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
Genetiker 
How did you determine that RISE416 is DE? I see that the guy is positive to Z1842, which is a SNP under haplogroup J1
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.
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.
Ok, thanks for your work.
Great job on this, I would love to see the downstream result for the I2a Yamnaya. Thanks!
Me too. I2a needs more data and mind-blowing results 🙂
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?
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.
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.
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.
Yes, I will do a post on the phenotype SNPs for the samples. I don’t know how long it will take though.
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
Apparently the data haven’t been uploaded yet, but I’ll analyze them when they are.
Thanks for all your analysis .
Can you look at russia RiSE 254 again (called IJK)?
Seems a bit downstream. Was there a resolution error?
You mean RISE554. No, nothing can be said beyond him being IJK. He was negative for downstream SNPs.
I did another analysis of RISE554’s Y-SNPs, and I found that he belonged to haplogroup N-Y6503.
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. ?
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