Time and place of European admixture into Ashkenazi Jews

[Angela]

Xue et al, for, I think, the third time.

See:
"[h=1]The time and place of European admixture in Ashkenazi Jewish history"[/h]
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006644

"The Ashkenazi Jewish (AJ) population is important in genetics due to its high rate of Mendelian disorders. AJ appeared in Europe in the 10th century, and their ancestry is thought to comprise European (EU) and Middle-Eastern (ME) components. However, both the time and place of admixture are subject to debate. Here, we attempt to characterize the AJ admixture history using a careful application of new and existing methods on a large AJ sample. Our main approach was based on local ancestry inference, in which we first classified each AJ genomic segment as EU or ME, and then compared allele frequencies along the EU segments to those of different EU populations. The contribution of each EU source was also estimated using GLOBETROTTER and haplotype sharing. The time of admixture was inferred based on multiple statistics, including ME segment lengths, the total EU ancestry per chromosome, and the correlation of ancestries along the chromosome. The major source of EU ancestry in AJ was found to be Southern Europe (≈60–80% of EU ancestry), with the rest being likely Eastern European. The inferred admixture time was ≈30 generations ago, but multiple lines of evidence suggest that it represents an average over two or more events, pre- and post-dating the founder event experienced by AJ in late medieval times. The time of the pre-bottleneck admixture event, which was likely Southern European, was estimated to ≈25–50 generations ago."


Let's see what's new.

 

[Angela]

I don't see any difference really from the last Xue paper in terms of conclusions, although they seem more confident of the results.

"Based on these arguments, we propose that a minimal model for the AJ admixture history should include substantial pre-bottleneck admixture with Southern Europeans, followed by post-bottleneck admixture on a smaller scale with Western or (more likely) Eastern Europeans. The estimates for the total European ancestry in AJ range from ≈49% using our previous whole-genome sequencing analysis [9], to ≈53% using the LAI analysis here, and ≈67% using the calibrated Globetrotter analysis. The proportion of Western/Eastern European ancestry was estimated between ≈15% (Globetrotter and the LAI-based localization method), and, if identified as the source of the post-bottleneck admixture, 23% (the IBD analysis). Therefore, the proportion of the Southern European (presumably pre-bottleneck) ancestry in AJ is between ≈26% to ≈52%, corresponding to [34,61]% ancestry at the time of the early admixture. Given these bounds, along with the admixture time estimate based on a single event (24–37 generations ago), we derived a constraint on the admixture times of the pre- and post-bottleneck events (Methods). We further assumed that post-bottleneck admixture happened at most 20 generations ago, when the effective population size has already recovered from the bottleneck (since our estimate of the post-bottleneck admixture proportions relied on the part of the genome not shared IBD; see the IBD analysis above and Methods). Finally, we assumed that post-bottleneck admixture happened no more recently than 10 generations ago, since no mass admixture events are known in the past 2–3 centuries of AJ history [52]. The results (Fig 6) show that given these constraints, the pre-bottleneck admixture time is between 24–49 generations ago. Our proposed model is shown in Fig 7."

I completely agree with what they say about Alder:
" We thus conclude that, perhaps due to the complex admixture history in Southern Europe, Alder cannot infer the true ancestral sources, and that the results are still consistent with a model of predominantly Southern European contribution."

Globetrotter also didn't work that well. I could have told them it wouldn't.

"The second lesson is the importance of evaluating the results of off-the-shelf tools using simulations when studying closely related populations. When simulating relatively old (≈1k years ago) Middle-Eastern and European admixture (particularly Southern European), we found many tools to be of limited utility (see, e.g., the section on Alder, f-statistics, and TreeMix and S1 Text sections 1 and 2 on LAMP and PCAMask). Further, while we eventually were able to extract useful information off RFMix’s local ancestries, the raw results were not very accurate: the accuracy per SNP was only ≈70%, the mean segment length was more than twice than expected, and the variance of the ancestry proportion per chromosome was overestimated. When jointly analyzing LAI and IBD sharing, the inferred proportion of IBD segments that were either not IBD or had a random ancestry assignment was as high as ≈35% ((1-λ) in Methods), although fortunately, we were able to account for that in our model. We note, though, that problems of this nature are not expected for recent admixture events between more diverged populations."

As always? I'll wait for the ancient dna.

 

[LeBrok]

Ah, my hopes are gone for juicy details. That much I've figured out from Harappa admixture runs.

