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View Full Version : Time and place of European admixture into the Ashkenazim-Xue et al



Angela
11-07-16, 19:27
Here we go again. :) Can't we just wait for the ancient dna which must surely be on its way?

Oh well, from Xue et al, (including Shai Carmi)

See the following pre-print:
http://biorxiv.org/content/biorxiv/early/2016/07/10/063099.full.pdf

"The Ashkenazi Jewish (AJ) population is important in medical genetics due to its high rate of Mendeliandisorders and other unique genetic characteristics. Ashkenazi Jews have appeared in Europe in the 10thcentury, and their ancestry is thought to involve an admixture of European (EU) and Middle-Eastern(ME) groups. However, both the time and place of admixture in Europe are obscure and subject tointense debate. Here, we attempt to characterize the Ashkenazi admixture history using a largeAshkenazi sample and careful application of new and existing methods. Our main approach is based onlocal ancestry inference, assigning each Ashkenazi genomic segment as EU or ME, and comparing allelefrequencies across EU segments to those of different EU populations. The contribution of each EUsource was also evaluated using GLOBETROTTER and analysis of IBD sharing. The time of admixture wasinferred using multiple tools, relying on statistics such as the distributions of EU segment lengths andthe total EU ancestry per chromosome and the correlation of ancestries along the chromosome. Oursimulations demonstrated that distinguishing EU vs ME ancestry is subject to considerable noise at thesingle segment level, but nevertheless, conclusions could be drawn based on chromosome-widestatistics. The predominant source of EU ancestry in AJ was found to be Southern European (≈60-80%),with the rest being likely Eastern European. The inferred admixture time was ≈35 generations ago, butmultiple lines of evidence suggests that it represents an average over two or more admixture events,pre- and post-dating the founder event experienced by AJ in late medieval times, with the prebottleneckadmixture event bounded between 25-55 generations ago."

So, around 800 AD? Is the speculation still that they were in Italy at that time? Does that mean they're not "Middle Eastern" at all? That doesn't seem right based on their yDna.

Of course, if it's closer to 50 generations ago we'd be talking about around 200 AD? Southern European converts to Judaism?

Well, I guess I'll be reading it today while I'm waiting in reception rooms.

davef
11-07-16, 21:06
I swear these studies kill my productivity!

Thanks for posting this but what makes this study special? We already know that doing admixture can make european jewish populations a certain percentage of Eastern European, Southern European and Mideast. That's what fire haired came up with using tools he probably downloaded for free. We don't know which populations are responsible for these scores.
Nothing on you for posting this, I'm just curious as to why they spent so much money to reach conclusions that may as well be reached (in my possibly clueless mind) using a cheap laptop and a few files and apps :).

davef
12-07-16, 02:43
I feel I've been overly harsh (that's how bad work days affect people). This is on fact one of the most interesting articles on this subject I've ever read because it estimates the pre founder admixture event as early as 8 hundred something AD. Assigning a time makes a huge difference and it could've happened while in what italy was back then. Where else could they have gotten the south european score? It certainly couldntve been from Central Europe (painfully obvious). There's the lack of ibd with italians as reported but that's with current day italians, Italy is very very diverse and very large so maby those italians jews do have ibd sharing haven't been found or tested yet (assuming they exist to begin with).

Or maybe they came from an old population that shared a lot with south euros. If the pre founding admixture event didn't happen in italy it would be odd if it happened in Germany assuming jews werent european shifted and purely Levantine.

Angela
12-07-16, 05:06
Some tidbits from the paper:

"Running RFMix on the AJ genomes with our European and Middle-Eastern reference panels and summing up the lengths of all tracts assigned to each ancestry, the genome-wide ancestry was ≈53% EU and ≈47% ME, consistent with an ADMIXTURE analysis (Methods) and our previous estimate based on a smaller sequencing panel."

The problems came when they did the IBD analysis, f4 statistics and even tree mix, and used Alder. Looking at the IBD sharing made it seem as if almost all the admixture was from eastern Europe. Also, there was more IBD sharing with Iberians, Western Europeans, and much more with Eastern Europeans than with Southern Europeans. If you go to the paper and scroll down to the IBD section, they have a graphic of it which is quite startling.

Alder and Tree Mix also produced results consistent with most of the European ancestry stemming from eastern Europeans.

As for f4 statistics, here is what they had to say:

"We measured the f4 statistic for the configuration (X,YRI;AJ,ME), where we used Yoruba (YRI) as an outgroup, and substituted different European regions for X (Figure S4A). The European region that gave the highest value of f4, Eastern Europe (closely matched by Western Europe), is theoretically the one closest to the true source of European gene flow. However, simulations with a dominant (or even exclusive) Southern European source resulted in highest f4 values for Eastern Europe as well. [This discrepancy might be explained, at least partly, by a strong Middle-East to Southern EU migration event [51] (Figure S5)]. Therefore, those results are still consistent with a dominant Southern EU source for AJ."

They then re-analyzed the data with computer simulations, and their conclusion was that "The results of all analyses (once calibrated by simulations) pointed to Southern Europe as the predominant source of European gene flow. At the same time, minor contributions from Western and/or Eastern Europe were also detected, with some analyses (IBD within AJ and between AJ and other sources, and Globetrotter) showing stronger support for an Eastern European source. Based on historical plausibility, these admixture events must have necessarily happened at different times, implying multiple historical events. The inferred admixture time, when modeled by a single event, was between ≈24-40 generations ago by the methods we examined (calibrated mean segment length and ancestry proportions, Alder, and Globetrotter), very close to the time of the AJ bottleneck, previously estimated to ≈25-35 generations ago [9, 16]. Therefore, admixture must have occurred both before and after the bottleneck, with the IBD and Alder analyses suggesting that the Eastern European admixture was more recent."

In terms of Globetrotter results, this is what they had to say.

" the overall European ancestry, ≈70% (or ≈67% after calibration by simulations; Supplementary Text S3), is about 15% higher than the LAI-based estimate, as well as our previous results based on whole-genome sequencing [9]. Our detailed calibration simulations (Supplementary Text S3) demonstrate that evidence exists to support either estimate, suggesting that the true fraction of EU ancestry is midway, around ≈60% (see Discussion)."

As to the programs which they attempted to use:

"In summary, we demonstrated that the raw results returned by Alder, the f-statistics, and TreeMix must only be interpreted in light of simulations. Using such simulations, the results were overall consistent with our previous model of an admixture event ≈35 generations ago involving predominantly Southern Europe, with minor contributions of either Western or Eastern Europe.

When simulating 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, the Methods section on ADMIXTURE, and Supplementary Texts S1 and S2 on LAMP and PCAMask). Further, while we were eventually able to extract useful information off RFMix’s local ancestries, the raw results were not very accurate: the accuracy per SNP was only ≈70- 80%, the mean segment length was more than twice than expected, and the variance of the ancestry proportion per chromosome was underestimated. When jointly analyzing LAI and IBD sharing, the inferred proportion of IBD segments that were either false or had random LAI was as high as ≈35% ((1-λ) in Methods), although fortunately, we were able to account for that in the model."

I've certainly been no fan of Alder (i.e. used in the Hellenthal/Busby papers on recent admixture) but I'll leave it to any "modelers" who read the paper to opine on whether they have an important point here. If they do, then even ancient dna might not give us reliable answers.

