Yes, I asked two different people to run the BAM files on all yDNA E samples from Swat, and both came up with the same results, all positive for Y31991. It appears two of them (I3262 and I1799) are also positive for PF4428. Since they are all related to each other (it's a family grave, in a clearly patriarchal and patrilocal setting) we can conclude all individuals are PF4428, or at the very least Y31991. I1992 is also related to the other men, so odds are the "E1a" is actually a "E1b" and also Y31991. Probably just an error in the S1 Table, that would be my guess. The other yDNA E individuals on the same table, who are not from the Swat Valley, are not E-Y31991 (for example that in LBA Armenia).
It's quite unfortunate that, eventhough the table has samples from Damgaard's study on Central Asia, they left out the two Central Saka outliers (unlike the other Sakas the outliers have very little "east Asian" ancestry, and present a very western-Steppe profile), one of which is the one you refered to before, DA19. I messaged Narasimhan about the Saka connection and he aknowledged it, but considering it is/was such a rare haplogroup I doubt we'll see it very often in the future, but who knows..I wasn't expecting to ever find my haplogroup and lo and behold there's a whole clan of them in Swat
PS: there's other clades under Y31991 which are not PF4428, those also seem to have Levantine and European connections, again suggesting an old migration from the Middle East to Europe, probably associated with early farming, or perhaps copper working. Naturally this is a bit speculatory, but not non-sensical, I hope.
It's quite unfortunate that, eventhough the table has samples from Damgaard's study on Central Asia, they left out the two Central Saka outliers (unlike the other Sakas the outliers have very little "east Asian" ancestry, and present a very western-Steppe profile), one of which is the one you refered to before, DA19. I messaged Narasimhan about the Saka connection and he aknowledged it, but considering it is/was such a rare haplogroup I doubt we'll see it very often in the future, but who knows..I wasn't expecting to ever find my haplogroup and lo and behold there's a whole clan of them in Swat
PS: there's other clades under Y31991 which are not PF4428, those also seem to have Levantine and European connections, again suggesting an old migration from the Middle East to Europe, probably associated with early farming, or perhaps copper working. Naturally this is a bit speculatory, but not non-sensical, I hope.
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