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Thread: Early Medieval aDNA from Poland coming soon

  1. #541
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    Quote Originally Posted by Generalissimo View Post
    So far they've only tested a handful of their samples for Y-hgs. They have to test the rest of them.
    What about the R1b-U106 sample from Wielbark culture in Drozdowo? Is that confirmed?

  2. #542
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    Quote Originally Posted by Radboud View Post
    What about the R1b-U106 sample from Wielbark culture in Drozdowo? Is that confirmed?
    Nope, not directly by any researcher.

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  4. #543
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    I have generated 24 BAM files from downloadable samples:

    Ancient_Polish Kow_8
    Ancient_Polish Kow_22
    Ancient_Polish Kow_24
    Ancient_Polish Kow_25
    Ancient_Polish Kow_26
    Ancient_Polish Kow_29
    Ancient_Polish Kow_36
    Ancient_Polish Kow_42
    Ancient_Polish Kow_45
    Ancient_Polish Kow_51
    Ancient_Polish Kow_55
    Ancient_Polish Mas_5
    Ancient_Polish Mas_19
    Ancient_Polish Mas_21
    Ancient_Polish Niem_2
    Ancient_Polish Niem_11
    Ancient_Polish Niem_18
    Ancient_Polish Niem_32
    Ancient_Polish Niem_34
    Ancient_Polish Niem_36
    Ancient_Polish Sow_6
    Ancient_Polish Sow_7
    Ancient_Polish Sow_11
    Ancient_Polish Sow_18

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  6. #544
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    Poland
    Quote Originally Posted by Vadim Verenich View Post
    I have generated 24 BAM files from downloadable samples:
    I'm excited. Have you started analysis yet?

  7. #545
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    The ratio of overlapping SNPs is rather small, however pileupCaller yields a handful of promising candidates for a downstream analysis (Niem_34,Kow_55, Kow_45).

    Niem_34

    Amerindian 0
    Arabian 0
    Armenian 0
    Basque 6.71
    Central_African 0
    Central_Euro 15.23
    East_African 0
    East_Asian 0
    East_Balkan 0
    East_Central_Asian 0
    East_Central_Euro 14.77
    East_Med 0
    Eastern_Euro 6.25
    Fennoscandian 32.13
    French 0
    Iberian 0.01
    Indo-Chinese 0
    Italian 0
    Malayan 0
    Near_Eastern 0
    North_African 0
    North_Atlantic 7.64
    North_Caucasian 0
    North_Sea 10.54
    Northeast_African 0
    Oceanian 0.01
    Omotic 0
    Pygmy 0
    Siberian 0
    South_Asian 0
    South_Central_Asian 0.9
    South_Chinese 0
    Volga-Ural 0
    West_African 0
    West_Caucasian 0
    West_Med 5.8


    First 20 Populations distance
    Sweden_north 1045.55
    Norway_north 1190.64
    Estonian 1672.49
    Sweden 10739.05
    Russian_Perm 11585.31
    Russian_Kostroma 12413.97
    Vepsian 12732.99
    Russian_Novgorod_Yaroslavl 12971.78
    Russian_North 14620.32
    Komi 15579.88
    Norway 17024.64
    Russian_Tver 18169.35
    Russian_Meshtchyora 27932.01
    Russian_Pinega 29175.10
    Denmark 29747.36
    Russian_Novgorod_Pskov 30636.40
    Latvian 30689.61
    Tatar_Kryashen 34012.66
    Russian_Bryansk 36945.09
    Russian_Center 37643.24
    (non extrapolated) % sum for first twenty pops

    Scandinavia 58.65
    Western Finns 20.41
    Russia North 14.70
    Eastern Finns 3.40
    Russia South 2.84


    North Europe 51.76
    NE Europe 31.43
    East Europe 6.66
    Volga-Ural 5.49
    East-Central Europe 4.65


    2 population sharing %
    Sweden_north 53.24
    Norway_north 46.76

    3 pop. sharing %
    Sweden_north 39.95
    Norway_north 35.08
    Estonian 24.97

    5 pop. sharing %
    Sweden_north 37.16
    Norway_north 32.63
    Estonian 23.23
    Sweden 3.62
    Russian_Perm 3.35

