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Thread: Population genomics of the Viking world (bioxiv, 2019, Copenhagen)

  1. #971
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    Quote Originally Posted by Williamson View Post
    I don't see any shared variants between VK333 and Gunn. I do see one shared variant Y13839 G>A (1A) found in the 1000 genomes kit HG00139. This variant doesn't show up in the BigY kits I have and I suspect it may be upstream.
    Much appreciated!
    R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>BY44243

    Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583;
    John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593;
    John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635

  2. #972
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    Quote Originally Posted by Williamson View Post
    Yes, I think the results for this one are fairly clear. There could be some debate on some of the others.

    Y17161 level: Y17161 G>A (1A)
    Y16889 level: no results
    A7992 level: A7993 T>C (2C)
    ~6111568-C-A level: no results
    FGC71023 level: FGC71023 T>C (2C)
    BY32418 level: no results

    This is still a fairly old branch. The men on these branches will have many unique variants which I'll check as well.

    Update: I checked the unique variants for the men on those branches and didn't see anything more.
    Thanks Williamson. It is very strange to find a relatively widespread Northern Italian clade like A7992 far south in Foggia (Apulia)... probably VK534 was more similar to Northern Italian people, than to Southern ones?

  3. #973
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    Quote Originally Posted by teepean47 View Post
    I redid just VK11. This sample is around 300 megabytes and takes about 30 minutes to process.

    https://drive.google.com/file/d/1qgA...ew?usp=sharing

    For info,

    FID IID MISS_PHENO N_MISS N_GENO F_MISS
    1 VK11.final.bam Y 1177433 1200343 0.9809


    FID IID MISS_PHENO N_MISS N_GENO F_MISS
    1 VK11 Y 1088196 1200343 0.9066

    (F_MISS is the ratio of missing SNPs. )
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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  5. #974
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    Nice visual map tool:
    https://mapalist.com/map/79314fae-b0...6-e27a07d87ba4

    Also see:
    http://haplotree.info/u5/

    I know one of the samples share my mtDNA line, but I will have a look tomorrow to see just how close we are.

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  7. #975
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    Quote Originally Posted by Ajeje Brazorf View Post
    I had omitted the non-Vikings.

     
    Object-ID Colloquial-Skeletal Y-Simple YTree Y-Haplotree-Variant YFull Mean date Location Country
    VK532 Kragehave Odetofter XL718 I1a2a I1-Z59 I-Z59 I-Z59 100 Sealand Denmark
    VK521 Sol941 Grav900 Brondsager Torsiinre I1a2a I1-Z2040 I-Z2040 I-Z2040 300 Sealand Denmark
    VK582 SBM1028 ALKEN ENGE 2013, X2244 I2a1b1a I2-CTS616 I-CTS616 I-CTS616 100 Jutland Denmark
    VK248 Faroe_22 I1 I1 I-M253 I1 1600 Faroes Faroes
    VK237 Faroe_15 R1aZ282 R1a-Z282 R-Z282 R-Z282 1600 Faroes Faroes
    VK45 Faroe_18 R1aZ284 R1a-Z284 R-Z284 R-Z284 1600 Faroes Faroes
    VK244 Faroe_12 R1aL448 R1a-L448 R-L448 R-L448 1600 Faroes Faroes
    VK238 Faroe_4 R1aZ287 R1a-CTS8401 R-CTS8401 R-CTS8401 1600 Faroes Faroes
    VK245 Faroe_16 R1aZ287 R1a-YP6099 R-YP6099 R-YP6099 1600 Faroes Faroes
    VK46 Faroe_19 R1aZ287 R1a-YP6099 R-YP6099 R-YP6099 1600 Faroes Faroes
    VK239 Faroe_5 R1bM269 R1b-M269 R-M269 R-M269 1600 Faroes Faroes
    VK44 Faroe_17 R1bDF13 R1b-Y2841 R-Y2841 R-Y2841 1600 Faroes Faroes
    VK242 Faroe_3 R1bDF13 R1b-L1065 R-L1065 R-L1065 1600 Faroes Faroes
    VK27 Faroe_10 R1bDF13 R1b-L513 R-L513 R-DF1 1600 Faroes Faroes
    VK234 Faroe_2 R1bS1194 R1b-A8041 R-A8041 R-L151 1600 Faroes Faroes
    VK25 Faroe_1 R1bS1194 R1b-A8041 R-A8041 R-L151 1600 Faroes Faroes
    VK538 Italy_Foggia-1249 L L L-M20 L 1150 Foggia Italy
    VK534 Italy_Foggia-869 R1bP312 R1b-P312 R-P312 R-P312 1150 Foggia Italy
    VK535 Italy_Foggia-891 R1bZ2109 R1b-Z2109 R-Z2109 R-Z2108 1237,5 Foggia Italy
    VK116 Norway_Trondheim_SK372 F F F-M89 F 1200 Nor_Mid Norway
    VK390 Norway_Telemark 1648-A R1aL448 R1a-L448 R-L448 R-L448 550 Nor_South Norway
    VK531 Norway_Troms 5001A R1bP297 R1b-P297 R-P297 R-P297 -2400 Nor_North Norway
    VK117 Norway_Trondheim_SK328 R1bP310 R1b-P310 R-P310 R-L52 1200 Nor_Mid Norway
    VK418 Norway_Nordland 1502 R1bZ19 R1b-Z18 R-Z18 R-Z19 350 Nor_North Norway
    VK210 Poland_Krakˇw-Zakrzˇwek gr. 24 I2a1 I2-L460 I-L460 I-L460 1150 Krakˇw Poland
    VK211 Poland_Cedynia gr. 435 R1bM269 R1b-M269 R-M269 R-M269 1150 Cedynia Poland
    VK579 Oland 1099 1785/67 35 N1aL1026 N1a-L1026 N-L1026 N-L1026 300 Oland Sweden
    VK541 Ukraine_Lutsk R1aM458 R1a-L1029 R-L1029 R-L1029 1250 Lutsk Ukraine
    The None Vikings list, contains a reference of VK116 Norway Trondheim 1200 AD, with Haplogroup F, and snp F-M89. Is this an older reference possibly pre 2014, as some Y Dna F haplogrops were changed, to Y H2. There are two references under the branch for Y H2 P96, with F-M89, on the FTDNA H Haplogroup listings.