To get back to simple basics, if they don't find any appreciable IBD sharing between Ashkenazim and any southern Europeans as defined as Bergamo, Tuscany, Abruzzo, Sicilians or Greeks, I fail to see how they could be responsible for the European admixture into the Ashkenazim. The only southern Europeans who do seem to have some substantial IBD sharing with the Ashkenazim are the Iberians. Is it possible it was Iberian Jews who moved to the Rhineland and formed the nucleus for the Ashkenazi Jews? I don't know why they didn't attempt to model them that way.

Taking the opposite view that the programs they ran without simulations were indeed accurate, and the admixture was mostly eastern European, one wonders what happened to all the eastern European yDna. If it is about 8% one could see that perhaps it just drifted out except for the I1 sub-group. I'm also unclear if it's definite that they picked up their Z93 subclade in the Near East. If it's about 50%, however, then it makes no sense.

Unless, of course, one were to dredge up that old theory that it was Jewish men who went to eastern Europe, and arrived there both without all that many women of their own, and at a time when there wasn't so much hostility and the church didn't yet have all that much control, and so they were able to take a lot of non-Jewish wives.

Well, all I can say is I wouldn't bet any money on any of this. I'll wait for the ancient dna, with the caveat that I want to know if some of these programs are indeed reliable.

Ed. It's late and it's been a long day, so if I made any misrepresentations as to their conclusions, just let me know.

davef
12-07-16, 05:33
Single most important paragraph:
"The results of all analyses (once calibrated by simulations) pointed to Southern Europe as the predominant source of European gene flow. At the same time, minor contributions from Western and/or Eastern Europe were also detected, with some analyses (IBD within AJ and between AJ and other sources, and Globetrotter) showing stronger support for an Eastern European source. Based on historical plausibility, these admixture events must have necessarily happened at different times, implying multiple historical events. The inferred admixture time, when modeled by a single event, was between ≈24-40 generations ago by the methods we examined (calibrated mean segment length and ancestry proportions, Alder, and Globetrotter), very close to the time of the AJ bottleneck, previously estimated to ≈25-35 generations ago [9, 16]. Therefore, admixture must have occurred both before and after the bottleneck, with the IBD and Alder analyses suggesting that the Eastern European admixture was more recent."

Admixture occurred both before and after the bottleneck. We know that after the bottleneck, it was from a Slavic population. But the mystery is whom it was with BEFORE the bottleneck. The southern euro score is the biggest mystery here and needs serious investigation. Its way higher than the Slavic. The first sentence says south Europe is the predominant source but we don't have the ibd data to figure out which Southern European population was the source though as you said, could be spain/portugal.
The Southern European score is the biggest trickster here.

Yeah I need that sleep thing as well.

davef
13-07-16, 01:49
Also, why did they mix in more northerly italians with abruzzo, Sicily and greek? I know abruzzo is more in the center but I question how many people were used in each group because if they used say 90 percent from bergarmo that would produce way different results than if they used 90 percent Sicily.

Sorry, but it never fails to blow my mind that on those gedmatch calculators european jews fit so well as italians (this is every calculator), levantines don't come close (some would be about maybe 5 to 10 percent south italian based on those oracles and often nothing at all) and even the Bronze Age levantines probably don't cut it (I haven't checked their results). I know there's no evidence of mixing with italians based on the weak ibd scores but the south european score couldn't have come from nowhere.

BTW I'm not vouching it came from Italy. And I apologize if I sound like a broken record but my mother has a broken record tendency as well

Angela
13-07-16, 05:19
I get the sense that a lot of effort was expended to get the results from this new method to match the results from their prior paper, and also to match a long held belief by a number of researchers that the Ashkenazi population was formed by the admixture of Jewish men and the Italian women (probably northern Italian women) whom they married and converted.

I'm not sure they're correct that the admixture was between a Middle Eastern population and a southern European population if by southern European they mean Italians and Greeks (Bergamo, Tuscany, Abruzzi, Sicily and Greece are the listed populations that were used). I don't see how it's possible for 50-60 % of the genome of the modern Ashkenazim to be from these people less than 2000 years ago and yet there is almost no IBD sharing with any of them. If the Ashkenazim stem from a southern European population then perhaps it is the Iberians, as there's much more sharing between Ashkenazi Jews and Iberians. (Unless the sharing with the Iberians is mostly gene flow from Jews into Iberian populations during the Moorish occupation?) Strangely, they never modeled the admixture with Iberians.

It's either that or Jewish men arriving in eastern Europe with very few wives and marrying a lot of gentile women before endogamy was enforced.

I also don't understand why the Ashkenazim share more IBD with Eastern Europeans not only in the last 1000 years or so, but also, presumably, 2000 years ago, and why, in the earlier time period they don't share all that much with Levantine populations?

I'd very much like for someone else to redo the IBD analysis on these specific samples, using both their methods and others.

7863



I have no idea what you're getting at with your first paragraph. Why wouldn't they include northern Italians? They tried to get a combined reference sample that would do a good job of covering all or at least most of Italian genetic variation so that they'd have a better chance of finding some IBD sharing. Even with samples from northern Italy, Tuscany, central Italy and the south, they couldn't find it, but they found it with Iberians even though the total number of samples was less.

As to the admixture utilities posted at gedmatch, and the Oracle results often provided, I'm afraid you seem to be a bit confused about how they should be interpreted. The fact that two groups of people share similar percentages of ancestry from very ancient populations doesn't at all mean that they necessarily share any gene flow in thousands of years. They might, but not necessarily. Nor are possible Oracle "admixtures" meant to be taken literally. This is as mistaken as to assume that because two groups of people cluster near one another on a PCA it means that they share any genes at all in even the last 10,000 years.

You might want to take a look at this article about how not to use Admixture. Even academic authors don't seem to be aware of some of the pitfalls. I posted it here as I think it's very helpful in interpreting or not misinterpreting Admixture results.
http://www.eupedia.com/forum/threads/31931-Why-Admixture-Calculators-Have-To-Be-Interpreted-Cautiously

The truth of the matter, of which many people seem to be totally unaware, is that with any of these analyses, including the ones using dstats like those done by Fire-Haired, if you plug in enough different populations you can get a number of patterns that are a "reasonable" fit, so you can prove just about anything you wish. That's why people have to be wary of the conclusions of even academic papers until they've really thought it through or tried to reproduce the results themselves. I'm waiting for some of the modelers in chief to do that with this paper. When hobbyists are involved, it's buyer beware, in my opinion.

One specific reason that I'm not spending too much time on this is all the calculations are, of course, based on modern genomes. The computations are based, for example, on modern Middle Easterners like Jordanians, Palestinians, Druze etc. However, how similar are these modern groups to the Jews of the first centuries of the Common Era, the period roughly corresponding to the time of the Roman Empire? From the current Lazardis et al paper, the ancient Levantine Bronze Age sample plots among modern Saudis and Egyptians. If the Jews of that era were close to them, then the Ashkenazim are perhaps even more "European" than the authors of this paper propose. What if, however, there has been additional SSA and other genetic intrusion into the Levant since the Jews were scattered? Then, the Ashkenazim may be less "European" admixed.