    10 pop. sharing %
    Sweden_north 31.87
    Norway_north 27.99
    Estonian 19.92
    Sweden 3.10
    Russian_Perm 2.88
    Russian_Kostroma 2.68
    Vepsian 2.62
    Russian_Novgorod_Yaroslavl 2.57
    Russian_North 2.28
    Komi 2.14

    First 20 Populations distance
    Sweden_north 188.63
    Norway_north 190.85
    Estonian 201.69
    Sweden 667.21
    Russian_Kostroma 690.27
    Russian_Novgorod_Yaroslavl 709.70
    Russian_Perm 723.88
    Russian_North 725.50
    Vepsian 814.19
    Norway 885.56
    Russian_Tver 915.53
    Komi 1017.67
    Russian_Pinega 1135.69
    Denmark 1230.27
    Russian_Meshtchyora 1258.59
    Tatar_Kryashen 1321.52
    Russian_Vyatka 1342.05
    Pl_Kashubians 1378.01
    Russian_Bryansk 1411.73
    Latvian 1423.77
    (non extrapolated) % sum for first twenty pops
    Regional sharing %
    Scandinavia 38.40
    Russia North 26.90
    Western Finns 18.69
    Russia South 8.06
    British Isles 7.94

    Area sharing %
    NE Europe 32.60
    North Europe 28.75
    East Europe 15.00
    East-Central Europe 13.16
    Volga-Ural 10.48

    Capture.PNG

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  9. #546
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    Poland
    I'm doing nMonte now. First observation. Very big distances. This sample is not closely similar to any modern population. But it's not big suprise.
    Last edited by lukaszM; 06-28-2017 at 08:52 AM.

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  11. #547
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    Poland
    Least-squares method.

    Using 1 population approximation:
    1 Estonian @ 17,560703
    2 Norway_north @ 19,330858
    3 Sweden_north @ 19,894275
    4 Russian_North @ 23,245507
    5 Russian_Kostroma @ 23,561229
    6 Russian_Novgorod_Yaroslavl @ 23,589842
    7 Russian_Tver @ 24,54382
    8 Russian_Perm @ 24,724274
    9 Sweden @ 25,07319
    10 Russian_Pinega @ 25,241099
    11 Pl_Kashubians @ 25,413996
    12 Vepsian @ 25,417291
    13 Russian_Vyatka @ 26,437303
    14 Norway @ 26,508029
    15 German_East @ 26,840821
    16 PL_Wielkopolska @ 27,255976
    17 Russian_Bryansk @ 27,450663
    18 Russian_Meshtchyora @ 27,534214
    19 PL_SE_Carpathia @ 27,713141
    20 Sorb_Lusatia @ 27,815398
    330 iterations.

    Using 2 populations approximation:
    1 Pl_north+Finnish_SW @ 15,08385
    2 Norway_north+Estonian @ 15,089804
    3 Sweden_north+Estonian @ 15,185013
    4 Pl_Kashubians+Finnish_SW @ 15,261346
    5 PL_Wielkopolska+Finnish_SW @ 15,360508
    6 Ukrainian_West+Finnish_SW @ 15,665331
    7 Finnish_SW+Sorb_Lusatia @ 15,989501
    8 Sweden_north+Vepsian @ 16,120843
    9 German_East+Finnish_SW @ 16,155785
    10 Czechs_Moravians+Finnish_SW @ 16,167073
    11 German_East+Karelian @ 16,265324
    12 PL_Mazovia+Finnish_SW @ 16,28873
    13 Pl_Kashubians+Karelian @ 16,339573
    14 South_Dutch+Karelian @ 16,418848
    15 PL_Podlasie_East_Mazovia+Finnish_SW @ 16,433465
    16 Pl_north+Karelian @ 16,452264
    17 Sweden+Vepsian @ 16,456091
    18 PL_average+Finnish_SW @ 16,487443
    19 Russian_Bryansk+Finnish_SW @ 16,552489
    20 South_Dutch+Vepsian @ 16,568986
    54615 iterations.