    There are four VK references,recently being shown on these posts, the above VK116, Norway Trondheim 1200 AD. The others are, VK411 Denmark 950 AD, VK161 Russia 1100 AD, VK304 Sweden 1050 AD, all these are referenced as Y DNA F, F-M89.

    There is a reference that indicates F-M89, was changed to represent Y H2, from 2005, upto 2014. See The Wikipedia page for F-M89, the chart is listed on the page, Y H2, was formerly F3. , but F-M89 is also referencing Y H2 P96, on FTDNA

    Is there any further SNPs or information that could check if any of these four Y F haplogroups, could possibly also reference Y H2 P96, as some previous F haplogroups F-M89 were updated and to now represent Y H2, was the snp P96 tested, and is F Haplogroup the correct identification today.
    Last edited by Paul333; 09-21-2020 at 04:42 PM.

  8. #976
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    Quote Originally Posted by Michalis Moriopoulos View Post
    Does the Willerslev lab usually release the raw genotype data without having to be lobbied? Seems odd not to for such a massive study.
    Yes, it does, but no one's even replying to emails this time.

    I don't think public relations is a strength of many of these labs.

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  10. #977
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    Quote Originally Posted by teepean47 View Post
    I redid just VK11. This sample is around 300 megabytes and takes about 30 minutes to process.

    https://drive.google.com/file/d/1qgA...ew?usp=sharing
    Looks much better.

    First try.

    Target: VK1:VK11
    Distance: 11.1677% / 0.11167695
    63.2 Yamnaya_RUS_Samara
    22.8 Anatolia_Barcin_N
    11.2 WHG
    2.8 Levant_PPNB

    VK1:VK11,0.140002,0.14319,0.048271,0.061047,0.0501 63,0.055778,0.028906,-0.017538,0.005727,-0.042643,0.003085,0.020232,0.006838,0.007982,0.045 195,0.01127,-0.008736,-0.005448,0.027151,0.028514,0.002745,0.004451,0.023 91,0.028799,-0.045864

    Second.

    Target: VK2:VK11
    Distance: 5.0433% / 0.05043288
    51.4 Yamnaya_RUS_Samara
    34.8 Anatolia_Barcin_N
    13.8 WHG

    VK2:VK11,0.120652,0.137096,0.064111,0.049742,0.042 777,0.025658,0.016451,0.001615,-0.009408,0.000729,-0.000325,0.005095,-0.001635,-0.009083,0.017372,0.011535,-0.008214,0.007095,0.004274,0.013006,0.004492,0.002 844,0.000863,0.016388,-0.007424

    Huge difference in the North Euro PCA too.

    https://vahaduo.github.io/g25views/#NorthEurope

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  12. #978
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    Nice. Might it be worthwhile for Teepean to convert some of the more novel samples using that more time-consuming method? Maybe the lab will release the genotype data soon so hopefully it wouldn't be necessary to convert all of the samples that way.
    Last edited by Michalis Moriopoulos; 09-21-2020 at 01:43 AM.
    Ελευθερία ή θάνατος.

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  14. #979
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    Quote Originally Posted by evon View Post
    Nice visual map tool:
    https://mapalist.com/map/79314fae-b0...6-e27a07d87ba4

    Also see:
    http://haplotree.info/u5/

    I know one of the samples share my mtDNA line, but I will have a look tomorrow to see just how close we are.
    From West Norway one of the authors of on the Vikings paper about the critics....and with a desert about the Longobards.....


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  16. #980
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    Quote Originally Posted by Finn View Post
    From West Norway one of the authors of on the Vikings paper about the critics....and with a desert about the Longobards.....

    I saw his post on Facebook, that he himself posted, but I have forgotten to view it. Thanks for the reminder. The northern Italian connection is very interesting and I will have a look at the paper again to check it out, maybe it can explain the southern signals in some Scandinavian samples using G25 online tools? He sounds like a Eastern Norwegian by the way, but I think he lives in ┼lesund by the looks of it.

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