Y haplogroups for prehistoric Eurasian genomes

Below are the Y haplogroups for the 55 newly available male genomes from prehistoric Eurasia.

RISE512  Russia          Andronovo    R1a1a1b2a2-Z2121/S3410
RISE94   Sweden          Battle Axe   R1a1a1b-V4100/Z651/F3044
RISE566  Czech Republic  Bell Beaker  R1b1a2a1a-P310/PF6546/S129
RISE560  Germany         Bell Beaker  R1b1a2a1a2-M12124(xM12050)
RISE563  Germany         Bell Beaker  R1b1a2a1a2b-PF6570/S28/U152
RISE564  Germany         Bell Beaker  R1b1a2a1-L51/M412/PF6536/S167
RISE434  Germany         Corded Ware  R1a1a1-F3159/M761
RISE436  Germany         Corded Ware  R1a1a1-CTS5648/M695
RISE446  Germany         Corded Ware  R1a1a1-M417*
RISE1    Poland          Corded Ware  R
RISE431  Poland          Corded Ware  R1a1a1-PF7532/F3398
RISE555  Russia          EBA          R1b1a2a2-CTS7340/Z2107
RISE492  Russia          Iron Age     R1a1a1b2a2a-Y431
RISE504  Russia          Iron Age     J2a2-PF5000(xP279/PF5065)
RISE600  Russia          Iron Age     Q1a1b-M25
RISE601  Russia          Iron Age     Q1a1b-M143
RISE602  Russia          Iron Age     J2a2-PF5000(xP279/PF5065)
RISE174  Sweden          Iron Age     ?
RISE493  Russia          Karasuk      Q1a1b1-L712
RISE494  Russia          Karasuk      R1a1a1b-V3726/Z650/CTS9754/PF6206
RISE495  Russia          Karasuk      R1a1a1b2a2-YP349
RISE397  Armenia         LBA          R1b1a2a2-Y4371/Z8128
RISE408  Armenia         LBA          J2b2a-Z590
RISE598  Lithuania       LBA          R1a1a1-M756
RISE553  Russia          LBA          R1a1a1
RISE554  Russia          LBA          N-Y6503-FGC28509/Y6499
RISE374  Hungary         Maros        G2a2a1a-PF6308
RISE413  Armenia         MBA          R1b1a2
RISE416  Armenia         MBA          E1b1b1b2a1a-L788
RISE423  Armenia         MBA          E1b1b1b2a1a-FGC18319/Y5413
RISE524  Russia          Meshovskaya  R1b1a2-PF6494
RISE525  Russia          Meshovskaya  R1a1a1b-Z649/CTS5508(xZ283)
RISE21   Denmark         Nordic BA    ?
RISE47   Denmark         Nordic BA    R1b1a2-PF6410/M520(xM12002,P312)
RISE175  Sweden          Nordic BA    I1-FGC2435/Z2698
RISE207  Sweden          Nordic BA    I1-M450/S109
RISE276  Denmark         Nordic LBA   R1b1a2a1a-CTS7650/PF6544/S1164
RISE42   Denmark         Nordic LN    R1
RISE179  Sweden          Nordic LN    I1-Z2765/CTS3506
RISE98   Sweden          Nordic LN    R1b1a2a1a1-M405/S21/U106*
RISE61   Denmark         Nordic MN B  R1a1a1b1a3b1-Z281
RISE546  Russia          Pit Grave    R1b1a2-PF6532/CTS12972
RISE547  Russia          Pit Grave    R1b1a2a2-CTS9416
RISE548  Russia          Pit Grave    R1b1a2a2-Z2105
RISE550  Russia          Pit Grave    R1b1a2a2-Z8129/M12145/Y12537
RISE552  Russia          Pit Grave?   I2a2a1b1b2-S12195
RISE486  Italy           Remedello    I2a1a1a-L672/S327
RISE487  Italy           Remedello    I2a1a1-Y2189
RISE489  Italy           Remedello    I2a1a1a-L672/S327
RISE386  Russia          Sintashta    R1a1a1b2a2-Z2124
RISE392  Russia          Sintashta    R1a1a1b2a2a-Y877
RISE139  Poland          Unetice      ?
RISE247  Hungary         Vatya        I2a2a-L368
RISE254  Hungary         Vatya        I2a2a-L59
RISE479  Hungary         Vatya        I2a2a1a2a2-SK1247/Y4915
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18 comments on “Y haplogroups for prehistoric Eurasian genomes
  1. Vincenzo says:

    How did you determine that RISE416 is DE? I see that the guy is positive to Z1842, which is a SNP under haplogroup J1

    • genetiker says:

      True. But he has two positive calls for DE (CTS1300/M5400/PF1423 and F1498/M5430/PF1428), is negative for F-P160/PF2618, and has no other positive J calls. So it’s safe to conclude that he was DE.

    • genetiker says:

      RISE489 and RISE600 also have positive calls for Z1842, and they definitely weren’t J.

      None of the RISE samples that I’ve done have negative calls for Z1842.

      The derived allele listed for Z1842 in the ISOGG Y-SNP index must be wrong.

      I’ve found other mistakes in the ISOGG Y-SNP index. I notified Thomas Krahn and others at ISOGG of these mistakes. I ended up having an email exchange with Krahn in which he acted like I was wrong, until I finally sent him an email making it perfectly clear that I was right. He simply stopped communicating with me at that point. To this day, ISOGG has not bothered to fix the mistakes that I notified them of.

  2. Matt says:

    Great job on this, I would love to see the downstream result for the I2a Yamnaya. Thanks!

  3. Me too. I2a needs more data and mind-blowing results 🙂

  4. You should specify what version of the ISOGG tree that is the reference of these haplogroup assignments. It is of utter importance since ISOGG branch names represents different branches in different versions of the ISOGG tree. So please make clear that you are referring to the current tree of 2015 (or some older version). You have assigned haplogroup I1a3a2 for RISE175 and RISE179. That means that you are saying that you have identified the SNPs BY351 or BY352, by reference to the current ISOGG tree of 2015. Can you confirm that you have identified BY351 or BY352 in RISE175 and RISE179?

    • genetiker says:

      No, there are no calls for BY351 or BY352.

      RISE175 is positive for non-ISOGG SNPs at positions 14769437, 16695752, 2683242, and 6646025.

      RISE179 is positive for the non-ISOGG SNP at position 14981302.

      I don’t know how the I1a3a2 haplogroup that is associated with these SNPs relates to the different versions of the ISOGG tree.

      • genetiker says:

        Apparently those are SNPs that were found in an I1a3a2 individual, but that are not necessarily specific to I1a3a2. So I’m going to change the haplogroups for RISE175 and RISE179.

  5. Rick says:

    Very nice. Any chance you could check the actual sequence reads for lactase persistence alleles? In the paper they only impute the genotypes from modern 1000 genomes samples. Which seems really backwards.

  6. Vincenzo says:

    genetiker, can you do something for the autosomal and Y-SNP calls of Oase 1? Here’s the link to the study: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14558.html

  7. genetiker says:

    You mean RISE554. No, nothing can be said beyond him being IJK. He was negative for downstream SNPs.

  8. genetiker says:

    I did another analysis of RISE554’s Y-SNPs, and I found that he belonged to haplogroup N-Y6503.

  9. Pete J. says:

    Yes I saw on anthrogenica. Very interesting.
    Can you clarify what you mean by R1a -CTS5508 for RISE 525. I cant find that anywhere on ISOGG or YFull. ?

  10. […] Y haplogroups for prehistoric Eurasian genomes […]

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