    Using 3 populations approximation:
    1 50% Pl_Kashubians +25% Sweden_north +25% Finnish_East @ 13,388059
    2 50% Pl_Kashubians +25% South_Dutch +25% Finnish_East @ 13,637605
    3 50% Pl_Kashubians +25% Sweden +25% Finnish_East @ 13,642815
    4 50% Pl_Kashubians +25% Norway +25% Finnish_East @ 13,664144
    5 50% Pl_Kashubians +25% Denmark +25% Finnish_East @ 13,737676
    6 50% Pl_Kashubians +25% Central_Dutch +25% Finnish_East @ 13,768636
    7 50% Pl_Kashubians +25% Norway_north +25% Finnish_East @ 13,804788
    8 50% Pl_north +25% Sweden_north +25% Finnish_East @ 13,818491
    9 50% PL_Wielkopolska +25% Sweden_north +25% Finnish_East @ 13,86732
    10 50% Sweden_north +25% PL_Sudovia +25% Finnish_East @ 13,915614
    11 50% Pl_north +25% Norway_north +25% Finnish_East @ 14,00492
    12 50% Pl_Kashubians +25% North_Dutch +25% Finnish_East @ 14,025822
    13 50% Sweden_north +25% PL_Sudovia +25% Finnish_Inkeri @ 14,082529
    14 50% Sweden +25% PL_Sudovia +25% Finnish_East @ 14,115754
    15 50% Pl_Kashubians +25% German_North +25% Finnish_East @ 14,121834
    16 50% Sweden_north +25% PL_Podlasie_East_Mazovia +25% Finnish_East @ 14,123338
    17 50% Sweden_north +25% Russian_Bryansk +25% Finnish_Inkeri @ 14,135842
    18 50% Russian_Bryansk +25% Central_Dutch +25% Finnish_East @ 14,144983
    19 50% Sweden_north +25% Russian_Bryansk +25% Finnish_East @ 14,154835
    20 50% PL_Wielkopolska +25% Norway_north +25% Finnish_East @ 14,169184
    15463227 iterations.

    Using 4 populations approximation:
    1 Sweden_north+Pl_Kashubians+Pl_Kashubians+Finnish_E ast @ 13,388059
    2 Sweden_north+Pl_Kashubians+Pl_north+Finnish_East @ 13,526345
    3 Sweden_north+PL_Wielkopolska+Pl_Kashubians+Finnish _East @ 13,587005
    4 South_Dutch+Pl_Kashubians+Pl_Kashubians+Finnish_Ea st @ 13,637605
    5 Sweden+Pl_Kashubians+Pl_Kashubians+Finnish_East @ 13,642815
    6 Norway+Pl_Kashubians+Pl_Kashubians+Finnish_East @ 13,664144
    7 South_Dutch+PL_Sudovia+Pl_Kashubians+Finnish_East @ 13,686547
    8 Sweden_north+Russian_Bryansk+Pl_Kashubians+Finnish _East @ 13,699355
    9 South_Dutch+Sweden_north+PL_Sudovia+Finnish_East @ 13,707622
    10 Sweden_north+Pl_Kashubians+PL_Podlasie_East_Mazovi a+Finnish_East @ 13,719303
    11 Sweden_north+Russian_Bryansk+Pl_north+Finnish_East @ 13,726542
    12 Sweden_north+PL_Sudovia+Pl_Kashubians+Finnish_East @ 13,735395
    13 Denmark+Pl_Kashubians+Pl_Kashubians+Finnish_East @ 13,737676
    14 Central_Dutch+PL_Sudovia+Pl_Kashubians+Finnish_Eas t @ 13,765609
    15 Central_Dutch+Pl_Kashubians+Pl_Kashubians+Finnish_ East @ 13,768636
    16 South_Dutch+Pl_Kashubians+PL_Podlasie_East_Mazovia +Finnish_East @ 13,774642
    17 Sweden_north+PL_Wielkopolska+Pl_north+Finnish_East @ 13,77977
    18 South_Dutch+Russian_Tver+Pl_Kashubians+Finnish_Eas t @ 13,780458
    19 South_Dutch+Russian_Bryansk+Pl_Kashubians+Finnish_ East @ 13,780672
    20 German_East+Sweden_north+PL_Sudovia+Finnish_East @ 13,78452
    21 Central_Dutch+Russian_Bryansk+Pl_Kashubians+Finnis h_East @ 13,794902
    22 Central_Dutch+Sweden_north+PL_Sudovia+Finnish_East @ 13,80075
    23 Sweden_north+Pl_north+PL_Podlasie_East_Mazovia+Fin nish_East @ 13,804622
    24 Norway_north+Pl_Kashubians+Pl_Kashubians+Finnish_E ast @ 13,804788
    25 Sweden_north+Ukrainian_West+Pl_Kashubians+Finnish_ East @ 13,812404
    26 Norway+Russian_Bryansk+Pl_Kashubians+Finnish_East @ 13,816199
    27 Sweden_north+Pl_north+Pl_north+Finnish_East @ 13,818491
    28 Sweden_north+PL_Sudovia+Pl_north+Finnish_East @ 13,822285
    29 Norway_north+Pl_Kashubians+Pl_north+Finnish_East @ 13,828289
    30 Norway+PL_Sudovia+Pl_Kashubians+Finnish_East @ 13,837048
    31 Central_Dutch+Pl_Kashubians+PL_Podlasie_East_Mazov ia+Finnish_East @ 13,839863
    32 Sweden+Russian_Bryansk+Pl_Kashubians+Finnish_East @ 13,842126
    33 Norway+Pl_Kashubians+PL_Podlasie_East_Mazovia+Finn ish_East @ 13,848176
    34 Denmark+Russian_Bryansk+Pl_Kashubians+Finnish_East @ 13,851294
    35 Sweden+Pl_Kashubians+Pl_north+Finnish_East @ 13,865357
    36 Sweden+Sweden_north+PL_Sudovia+Finnish_East @ 13,866953
    37 Sweden_north+PL_Wielkopolska+PL_Wielkopolska+Finni sh_East @ 13,86732
    38 Denmark+PL_Sudovia+Pl_Kashubians+Finnish_East @ 13,868791
    39 Sweden+Pl_Kashubians+PL_Podlasie_East_Mazovia+Finn ish_East @ 13,870115
    40 Sweden_north+Russian_Don_Cossack+Pl_Kashubians+Fin nish_East @ 13,871279
    394648203 iterations.