So, for me, I'm not looking for ultimate answers from this paper. More important to me is whether their criticism of some of these programs for use on southern Europeans, and Jews, is justified, because the tools will be used on ancient dna as well.

davef
13-07-16, 07:33
I get the sense that a lot of effort was expended to get the results from this new method to match the results from their prior paper, and also to match a long held belief by a number of researchers that the Ashkenazi population was formed by the admixture of Jewish men and the Italian women (probably northern Italian women) whom they married and converted.

I'm not sure they're correct that the admixture was between a Middle Eastern population and a southern European population if by southern European they mean Italians and Greeks (Bergamo, Tuscany, Abruzzi, Sicily and Greece are the listed populations that were used). I don't see how it's possible for 50-60 % of the genome of the modern Ashkenazim to be from these people less than 2000 years ago and yet there is almost no IBD sharing with any of them. If the Ashkenazim stem from a southern European population then perhaps it is the Iberians, as there's much more sharing between Ashkenazi Jews and Iberians. (Unless the sharing with the Iberians is mostly gene flow from Jews into Iberian populations during the Moorish occupation?) Strangely, they never modeled the admixture with Iberians.

It's either that or Jewish men arriving in eastern Europe with very few wives and marrying a lot of gentile women before endogamy was enforced.

I also don't understand why the Ashkenazim share more IBD with Eastern Europeans not only in the last 1000 years or so, but also, presumably, 2000 years ago, and why, in the earlier time period they don't share all that much with Levantine populations?

I'd very much like for someone else to redo the IBD analysis on these specific samples, using both their methods and others.

7863



I have no idea what you're getting at with your first paragraph. Why wouldn't they include northern Italians? They tried to get a combined reference sample that would do a good job of covering all or at least most of Italian genetic variation so that they'd have a better chance of finding some IBD sharing. Even with samples from northern Italy, Tuscany, central Italy and the south, they couldn't find it, but they found it with Iberians even though the total number of samples was less.

As to the admixture utilities posted at gedmatch, and the Oracle results often provided, I'm afraid you seem to be a bit confused about how they should be interpreted. The fact that two groups of people share similar percentages of ancestry from very ancient populations doesn't at all mean that they necessarily share any gene flow in thousands of years. They might, but not necessarily. Nor are possible Oracle "admixtures" meant to be taken literally. This is as mistaken as to assume that because two groups of people cluster near one another on a PCA it means that they share any genes at all in even the last 10,000 years.

You might want to take a look at this article about how not to use Admixture. Even academic authors don't seem to be aware of some of the pitfalls. I posted it here as I think it's very helpful in interpreting or not misinterpreting Admixture results.
http://www.eupedia.com/forum/threads/31931-Why-Admixture-Calculators-Have-To-Be-Interpreted-Cautiously

The truth of the matter, of which many people seem to be totally unaware, is that with any of these analyses, including the ones using dstats like those done by Fire-Haired, if you plug in enough different populations you can get a number of patterns that are a "reasonable" fit, so you can prove just about anything you wish. That's why people have to be wary of the conclusions of even academic papers until they've really thought it through or tried to reproduce the results themselves. I'm waiting for some of the modelers in chief to do that with this paper. When hobbyists are involved, it's buyer beware, in my opinion.

One specific reason that I'm not spending too much time on this is all the calculations are, of course, based on modern genomes. The computations are based, for example, on modern Middle Easterners like Jordanians, Palestinians, Druze etc. However, how similar are these modern groups to the Jews of the first centuries of the Common Era, the period roughly corresponding to the time of the Roman Empire? From the current Lazardis et al paper, the ancient Levantine Bronze Age sample plots among modern Saudis and Egyptians. If the Jews of that era were close to them, then the Ashkenazim are perhaps even more "European" than the authors of this paper propose. What if, however, there has been additional SSA and other genetic intrusion into the Levant since the Jews were scattered? Then, the Ashkenazim may be less "European" admixed.

So, for me, I'm not looking for ultimate answers from this paper. More important to me is whether their criticism of some of these programs for use on southern Europeans, and Jews, is justified, because the tools will be used on ancient dna as well.

You said if you plug in enough different populations you can get enough different patterns that are a "reasonable" fit...not quite understanding what you mean.

And I don't quite understand the link you posted. It's not getting through to my skull. I'm good at admitting I'm too "dumb" or inexperienced to understand anything written with regards to this subject. It's gobbledygook to me lol.

The while ibd with Eastern Europeans within the last 2000 years doesn't seem right at all. Weren't jews in Rome at that time? That's ridiculous. Now the Southern European source is Iberian...it keeps changing every year. Sorry to sound this way but with the sub par week I've been cursed with and this, I'm feeling frustrated. Nothing on you, but wait till next year and they'll conclude that Ashkenazim are from a sacred order of lizard people. :p

Pulling hair out in three...two...one.,,
:p

davef
13-07-16, 08:01
These posts are merely frustrations of someone who descends from endogamous groups and thus I don't know how I came to be throughout these thousands of years. All of my ancestors are from "backwoods" villages lol. By backwoods, think the equivalent of Appalachia in the US. Endogamous to the extreme.
Dont know the better word for backwoods in case someone doesn't approve of that word. I apologize.

davef
13-07-16, 15:28
But for one thing I do know better than to take oracle results literally, so if someone from france posts an oracle result of 50% English 50% Spanish I'm not going to assume that this french individual has one spanish parent and one english parent and neither should he/she. I think once Alan explained why a neolithic Levantine individual scored 30 percent sardinian I think i started getting what these things are telling us, that is 30 percent of a Sardinians genome is from these neolithic Levantine individuals. Obviously it's not the case that the neolithic Levantine had one parent who was 100 percent Yemenite jewish and one who was 40 percent Yemenite jewish 60 percent sardinian. Common sense really, were there Yemenite Jews (or Jews at all) and Sardinians in the Stone Age? Of course not.
EDIT: I might add that I'm absolutely disgusted with people who manipulate the data in order to fulfill their prophecies because if Joe Bob uses a calculator that is way off center against his 23 and me results and winds up getting a bit of a "surprise" (such as getting 3 percent Native American when his ancestors were colonials from England and Germany for centuries and millennia) he's going to be convinced that he has Native ancestry when it could just be a preshistoric connection. He'll be digging thru papers for years trying to find that Indian in the tree only to realize he's been wasting time. Note there are countless colonial Americans who wish to join a tribe.
In my view, if you convince someone that he isn't of the ethnic background (s) he always believed he was a part of, that could change how he sees himself. Do you get my drift?

LeBrok
13-07-16, 16:51
These posts are merely frustrations of someone who descends from endogamous groups and thus I don't know how I came to be throughout these thousands of years. All of my ancestors are from "backwoods" villages lol. By backwoods, think the equivalent of Appalachia in the US. Endogamous to the extreme.
Dont know the better word for backwoods in case someone doesn't approve of that word. I apologize. We all came from hunter gatherers groups and later farmers, mostly secluded in their small villages. All pretty much endogamous for long periods, except short times of mixing with new blood.
Watch any Amazon tribes video on Youtube, the ones still separated from civilization in strict reserves. They've been endogamous for thousands of years. All people in the tribe looks like bunch of brother and sisters, almost twins. And yet they existed like this for thousands of years. Being endogamous can't be that bad as people say?

davef
13-07-16, 22:42
Oh no, I'm not ashamed of being from endogamous groups or saying its a bad thing...it's just hard to figure out the origins of endogamous groups.

