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Saturday, April 8, 2023

Dear Harald...

I've started analyzing the Identity-by-Descent (IBD) data from the recent Ringbauer et al. preprint (see here). Unfortunately, it'll take me a few weeks to do this properly, so I won't be able to write anything detailed on the topic for a while.

Meantime, this is the comment that I left for the authors at bioRxiv (at this time it's still being approved, but it should appear there within a day or so, possibly along with a reply from the authors):

Hello authors,

Thanks for the interesting preprint and data. However, I'd like to see you address a couple of technical issues and perhaps one theoretical issue in the final manuscript:

- the output you posted shows some unusual results, which are potentially false positives that appear to be concentrated among the shotgun and noUDG samples. I'm guessing that this is due to the same types of ancient DNA damage creating IBD-like patterns in these samples. If so, isn't there a risk that many or even most of the individuals in your analysis are affected by this problem to some degree, which might be skewing your estimates of genealogical relatedness between them?

- many individuals from groups that have experienced founder effects, such as Ashkenazi Jews, appear to be close genetic cousins, even though they're not genealogical cousins. Basically, the reason for this is reduced haplotype diversity in such populations. Have you considered the possibility that at least some of the close relationships that you're seeing between individuals and populations might be exaggerated by founder effects?

- thanks to ancient DNA we've learned that the Yamnaya phenomenon isn't just an archeological horizon, but also a closely related and genetically very similar group of people. Indeed, in my mind, ancient DNA has helped to redefine the Yamnaya concept, with Y-chromosome haplogroup R1b-Z2103 now being one of the key traits of the Yamnaya identity. So considering that the Corded Ware people are not rich in R1b-Z2103, and even the earliest Corded Ware individuals are somewhat different from the Yamnaya people in terms of genome-wide genetic structure, it doesn't seem right to keep claiming that the Corded Ware population is derived from Yamnaya. I can't see anything in your IBD data that would preclude the idea that the Corded Ware and Yamnaya peoples were different populations derived from the same as yet unsampled pre-Yamnaya/post-Sredny steppe group.

See also...

Dear Harald #2

On the origin of the Corded Ware people