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Razib Khan has posted on the paper. See:
See: http://www.unz.com/gnxp/the-origins-of-ashkenazi-jews-near-resolution/#comments
A few tidbits:
"The likely parental populations of Ashkenazi Jews are Roman period peoples of the eastern Mediterranean, particularly the swath of territory from Alexandria up to Anatolia, and, the peoples of the western Mediterranean. That is, Levantines and Iberians & Italians."
Well, maybe it's likely, but we still don't have the proof, in my opinion, whatever the authors may claim.
"Additionally, the more and more we learn about the Middle East, the more likely it seems that Muslim populations, who are often modeled as a parental group, are highly cosmopolitan compared to ancient groups. Recall that Neolithic farmers from the Levant resemble Sardinians more than they do locals, because of later migration from further east in Eurasia, as well as later African gene flow. Using imperfect reference populations will probably skew the results appropriately."
This is probably why we won't solve this mystery until we get ancient dna from the right periods.
"The major change in the past few years is the usage of more genetic information than common genotypes. This paper for example looks at haplotype information. Sequences of variants across the genome. This preserves more recent genetic variation. In other cases you can look at whole genome sequences, and focus on low frequency variants which are extremely informative of recent population differentiation."
I wish he'd addressed the concerns expressed in the paper about how problematic and unhelpful some of these programs are when analyzing southern European genetics.
This person offered one possible explanation:
"Priori assumptions about ME|Euro 50|50 … SW Asian in Ashkenazi is 11-13% … W-Asian in Jews 17-22% and not entirely derivative of the Levant. 252K is fine for Admixture or PCA but rather light for Alder, ChromoPainter and IBD. Ashkenazi ethnogenesis far more nuanced than presented here."
"Priori assumptions about ME|Euro 50|50 … SW Asian in Ashkenazi is 11-13% … W-Asian in Jews 17-22% and not entirely derivative of the Levant."
Why is he insisting "not entirely derivative of the Levant?" Just curious
Razib also said:
"Ultimately the only reason I’d suggest that this paper is lacking is the imperfection of Middle Eastern source populations. That’s probably increasing the European and decreasing the Middle Eastern fraction somewhat on the margins"
Could you also explain why he said this?
Percentages at the margins? Don't know what that means. Plus, you mentioned that if they were more like "northern near east" then they would've picked up less European admixture...does this mean that the northern near east had more in common with modern europeans?
Ashkenazim sat pretty close to the Anatolians. They are about on par with Sicilians when it comes to Anatolian-ness. Don't take this as suggesting they have sicilian ancestry. Yeah, Sardinians are definitely the closest.
They could've used cypriots and crete for their south european sample pool. It would've been the more common sense approach. It helps that those two islands are way closer to the levant than italy.
Crete similar autosomally? Do you have data and papers to back this?
Yes I don't subscribe to italian anvestry in jews either.
In terms of autosomal DNA Cretans are close to Sicilians (but again, their y-dna pool shows Slavic influence via R1a and I2), Cypriots are not even in the European cluster on any PCA plot, they are basically Levantines themselves.
Oh actually you caught my eye when you said Cretans are autosomally similar to Ashkenazim, so I asked if you have a paper to confirm. It would be interesting if ibd sharing is higher there in comparison to the low ibd sharing reported in the paper with south europeans.
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