Tomenable
16-07-16, 19:14
one wonders what happened to all the eastern European yDna.

We do have few Y-DNA samples from the Khazar Khaganate (the Saltovo-Mayaki archaeological culture).

Saltovo-Mayaki archaeological culture was located in South-Eastern Europe (Pontic-Caspian region):

https://www.academia.edu/15713987/Афанасьев_Г.Е._Вень_Ш._Тун_С._ Ван_Л._Вэй_Л._Добровольская_ .В._Коробов_Д.С._Решетова_И.К ._Ли_Х.._Хазарские_конфедера ы_в_бассейне_Дона_Естестве нонаучные_методы_исследов ния_и_парадигма_современно й_археологии._М._2015._С.146-153

Individual - haplogroups (all samples dated to years ca. 800 - 900 AD):

A80301 - R1a1a1b2a (Y-DNA), I4a (mtDNA)
A80302 - D4m2 (mtDNA)
A80410 - G (Y-DNA)
A80411 - J2a (Y-DNA)

The population of the Khazar Khaganate / of the Saltovo-Mayaki culture, was ethnically heterogeneous:

https://en.wikipedia.org/wiki/Saltovo-Mayaki

"Saltovo-Mayaki is the name given by archaeologists to the early medieval culture of the Pontic steppe region roughly between the Don and the Dnieper Rivers. Their culture was a melting pot of Onogur, Khazar, Pecheneg, Magyar, Alan, and Slavic influences. During the ninth century the Saltovo-Mayaki culture was closely associated with the Khazar Khaganate, and archaeological sites from this period are one way that historians track the geographic scope of Khazar influence."

====================

The most common Jewish subclade of R1a, is this: R1a1a1b2a2b1a1 M582 (aka CTS6).

It descends from R1a1a1b2a Z94 - one sample of which was found in Saltovo-Mayaki.

Angela
16-07-16, 20:05
We do have few Y-DNA samples from the Khazar Khaganate (the Saltovo-Mayaki archaeological culture).

Saltovo-Mayaki archaeological culture was located in South-Eastern Europe (Pontic-Caspian region):

https://www.academia.edu/15713987/Афанасьев_Г.Е._Вень_Ш._Тун_С._ Ван_Л._Вэй_Л._Добровольская_ .В._Коробов_Д.С._Решетова_И.К ._Ли_Х.._Хазарские_конфедера ы_в_бассейне_Дона_Естестве нонаучные_методы_исследов ния_и_парадигма_современно й_археологии._М._2015._С.146-153 (https://www.academia.edu/15713987/%D0%90%D1%84%D0%B0%D0%BD%D0%B0%D1%81%D1%8C%D0%B5%D 0%B2_%D0%93.%D0%95._%D0%92%D0%B5%D0%BD%D1%8C_%D0%A 8._%D0%A2%D1%83%D0%BD_%D0%A1._%D0%92%D0%B0%D0%BD_% D0%9B._%D0%92%D1%8D%D0%B9_%D0%9B._%D0%94%D0%BE%D0% B1%D1%80%D0%BE%D0%B2%D0%BE%D0%BB%D1%8C%D1%81%D0%BA %D0%B0%D1%8F_%D0%9C.%D0%92._%D0%9A%D0%BE%D1%80%D0% BE%D0%B1%D0%BE%D0%B2_%D0%94.%D0%A1._%D0%A0%D0%B5%D 1%88%D0%B5%D1%82%D0%BE%D0%B2%D0%B0_%D0%98.%D0%9A._ %D0%9B%D0%B8_%D0%A5.._%D0%A5%D0%B0%D0%B7%D0%B0%D1% 80%D1%81%D0%BA%D0%B8%D0%B5_%D0%BA%D0%BE%D0%BD%D1%8 4%D0%B5%D0%B4%D0%B5%D1%80%D0%B0%D1%82%D1%8B_%D0%B2 _%D0%B1%D0%B0%D1%81%D1%81%D0%B5%D0%B9%D0%BD%D0%B5_ %D0%94%D0%BE%D0%BD%D0%B0_%D0%95%D1%81%D1%82%D0%B5% D1%81%D1%82%D0%B2%D0%B5%D0%BD%D0%BD%D0%BE%D0%BD%D0 %B0%D1%83%D1%87%D0%BD%D1%8B%D0%B5_%D0%BC%D0%B5%D1% 82%D0%BE%D0%B4%D1%8B_%D0%B8%D1%81%D1%81%D0%BB%D0%B 5%D0%B4%D0%BE%D0%B2%D0%B0%D0%BD%D0%B8%D1%8F_%D0%B8 _%D0%BF%D0%B0%D1%80%D0%B0%D0%B4%D0%B8%D0%B3%D0%BC% D0%B0_%D1%81%D0%BE%D0%B2%D1%80%D0%B5%D0%BC%D0%B5%D 0%BD%D0%BD%D0%BE%D0%B9_%D0%B0%D1%80%D1%85%D0%B5%D0 %BE%D0%BB%D0%BE%D0%B3%D0%B8%D0%B8._%D0%9C._2015._% D0%A1.146-153)

Individual - haplogroups (all samples dated to years ca. 800 - 900 AD):

A80301 - R1a1a1b2a (Y-DNA), I4a (mtDNA)
A80302 - D4m2 (mtDNA)
A80410 - G (Y-DNA)
A80411 - J2a (Y-DNA)

The population of the Khazar Khaganate / of the Saltovo-Mayaki culture, was ethnically heterogeneous:

https://en.wikipedia.org/wiki/Saltovo-Mayaki

"Saltovo-Mayaki is the name given by archaeologists to the early medieval culture of the Pontic steppe region roughly between the Don and the Dnieper Rivers. Their culture was a melting pot of Onogur, Khazar, Pecheneg, Magyar, Alan, and Slavic influences. During the ninth century the Saltovo-Mayaki culture was closely associated with the Khazar Khaganate, and archaeological sites from this period are one way that historians track the geographic scope of Khazar influence."

====================

The most common Jewish subclade of R1a, is this: R1a1a1b2a2b1a1 M582 (aka CTS6).

It descends from R1a1a1b2a Z94 - one sample of which was found in Saltovo-Mayaki.

It's also found in the Near East, isn't it? If so, it could have entered the Jewish genome with "Iranian like" migrations into the Near East. So, again, inconclusive.

Also, it doesn't form a large enough percentage of the y lineages of Ashkenazim to account for 50-60% of their autosomal inheritance, although if it entered their population in eastern Europe it might explain the 15% or so that is proposed with some of these Xue models.

I suppose I should say that I do think it is possible that the ancient Hebrews had rather more eastern Anatolian inheritance than the "Canaanites", since the mythology of their origins as expressed in the Old Testament would allow for that, with the connections to the upper Euphrates and Hurrian culture.* However, I do think there was some ancient interaction with Egyptians, so you would think it would have been somewhere in between these people and the Bronze Age Levantine sample, but again, who knows.

*http://www.jewishvirtuallibrary.org/jsource/History/hebrews.html

Tomenable
16-07-16, 20:22
^ I think testing some ancient DNA samples from actual Jewish burials could help.