 

[davef]

The Canaanite abstract suggested 45 percent Neolithic Central European as well

 

[davef]

Wait what i find interesting is that it says the rest of the European admixture is likely Eastern European, yet not every ashkenazi community is based in Eastern Europe.

 

[Angela]

Wait what i find interesting is that it says the rest of the European admixture is likely Eastern European, yet not every ashkenazi community is based in Eastern Europe.

Well, they certainly used to be.

The Canaanite abstract suggested 45 percent Neolithic Central European as well

I don't understand what you mean by that. There's a big difference between "European" populations of any area and the Early or Middle Neolithic farming populations of Central Europe.

That's why I no longer pay attention to any modeling with modern populations. It's just always going to be wrong to one degree or another.

 

[Angela]

I'm not as convinced as Razib Khan that this analysis is completely accurate.

See:
https://www.gnxp.com/WordPress/2018...europe/?utm_source=dlvr.it&utm_medium=twitter

I do agree with some of the things he says, as, for example, that the original Jews of the Near East might have been very much like the Lebanese given how similar they seem to be to the Bronze Age Canaanites. Also, I've held for a long time that the Palestinians and the Jordanians, the latter of whom, if they weren't Palestinian originally, are Palestinian since the Arab-Israeli Wars and resettlement there, are different from the Lebanese. Even 23andme has shown that. I even agree that the Palestinian Christians may be more like the Lebanese, although it depends how much they shared in the post Muslim area migrations from the south.

Where I disagree is with his conclusion that if the ethnogenesis of the European Jews took place after the establishment of Christianity (I'm not so sure I trust any of this dating), it points to the "weakness" of Christianity at that time, as does the subsequent spread of heresies like that of the Cathars.

First, just as a generality, religions evolve and change, "heresies" develop, or other kinds of conflicts. It doesn't mean the religion is "weak", necessarily.

Second of all, if this initial admixture took place in Italy, as he seems to think probable, with Italian women admixing with Jewish men, it must have taken place a couple of hundred years before 1000 AD, as already during the pontificate of Pope Gregory, he is sending admonitions to Bishop Venanzio of Luni to make sure that Jews do not proselytize their Christian slaves or servants, and that in fact Jews not be permitted to have Christians in their households.

https://books.google.com/books?id=O...1gQ6AEINDAC#v=onepage&q=ebrei in Luni&f=false

Of course, given the Italian propensity to place the personal above the institutional, perhaps enforcement was lax. Still, lax even hundreds of years into the future?

Then, there is the leak about the findings of the upcoming paper on the ancient Jews to consider. While such Italian groups would have been high in EEF like ancestry, one would think they would have Central European Indo-European ancestry by that time.

 

[davef]

Just a guess, but maybe the Eastern European and Western European is just more northern ancestry from from say hunter gatherers within that 45 percent "Neolithic Central European"?

 

[Pax Augusta]

 

[Tomenable]

Did they manage to identify the source(s) of their Northern Euro admixture?

 

[Yaahobi Oded]

I wonder if some of the "South European" Admixture couldn't have come into the Jewish gene-pool at a much earlier stage - through the Philistines ("sea people")... After-all, we know that some of them, like the Sherden and the Shekelesh, might have come from Sardinia and Sicily... We also know that at least in the beginning of the Second Temple Period - in between the 6th and 4th centuries BCE - the Jews in Judea took many wives from Philistine cities like Ashdod:

"..in those days I saw men of Judah who had married women from Ashdod, Ammon and Moab.Half of their children spoke the language of Ashdod or the language of one of the other peoples, and did not know how to speak the language of Judah.I rebuked them and called curses down on them. I beat some of the men and pulled out their hair. I made them take an oath in God’s name and said: “You are not to give your daughters in marriage to their sons, nor are you to take their daughters in marriage for your sons or for yourselves.Was it not because of marriages like these that Solomon king of Israel sinned?" (Nehemiah 13: 23 - 26)...

So, couldn't it be that some "South-European" DNA came from them (in fact, in all Autosomal DNA Analysis we can see some "European Admixture" in non-Ashkenazi Jews, and even among Samaritans, Palestinians, and other Levant populations, as well)?...

 

[Angela]

I've already speculated here that this might be a possibility, but the answer will come only with the paper on the Philistines and the ancient Judeans.

 

[William Tell]

I've already speculated here that this might be a possibility, but the answer will come only with the paper on the Philistines and the ancient Judeans.

Interesting, does this mean this paper will show Celtic-like ancestry in Jews? Also, when is this paper coming out, I could only find a paper of pig DNA??

I think maybe the reason Jews don't eat pork is because of the Philistines.