    Gaussian method.
    Noise dispersion set to 0,130062
     

    Using 1 population approximation:
    1 South_Dutch @ 6,343965
    2 German_East @ 6,480591
    3 Central_Dutch @ 6,699094
    4 Russian_Novgorod_Pskov @ 6,745171
    5 Czechs_Moravians @ 6,881765
    6 SE_England @ 7,02363
    7 Slovak @ 7,057514
    8 PL_SE_Carpathia @ 7,118933
    9 Russian_Smolensk @ 7,141036
    10 PL_Upper_Silesia @ 7,143078
    11 Ukrainian_West @ 7,209591
    12 German_North @ 7,255543
    13 Carpathian_Rusyns @ 7,266248
    14 Belarusian_West @ 7,306556
    15 Norway @ 7,323025
    16 PL_South_Poland @ 7,407969
    17 Slovenian @ 7,408418
    18 South_Germany @ 7,430541
    19 German_West @ 7,443366
    20 Welsh @ 7,459936
    330 iterations.

    Using 2 populations approximation:
    1 France_NorthWest+Estonian @ 5,680869
    2 France_South+Estonian @ 5,744096
    3 South_Dutch+Estonian @ 5,821826
    4 France_Central+Estonian @ 5,836554
    5 Swiss_German+Estonian @ 5,837643
    6 France+Estonian @ 5,862822
    7 South_Dutch+Russian_Novgorod_Pskov @ 5,876013
    8 France_SW+Estonian @ 5,9523
    9 Spain_Baleares+Estonian @ 5,959641
    10 France_NorthWest+Vepsian @ 5,960748
    11 Spain_Valencia+Estonian @ 5,9729
    12 Austria_Tyrol+Estonian @ 5,976937
    13 Spain_Centabria+Estonian @ 5,978764
    14 South_Dutch+Latvian @ 6,005569
    15 Czechs_Moravians+Finnish_SW @ 6,020592
    16 France_NorthWest+Karelian @ 6,033282
    17 Central_Dutch+Russian_Novgorod_Pskov @ 6,041002
    18 Asturia+Estonian @ 6,042744
    19 South_Dutch+Lithuanian @ 6,043373
    20 Spain_Aragon+Estonian @ 6,047303
    54615 iterations.