There are old Jewish graves in Roman catacombs, and there are also these graves:

http://www.eupedia.com/forum/threads/31980-Ancient-Ashkenazi-Jewish-DNA?p=475572&viewfull=1#post475572


It's also found in the Near East, isn't it?

Yes. R1a-Z94 has a very widespread distribution.

We need higher resolution of SNPs to determine where did the Jewish branch come from.

davef
16-07-16, 20:39
It's also found in the Near East, isn't it? If so, it could have entered the Jewish genome with "Iranian like" migrations into the Near East. So, again, inconclusive.

Also, it doesn't form a large enough percentage of the y lineages of Ashkenazim to account for 50-60% of their autosomal inheritance, although if it entered their population in eastern Europe it might explain the 15% or so that is proposed with some of these Xue models.

I suppose I should say that I do think it is possible that the ancient Hebrews had rather more eastern Anatolian inheritance than the "Canaanites", since the mythology of their origins as expressed in the Old Testament would allow for that, with the connections to the upper Euphrates and Hurrian culture.* However, I do think there was some ancient interaction with Egyptians, so you would think it would have been somewhere in between these people and the Bronze Age Levantine sample, but again, who knows.

*http://www.jewishvirtuallibrary.org/jsource/History/hebrews.html
I don't think we can prove that those Bronze Age levantines represented the majority of Canaanites well. And the low ibd sharing with Italy and ironically the Middle East (the Middle East ibd being even lower) in and with the Ashkenazim being more Southern European and middle eastern than Northern European (some of the northerly stuff could've came later) according to the admixture test might just lead to the possibility that some of the Middle East was more european like than it is today. I've seen gedmatch numbers from today's levantines and they don't get much of any EEF in some calculators and if they get any european percentages it would be something like 5 percent some southern euro group.
My biggest bet favors that the Southern European score did not come from Southern Europeans, that includes greeks, italians, sicily, etc though the Iberian ibd could indicate some spanish but in this study Southern European means italian or greek.
I'm not insisting on the idea in the previous paragraph above, it's just something i kinda have more faith in. I can't insist on anything without more actual genomes, but I won't bet as much on the "South European" coming from Europe.

Btw I was only suggesting that perhaps parts of the Middle East was more euro like. I'm not like those boneheads on other forums who try to claim that all the great civilizations of the Middle East were once like eiropeans until they started mixing with slaves or some other quacky idea. If I wanted to convince people that events like these happened, I wouldn't post them here since Angela knows all the tricks in the book.

Angela
16-07-16, 21:32
I don't think we can prove that those Bronze Age levantines represented the majority of Canaanites well. And the low ibd sharing with Italy and ironically the Middle East (the Middle East ibd being even lower) in and with the Ashkenazim being more Southern European and middle eastern than Northern European (some of the northerly stuff could've came later) according to the admixture test might just lead to the possibility that some of the Middle East was more european like than it is today. I've seen gedmatch numbers from today's levantines and they don't get much of any EEF in some calculators and if they get any european percentages it would be something like 5 percent some southern euro group.
My biggest bet favors that the Southern European score did not come from Southern Europeans, that includes greeks, italians, sicily, etc though the Iberian ibd could indicate some spanish but in this study Southern European means italian or greek.
I'm not insisting on the idea in the previous paragraph above, it's just something i kinda have more faith in. I can't insist on anything without more actual genomes, but I won't bet as much on the "South European" coming from Europe.

Btw I was only suggesting that perhaps parts of the Middle East was more euro like. I'm not like those boneheads on other forums who try to claim that all the great civilizations of the Middle East were once like eiropeans until they started mixing with slaves or some other quacky idea. If I wanted to convince people that events like these happened, I wouldn't post them here since Angela knows all the tricks in the book.

Interesting choice of words: are a knowledge of archaeology, history, and genetics, and the use of reason and logic "tricks"???

As to the Canaanites, what better evidence could there be about the autosomal signature of the Canaanites than an ancient sample from the same time and place as the Canaanites? I don't think it gets any better than that. That indicates the Canaanites and other peoples of the Levant at that time were probably very Saudi like and Egyptian like, and lo and behold, the Palestinians and Jordanians in the analysis at 23andme cluster not with Anatolians or Syrians or Iranians or people from the Caucasus, but with Saudis and Egyptians, although they plot a bit "north" of them (not that much, however). I used to think that was because of a lot of influx from Arabia into the Levant with the Muslim migrations, but maybe not, or at least not to any great extent. The Lebanese are probably a decent example of a "Canaanite" like population. They plot a bit north of the Jordanians, etc., but they might have a bit of "Hellenic" admixture and/or a bit of Crusader.

If Iranians are still mostly Iranian Chalcolithic, and some of the Bedouin, if you subtract out the recent SSA are pretty darn Natufian like, then I think it's possible that Canaanites (Lebanese) and Palestinians aren't that far removed from the Levantine Bronze.

The Jews might have been different. Did you read the article from the Jewish Virtual Library? High levels of admixture from the more northern Near East are indeed possible for them, and given their extreme endogamy might have become fixed. It may also be that they absorbed some ancestry from the Sea Peoples as they were very close to the coast at the time. I think we may be able to get a hint about their admixture at that time by looking at the Samaritans and the Druse, who are quite different from the Palestinians and the Jordanians.

All of this is going to have to wait for ancient dna.

Btw, I have no idea how you could think the Jews of that time might have been "European" like, a statement you've made before. There is to my knowledge no documented "European" migration to the Levant large or small in the relevant time frame. Until these "Sea Peoples" dna is analyzed we won't know if they came from Crete or Anatolia, and we certainly won't know how much ancestry they could have contributed to the Jews and whether that would have been enough to turn them into a "European" population. We'll have to wait and see. Even most of the "Hellenic" people were just Hellenized Near Easterners. Did these "European like" Jews drop out of the sky from a space ship? Even wild speculations have to be based on some data.

No offense meant, but you place way too much emphasis on admixture runs from gedmatch, in my opinion. They're one, and not the most reliable, of the genetic tools available. Also, the fact that today's Near Easterners get so little "EEF", or maybe you mean "Anatolian Neolithic", or Early European farmer" just shows they aren't "European". EEF is preeminently a European marker today, although the majority of the genes in that cluster entered Europe with farmers from Anatolia. After the Anatolian farmers left the Near East ten thousand or so years ago there were massive demographic changes there, although mainly through the agency of another "Basal Eurasian" rich farmer group, and then more minor amounts of ancestry from EHG through the Indo-Europeans. You can also add in some additional ASI and SSA. Now, during the latter part of the first millennium, and then into the Roman Era, they increasingly became traders, and there was at that time no prescription on marriage with "foreign" women, so the genome of diaspora Jews could have been different from that of the Palestine Jews. That's why we need their genomes as well, although again, if the admixture was with Italians or Greeks why is there no real IBD sharing? Italians definitely seem out, which will disappoint all my Ashkenazi friends, but perhaps the "Greek" population used for the comparison did not include island Greeks, Cretans, or Pontic Greeks, and that would make a difference.

davef
16-07-16, 22:18
Thanks!
Yeah, I meant that you can't be fooled easily when I made the tricks in the book statement.

Ok so around the time when the Bronze Age levantines were around, nobody in the Mideast during that time had much (if at all) to share with europeans. The anatolian farmers were gone from there thousands of years prior.

