% Chalcolithic_Anatolia_(n=35) + 40.40% Hallstatt_Celts_(n=2)
    4.07435708 44.00% Middle-Late_Bronze_Age_Hittites_(n=2) + 56.00% Late_Medieval_Latium_(n=16)
    4.07518989 59.00% Chalcolithic_Anatolia_(n=35) + 41.00% Bronze_Age_Germany_(n=26)
    4.11611037 13.00% Late_Bronze_Age_North_Caucasus_(n=4) + 87.00% Imperial_Roman_Marche_(n=2)
    4.12911941 60.80% Middle_Bronze_Age_Anatolia_(n=2) + 39.20% Ostrogoths_(n=3)
    4.13433359 39.40% Kura-Araxes_culture_(n=8) + 60.60% Villanovans_(n=2)
    4.18417664 29.60% Battle-Axe_culture_(n=3) + 70.40% Middle_Bronze_Age_Anatolia_(n=2)
    4.21366413 57.40% Chalcolithic_Anatolia_(n=35) + 42.60% Bell_Beaker_Bavaria/Saxony_(n=20)
    4.34682086 62.20% Chalcolithic_Anatolia_(n=35) + 37.80% Iron_Age_Briton_(n=2)

  25. #225
    Regular Member italouruguayan's Avatar
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    21-04-17
    Location
    Montevideo, Uruguay
    Posts
    273

    Y-DNA haplogroup
    R1B U106 L44
    MtDNA haplogroup
    A2

    Ethnic group
    Mixed , mostly Italian
    Country: Uruguay



    My updates...

    Distance to: italouruguayan

    11.56324781 Western_Scythians_(n=28)
    14.69083047 Late_Medieval_Latium_(n=16)
    16.23768764 Roman_&_Visigothic_Iberia_(n=31)
    16.25998155 Bell_Beaker_Hungary_(n=6)
    16.91561409 Ostrogoths_(n=3)
    17.22619517 Medieval_Andalusia_(n=14)
    17.28995084 Bronze_Age_Illyrians
    17.89198424 Medieval_Catalonia_Valencia_(n=9)
    18.33555017 Early_Medieval_Latium_(n=5)
    18.58682060 Late_Antiquity_Latium_(n=24)
    19.14316327 Villanovans_(n=2)
    19.86298819 Etruscans_(n=3)
    20.81990874 Bell_Beaker_Poland_(n=6)
    21.62285365 Gauls_Belgae_(n=16)
    21.86751929 Bell_Beaker_Bavaria/Saxony_(n=20)
    21.87160488 Imperial_Roman_Marche_(n=2)
    21.99280109 Middle_Bronze_Age_North_Alps_(n=7)
    22.57669816 Cimmerians_(n=6)
    22.99249008 Bell_Beaker_Gaul_(n=13)
    23.87470209 Early_Bronze_Age_Swabia_(n=24)
    24.40309612 Bronze_Age_Germany_(n=26)
    24.58744802 Latins_(n=4)
    25.13049741 Chernyakhiv_culture_Goths_(n=3)
    25.24729094 Bell_Beaker_Czechia_(n=15)
    25.33739134 Suebi_Alemmani_(n=20)
    26.52373842 Iron_Age_Kangju_(n=4)
    26.82286897 Hallstatt_Celts_(n=2)
    27.12488894 Roman_Britain_(n=8)
    27.15390580 Lombards_(n=28)
    27.68604522 Italian_Greeks_(n=2)

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