    Using 3 populations approximation:
    1 50% Pl_north +25% Spanish_Basque +25% Finnish_East @ 5,070976
    2 50% Pl_north +25% Spanish_Basque +25% Finnish_Inkeri @ 5,193782
    3 50% Pl_north +25% France_SW +25% Finnish_East @ 5,198451
    4 50% Estonian +25% Spanish_Basque +25% Lithuanian @ 5,201701
    5 50% Pl_north +25% Spain_Centabria +25% Finnish_East @ 5,206306
    6 50% PL_Sudovia +25% Spanish_Basque +25% Finnish_East @ 5,209296
    7 50% Lithuanian +25% Spanish_Basque +25% Finnish_East @ 5,22045
    8 50% Pl_north +25% France_South +25% Finnish_East @ 5,230519
    9 50% Pl_north +25% French_Basque +25% Finnish_East @ 5,230794
    10 50% Estonian +25% Spanish_Basque +25% PL_Sudovia @ 5,236793
    11 50% Lithuanian +25% Spanish_Basque +25% Finnish_SW @ 5,240247
    12 50% Pl_north +25% Finnish_East +25% Spain_La-Rioja @ 5,247062
    13 50% PL_Podlasie_East_Mazovia +25% Spanish_Basque +25% Finnish_East @ 5,255406
    14 50% Lithuanian +25% Spanish_Basque +25% Estonian @ 5,264719
    15 50% Estonian +25% Spanish_Basque +25% Sweden_north @ 5,266936
    16 50% Pl_north +25% Spain_Aragon +25% Finnish_East @ 5,267507
    17 50% Pl_Kashubians +25% Spanish_Basque +25% Finnish_East @ 5,271351
    18 50% PL_Wielkopolska +25% Spanish_Basque +25% Finnish_East @ 5,272782
    19 50% Estonian +25% Spanish_Basque +25% Pl_north @ 5,276807
    20 50% Estonian +25% Spanish_Basque +25% PL_Wielkopolska @ 5,279113


    In admix4 looks Finno-Germano-Slavic...

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  13. #548
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    Y-DNA (P)
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    Poland
    nMonte restrcited

    Sweden_north 37.4
    PL_Sudovia 28.9
    Finnish_East 23.1
    IT_Sardinia 4.2
    Pl_Kashubians 3.0
    GR_Thrace 1.8
    France_SW 1.6

    nMonte full
     


    Sweden_north 35.85
    PL_Sudovia 26.25
    Finnish_East 23.15
    Pl_Kashubians 7.00
    IT_Sardinia 4.15
    France_SW 1.30
    GR_Thrace 1.00
    Brahui_PAK 0.70
    North_Dagestan 0.20
    Spanish_Basque 0.15
    Telugu_IND 0.10
    North_Amerind 0.10
    Brahmin_Nepali 0.05


    Also very big distances

    [1] "1. CLOSEST SINGLE ITEM DISTANCES"
    Estonian Norway_north
    17.55858 19.32280
    Sweden_north Russian_North
    19.88559 23.24059
    Russian_Kostroma Russian_Novgorod_Yaroslavl
    23.55544 23.58362
    Russian_Tver Russian_Perm
    24.53780 24.71749

    [/spoiler]

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  15. #549
    Registered Users
    Posts
    745
    Sex
    Location
    Estonia
    Ethnicity
    Belarusian
    Y-DNA (P)
    I2-A1328
    mtDNA (M)
    J1c

    Kow_55 (Goth?)

    Code:
    Amerindian	0.32
    Arabian	0
    Armenian	0
    Basque	5.33
    Central_African	0
    Central_Euro	15.71
    East_African	0
    East_Asian	0
    East_Balkan	7.77
    East_Central_Asian	0
    East_Central_Euro	12.56
    East_Med	0
    Eastern_Euro	6.35
    Fennoscandian	4.68
    French	3.08
    Iberian	4.8
    Indo-Chinese	0.02
    Italian	0
    Malayan	0
    Near_Eastern	0
    North_African	0
    North_Atlantic	21.06
    North_Caucasian	0
    North_Sea	11.24
    Northeast_African	0
    Oceanian	0
    Omotic	0
    Pygmy	0
    Siberian	0
    South_Asian	1.38
    South_Central_Asian	0
    South_Chinese	2.13
    Volga-Ural	0
    West_African	0
    West_Caucasian	0
    West_Med	3.59
    