Now that you brought that up, the Southern European score could've in fact been from mixing with an actual, unknown european population, since jews seem to have much more in common with europeans than modern levantines. It's just a matter of getting ancient genomes at this stage.

I know by now that gedmatch or admixture isn't the ultimate predictor, but it does point out that jews have more in common with Southern Europe than levantines do, at least to me it does. That's as far as it goes. It fails to point out the source. Ancient genomes and ibd would be pretty much the only way short of a time machine we can figure out the population that contributed to the "south european score."

srdceleva
18-07-16, 20:23
one majory counfusion in this thread for this whole discussion is the IBD sharing between Aj and the other ME and EU populations. When i was reading the study, when they were discussing IBD sharing between the populations it didnt seem to be an issue at all for the authors that AJ shared the largest IBD segments with Eastern europeans, then next with Iberians, then next with southern europeans, and then next with middle easterners. This makes total sense according to the evidence suggested in the study, that AJ had more recent ancestry from Eastern europeans then slightly older or pre bottleneck ancestry southern europeans, and then ancestry from the original levantine Jews. Obviously you will share the longest strands of your dna with recent people who admixed with you, so this makes total sense that if Eastern eurpeans mixed most recently with AJ that they will share the largest identical strands of dna with them. If admixture was from along time ago such as the ME admixture in AJ then you would expect for modern ME and AJ to share very little IBD segments as the length of Identically shared ancestry would be broken up thousands of times and would not remain identical anymore. Higher shared IBD with Iberia is easily explained away by the recent gene flow in Iberia from Sephardic Jews. The sephardic Jewish ancestry in modern Iberians is quite significant. Maybe I dont understand how it all works quite well enough but thats what I understood from it. I still do think its best to wait for ancient dna evidence.

davef
18-07-16, 21:09
Srdceleva, that was absolutely brilliant. If you relate the order of the ibd lengths to the order of the proposed admixture events, you'll see how they match. The shortest is with levantines, but jews are from the Middle East, and derive from Bronze Age levantines. When they left, their Levantine cousins became Lebanese, etc and formed different sequences and eventually would drift from the jews overtime. Southern European (one that is about as southerly as south italians, not saying its from them) came next, and over time the south euro contributors drifted out genetically from European Jews so ibd got worse overtime. Pattern applies with the other contributors.
Not saying this happened for sure, we lack hard evidence but your idea is very interesting and makes a lot of sense.

Angela
18-07-16, 22:42
one majory counfusion in this thread for this whole discussion is the IBD sharing between Aj and the other ME and EU populations. When i was reading the study, when they were discussing IBD sharing between the populations it didnt seem to be an issue at all for the authors that AJ shared the largest IBD segments with Eastern europeans, then next with Iberians, then next with southern europeans, and then next with middle easterners. This makes total sense according to the evidence suggested in the study, that AJ had more recent ancestry from Eastern europeans then slightly older or pre bottleneck ancestry southern europeans, and then ancestry from the original levantine Jews. Obviously you will share the longest strands of your dna with recent people who admixed with you, so this makes total sense that if Eastern eurpeans mixed most recently with AJ that they will share the largest identical strands of dna with them. If admixture was from along time ago such as the ME admixture in AJ then you would expect for modern ME and AJ to share very little IBD segments as the length of Identically shared ancestry would be broken up thousands of times and would not remain identical anymore. Higher shared IBD with Iberia is easily explained away by the recent gene flow in Iberia from Sephardic Jews. The sephardic Jewish ancestry in modern Iberians is quite significant. Maybe I dont understand how it all works quite well enough but thats what I understood from it. I still do think its best to wait for ancient dna evidence.

Take a look at the graphic of the IBD sharing, and also read the caption:

7878
Both the less than 7cm and more than 7cm sharing is highest with Eastern Europeans.

Also, the length of the segments is not the only important factor; one also has to consider the mean number of segments.

srdceleva
19-07-16, 01:07
Srdceleva, that was absolutely brilliant. If you relate the order of the ibd lengths to the order of the proposed admixture events, you'll see how they match. The shortest is with levantines, but jews are from the Middle East, and derive from Bronze Age levantines. When they left, their Levantine cousins became Lebanese, etc and formed different sequences and eventually would drift from the jews overtime. Southern European (one that is about as southerly as south italians, not saying its from them) came next, and over time the south euro contributors drifted out genetically from European Jews so ibd got worse overtime. Pattern applies with the other contributors.
Not saying this happened for sure, we lack hard evidence but your idea is very interesting and makes a lot of sense.

thanks for the nice comments


Take a look at the graphic of the IBD sharing, and also read the caption:

7878
Both the less than 7cm and more than 7cm sharing is highest with Eastern Europeans.

Also, the length of the segments is not the only important factor; one also has to consider the mean number of segments.

i still think it falls in line with what I said, and in the description above the graph it says also the same conclusion, that this shows that most of the recent genetic influence in AJ is from Eastern Europe.

davef
19-07-16, 01:22
thanks for the nice comments



i still think it falls in line with what I said, and in the description above the graph it says also the same conclusion, that this shows that most of the recent genetic influence in AJ is from Eastern Europe.

Yeah, they both show Eastern Europe>(Iberia or Western Europe-they seem to have different ranks in both charts, but they are somewhat close)>Southern Europe>MidEast
which makes sense given what we believe happened during the European journey.

And I don't know if we should say low ibd leads to not having any gene flow from a certain place. To say they haven't gotten any from Southern Europe is like saying they haven't gotten any from the MidEast, which is odd since that's where they are from...but we have the challenge of using modern populations for comparison, since Jews have been endogamous for centuries and other populations, even the ones where the Jews MAY have gotten what they got went their own separate ways genetically and drifted out. If they would be so kind as to replace the modern Levantines with Bronze Age Levantines, and the modern Southern Euros with ancient ones (Angela brought up the island types) the IBD should be higher between either of these populations or both. Jews descend from non-Jews. Period. It's not like they're a separate hominid species, or crash landed on Planet Earth from the outer reaches of the galaxy.

"We...bring...you...peace" (finger glows)

Let me know any issues you have with what I have said

srdceleva
19-07-16, 01:45
Yeah, they both show Eastern Europe>(Iberia or Western Europe-they seem to have different ranks in both charts, but they are somewhat close)>Southern Europe>MidEast
which makes sense given what we believe happened during the European journey.

And I don't know if we should say low ibd leads to not having any gene flow from a certain place. To say they haven't gotten any from Southern Europe is like saying they haven't gotten any from the MidEast, which is odd since that's where they are from...but we have the challenge of using modern populations for comparison, since Jews have been endogamous for centuries and other populations, even the ones where the Jews MAY have gotten what they got went their own separate ways genetically and drifted out. If they would be so kind as to replace the modern Levantines with Bronze Age Levantines, and the modern Southern Euros with ancient ones (Angela brought up the island types) the IBD should be higher between either of these populations or both. Jews descend from non-Jews. Period. It's not like they're a separate hominid species, or crash landed on Planet Earth from the outer reaches of the galaxy.

"We...bring...you...peace" (finger glows)

Let me know any issues you have with what I have said

yes i think were on the right track. From my understanding IBD and proving recent genetic relatedness in general, for example between cousins or close family, is based on the fact that you share large portions of identical dna with that person, and as angela pointed out, the frequency of these segments. This proves that you have a recent genetic relationship. You may be almost one hundred percent of a different ethnicity as someone but if you have a recent common ancestor from not too long ago you will share higher rates of IBD with that person than with someone of your own ethnicity who isnt as close of a cousin because youve been seperated from them for a long time. The Jews have literally been seperated form levantine peoples for over 2000 years. As time goes on that dna gets broken up into so many parts that the length of identical dna becomes very small, though you are of the same ethnic group. This makes total sense. My overall genetic make up may resemble a guy from eastern europe, but because im a quarter american there maybe be many americans who i share more recent ancestry with than many eastern europeans.

davef
19-07-16, 02:18
I know, it makes total sense. They are descended from Bronze Age levantines and I bet if the calculator used in this student were used on the Bronze Age, they might not get any european. Maybe a small percentage of south european in the single digits. Ibd sharing with modern south Europe is small but it's certainly higher than with the modern Middle East.

Yeah ibd is "enough" sharing in a row as opposed to scattered short segments here and there, which admixture calculators go by (by state). The 47 percent Mideast is IBS sharing with the levant so 47 percent of the total genome is admired with levant, and one can be tricked into thinking that a gang of people who were 3/4 south italian 1/4 north euro mingled with a group of people who were of full Lebanese descent and together they formed Ashkenazim.

Also you said you are 1/4 American...you mean Native American ,colonial (English/german or some other northern descent), or having a grandparent born in the US of another background besides the colonial/native?

srdceleva
19-07-16, 02:41
I know, it makes total sense. They are descended from Bronze Age levantines and I bet if the calculator used in this student were used on the Bronze Age, they might not get any european. Maybe a small percentage of south european in the single digits. Ibd sharing with modern south Europe is small but it's certainly higher than with the modern Middle East.

Yeah ibd is "enough" sharing in a row as opposed to scattered short segments here and there, which admixture calculators go by (by state). The 47 percent Mideast is IBS sharing with the levant so 47 percent of the total genome is admired with levant, and one can be tricked into thinking that a gang of people who were 3/4 south italian 1/4 north euro mingled with a group of people who were of full Lebanese descent and together they formed Ashkenazim.

Also you said you are 1/4 American...you mean Native American ,colonial (English/german or some other northern descent), or having a grandparent born in the US of another background besides the colonial/native?

Well I think to truely see how really middle eastern Ashkenazi Jews are we will have to wait for more ancient DNA to be sampled as many people on this website have said many times, modern populations are not always the best representation of ancient ones. Modern levantine people may have had alot of genetic influence from the Islamic arab expansions while ancient levantine people had more influence from southern european/ Mediterranean cultures ( possibly the philistines?). Well just have to wait.

My American grandmothers ancestry is very colonial after having done her family tree I can definitely say her family has been in the US in some places before the revolution. She does have more recent ancestry though ( but still a couple generations back) from Germany, Switzerland, and France . She didn't hsve any native American according to her DNA results.

davef
19-07-16, 03:12
It would really be great if they compare modern european jews with the philistines that were picked up about a week ago. I would definitely expect big ibd there and would explain the Southern European plotting that jews get. Using modern italians is pretty much a lost cause and I would be mad if I see a new study that uses them again. I would ask if they even bothered reading any other study that tries to figure out european admixture sources.
Not to mention Ashkenazim/sephardics score high european/Anatolian farmer, about on par with south euros unlike today's leventines who sit more with the Bronze Age leventines.

Vallicanus
19-07-16, 09:54
An Anthrogenica thread on the 23andMe results of 6 North African Jews gives Italian readings of 29pc, 17.5pc, 18.5pc, 25.1pc, 29.4pc and 23.8pc.Iberian readings were very low, generally 0.1pc with a single example reaching 2.2pc.

Vallicanus
19-07-16, 10:46
Genetic differences between Sephardi and Ashkenazi Jews are not great.

davef
19-07-16, 15:56
Whoa! I think 23 and me tests for ibd so that's freakishly high. 29 percent? That's insane! I think the jews who stuck around in italy picked up more recent Italiano blood and some moved to Africa. Or they're not fully jewish but mixed with italian.
I think I've seen maps where the researcher would pull some trick where Sephardim would still cluster with sicilans and cypriots whereas Ashkenazim would plot far from everyone and i think this is a result of testing longer ibd strands but i could be wrong.
Ashkenazim do have the greatest ibd with Sephardim

davef
19-07-16, 19:39
Uh it was redundant for me to say that they aren't fully jewish after mixing with italians because i already pointed out that they picked up more recent italian blood (those North African ones you posted). Lol. But yeah there's definitely recent italian in those, because most ashkenazi get 95 percent or more ashkenazi from 23and me, its own category.
I think if you take out all the jewish samples in 23andme I don't know if it would be able to figure out anything about a new ashkenazi customer.

Vallicanus
19-07-16, 20:12
Uh it was redundant for me to say that they aren't fully jewish after mixing with italians because i already pointed out that they picked up more recent italian blood (those North African ones you posted). Lol. But yeah there's definitely recent italian in those, because most ashkenazi get 95 percent or more ashkenazi from 23and me, its own category.
I think if you take out all the jewish samples in 23andme I don't know if it would be able to figure out anything about a new ashkenazi customer.


Where does that high Italian reading come from in these North African Jews on 23andMe?

These 6 samples also get 2 to 5pc of Ashkenazi.

Vallicanus
19-07-16, 20:21
Reference:
anthrogenica.com/showthread.php?5048-23andme-results-of-North-African-Jews/page3

davef
19-07-16, 20:32
2-5 percent means they and Ashkenazim drifted off genetically. Those high italian scores tell me that they have recent italian ancestry and i think they were more open to conversions. Ashkenazim who are full blooded shouldn't score much of any italian in this test, maybe 1-2 percent in an oddball.
What else did they score besides italian, Iberian, or Ashkenazim? Likely Mideast, but european jews left the Mideast long ago and are supposed to be drifted off, this is really strange. Ibd with Middle East can't be that high..,,
Or they're converts!

davef
19-07-16, 20:34
Oh I see you posted that thread. I'll read it later, but this is getting even more interesting. I love interesting.

Angela
19-07-16, 21:13
Uh it was redundant for me to say that they aren't fully jewish after mixing with italians because i already pointed out that they picked up more recent italian blood (those North African ones you posted). Lol. But yeah there's definitely recent italian in those, because most ashkenazi get 95 percent or more ashkenazi from 23and me, its own category.
I think if you take out all the jewish samples in 23andme I don't know if it would be able to figure out anything about a new ashkenazi customer.

Yes, you finally got my attention. Don't expect it to continue, however, Sikeliot.

No, there isn't recent "Italian" in North African Jews. Please familiarize yourself with their history. You may also be confusing North African Jews with Sephardic Jews; they aren't the same even when they use the same religious rite and despite the fact that there was Sephardic migration into North Africa.
https://en.wikipedia.org/wiki/History_of_the_Jews_in_Algeria
https://en.wikipedia.org/wiki/History_of_the_Jews_in_Tunisia
https://en.wikipedia.org/wiki/Berber_Jews

Plus we have just finished discussing ad nauseam the fact that no academic study has found any appreciable IBD sharing between any Italians and any Jews. Certainly, it seems pretty settled that the only recent IBD sharing between Jews and European populations is with Eastern Europeans, and there isn't much of that.