    
    First 20 Populations	distance
    German_North	1112.94
    Welsh	1443.77
    South_Dutch	1475.63
    NW-England	1514.72
    British_mixed	1546.92
    Orcadian	1677.83
    Scotland	1824.52
    Ireland	2032.76
    German_East	2091.99
    SE_England	2130.52
    Denmark	2422.54
    Ukrainian_West	2481.84
    Central_Dutch	2517.44
    Pl_north	2627.23
    England_Cumberland	2865.76
    Northern Ireland	3263.92
    Sorbs_Lusatia	3307.03
    Norway	3421.12
    NE-England	3928.14
    PL_Wielkopolska	4234.03
    	(non extrapolated) % sum for first twenty pops
    	
    British Isles	52.37
    Holland & N. German 	21.51
    Poland north-west	10.69
    Scandinavia	9.03
    Ukraine&Moldavia	6.40
    	
    	
    British Isles 	40.02
    North Europe	23.34
    East-Central Europe	20.88
    East Europe	9.07
    Western Europe	6.69
    
    2 population sharing %	
    German_North	56.47
    Welsh	43.53
    	
    3 pop. sharing %	
    German_North	39.60
    Welsh	30.53
    South_Dutch	29.87
    	
    5 pop. sharing %	
    German_North	25.13
    Welsh	19.37
    South_Dutch	18.95
    NW-England	18.46
    British_mixed	18.08
    	
    10 pop. sharing %	
    German_North	13.67
    Welsh	10.54
    South_Dutch	10.31
    NW-England	10.05
    British_mixed	9.84
    Orcadian	9.07
    Scotland	8.34
    Ireland	7.49
    German_East	7.27
    SE_England	7.14
    	
    	First 20 Populations	distance
    1	German_East	34.91
    2	German_North	38.30
    3	Ukrainian_West	38.45
    4	Pl_north	39.27
    5	Czechs_Moravians	39.91
    6	Welsh	40.55
    7	Orcadian	41.03
    8	Sorbs_Lusatia	41.97
    9	South_Dutch	42.41
    10	Ireland	43.46
    11	Norway	44.25
    12	British_mixed	44.28
    13	PL_Wielkopolska	44.57
    14	NW-England	44.58
    15	Central_Dutch	44.84
    		(non extrapolated) % sum for first twenty pops
    	Regional sharing %	
    1	British Isles	37.88
    2	East-Balkan	18.10
    3	Holland & N. German 	14.73
    4	Scandinavia	14.68
    5	Poland north-west	14.61
    		
    	Area sharing %	
    1	East-Central Europe	25.86
    2	Balkan	19.60
    3	Western Europe	18.42
    4	East Europe	18.16
    5	British Isles 	17.96
    Attached Images Attached Images

  16. The Following 8 Users Say Thank You to Vadim Verenich For This Useful Post:

     Kurd (06-28-2017),  leonardo (06-28-2017),  lukaszM (06-28-2017),  Michał (06-28-2017),  Rethel (06-28-2017),  Tomenable (06-28-2017),  Underworld (06-28-2017),  Waldemar (06-28-2017)

  17. #550
    Banned
    Posts
    6,336
    Sex
    Location
    Torun
    Ethnicity
    Central 75% + 25% Mazovia
    Nationality
    Pole
    Y-DNA (P)
    R1a > M198 > YP 1337

    Poland
    And for Niemcza_34 nMonte based on medians not averages for reference samples. Looks more Slavic in such way.

    Sweden_north 36.65
    PL_Podlasie_East_Mazovia 22.80
    Finnish_East 22.75
    PL_Sudovia 11.15
    IT_Sardinia 4.45
    France_SW 2.20
    Pl_north 0.00

  18. The Following 7 Users Say Thank You to lukaszM For This Useful Post:

     Brent.B (06-28-2017),  Huijbregts (06-28-2017),  leonardo (06-28-2017),  Michał (06-28-2017),  Rethel (06-28-2017),  Tomenable (06-28-2017),  Waldemar (06-28-2017)

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