I've urged you before to study the 23andme white paper in order to understand their proprietary algorithm.
https://www.23andme.com/ancestry_composition_guide/

Please familiarize yourself with the recall and precision numbers for "Italian" in 23andme results. It's in the white paper they've provided. Commenting without taking these things into consideration isn't very helpful.

As I've also told you many times, I put very little credence in posted results "supposedly" from 23andme, by people "claiming" to be all sorts of nationalities. They don't seem to have caught on at Anthrogenica that people posting there can claim to be all sorts of nationalities and there's no way to verify it, just as there is no way to verify the posted "results" are not doctored. Even if the posts are "honest", 23andme does not represent a randomly chosen, scientific set. It's all self selected people who may or may not be representative of their groups.

@Vallicanus,
Ah, our Iberian obsessed Scot is back. Perhaps you might consider contacting the authors of Xue et al and Behar and all the others who have looked at the issue of IBD sharing between Jews and Europeans and tell them that they're dead wrong; there is no IBD sharing between Jews and Iberians, and the proof is some unsourced individual sets of results from 23andme. Good luck with that, and please report back. I'm dying to hear the response.

Now, stop repeating the same things over and over again, and get back on topic.

davef
19-07-16, 21:57
Ok I appreciate the response, I just thought that non-Ashkenazic jews mixed more with their hosts and wasnt aware of 23-and me's quirks. It's my fault for not doing my homework, I'll admit. And I was aware from the beginning that Ashkenazim have no recent italian ancestry, this isn't anything new to me or anything I'm pushing to argue against. I mistakenly thought that North African jews were more open to mixing and incorporated italians into their troupe.

Try not to confuse me for someone else, please. I'm not sikeliot.

Vallicanus
19-07-16, 23:16
Sorry, everybody but I'm still in the dark why 23andMe's North African Jewish sample has such a high "Italian" reading.

What does "Italian" mean in 23andMe?

Remember Fiorito et alia (2015) found high IBD sharing between Italians, especially South Italians and Sardinians, and Northwest Africans.

srdceleva
20-07-16, 00:01
Sorry, everybody but I'm still in the dark why 23andMe's North African Jewish sample has such a high "Italian" reading.

What does "Italian" mean in 23andMe?

this thread is getting too confusing for me, i think angela was right earlier, we have to wait for the ancient samples. The ashkenazi have to complex of a history it seems, I also dont understand why those people from 23 and me show such high italian. Maybe because they are new york AJ and are a quarter Italian haha who knows, or maybe when europeans mix with middle easterners some parts of their dna can be easily confused with Italians lol. Im just gunna wait for the ancient DNA

Angela
20-07-16, 02:14
Ok I appreciate the response, I just thought that non-Ashkenazic jews mixed more with their hosts and wasnt aware of 23-and me's quirks. It's my fault for not doing my homework, I'll admit. And I was aware from the beginning that Ashkenazim have no recent italian ancestry, this isn't anything new to me or anything I'm pushing to argue against. I mistakenly thought that North African jews were more open to mixing and incorporated italians into their troupe.

Try not to confuse me for someone else, please. I'm not sikeliot.

I apologize, Davef. The preoccupations are his, and indeed some of the arguments echo things he has posted on 23andme, so the name just floated to the surface of my mind I guess. I'll be more careful in the future.

Again, sorry.

davef
20-07-16, 03:12
Not a problem, Angela! Apology accepted!

davef
21-07-16, 00:53
Vallicanus,
Angela pointed out that North African Jews do not have italian ancestry and I agree with her. The "italian" could be explained by bad methodology on 23andme's part,the possibility that the poster had flat out lied about their ancestry, or that they aren't fully North African jewish, but mixed with italian unlike anyone who is full blooded North African jewish. I had to coin my words precisely so no one misreads them and thinks I was implying that North African jews have italian ancestry which isn't the case.

There isn't ibd sharing between North African jews and italians and I wouldn't gloss too hard over those results.

I apologize for veering off topic.

Angela
21-07-16, 17:18
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."

There's also some interesting discussion in the comments about what caused the bottleneck. I agree with the posters who hold it's probably small population size to begin with, combined with the pogroms.

There's also an amusing bit where Khan typically loses his temper again when confronted with the same old argument, made, I would be willing to bet, by the same person who used to repeat this stuff over and over again on this forum, that Italians are the product of at least a partial replacement by Middle Easterners during the Roman Empire, and all based on the fact that there is an increasing number of grave inscriptions with "Greek" names in that period.

I could have written the response myself, although, unlike Khan, I haven't looked at thousands of Italian genomes. :)

I also don't agree with even "possible" parity in Sicily, given the uniparental story.

Anyway, it's off topic for this thread, so I won't include it here, but the exchange is worth a read.

davef
21-07-16, 17:30
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."

WOW!!! I just scoped the date of the article and it came out two days ago!!! Im reading it later, thanks Angela!!!!!

davef
21-07-16, 18:17
"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?

Angela
22-07-16, 03:39
"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?

The Middle Eastern source populations being used are imperfect, as we've already said may times, because they're modern samples, and we don't know how close the Jews of the first millennium BC and the early centuries of the Common Era were to modern Palestinians/Jordanians, or even Druze, although they may be closer, as they have more northern Near East admixture.

If the Jews of the beginning of the Common Era were like modern Palestinians, that's one thing. If they were more like the Druze, for example, being less SSA, more northern Near East, then they probably picked up less admixture in Europe.

The Levant Bronze Age clustered with Saudis. We don't know, however, the genetic signature of any of the inhabitants of the Levant by the late Iron Age. Did they by that time have more Northern Near Eastern affinities, and then they changed again with the Arab invasions and the slave trade?

Even if they were still Levant Bronze Age like in the first millennium BC, had the Jews, in particular, given that a good number of them had become merchants, and now actively proselytized or at least willingly absorbed a lot of non Jewish women into their communities, already changed to a certain degree by the first centuries of the Common Era, particularly in the communities in Anatolia? We just don't know.

In this regard, there were at that time large communities of Jews throughout Anatolia, and a large one even in Cyprus. When the Apostles and other disciples of Jesus traveled the ancient world to preach the Gospel, they worked from the Jewish communities in the beginning. When the Jews of the Levant, after two disastrous wars with Rome, were by the tens of thousands either killed or sold into slavery, the future of the Jewish people may have rested on these already slightly changed diaspora communities.

In that regard I've often wondered why more analysis isn't done with the Italian Jews, who were in Rome from very early times. I suppose by now there's been intermarriage with other European Jews, and so the waters are muddied.

We just don't know. Khan seems to be leaving the possibility open that the Jews had already become a bit more northern and western by the time of the major diaspora movements, although he thinks the differences might be small given that he says it would only change the percentages at the margins.

Of course, none of this answers why we're not seeing any significant IBD sharing from that period with any southern European populations.

davef
22-07-16, 04:08
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?

davef
22-07-16, 05:12
If the jews descend from Bronze Age Canaanites, then a little Slavic won't be enough for them to plot in Europe. There had to be some intervention, and its doubtful that it was from " italians". Im not fooled by the " jews are descended from italians/Romans" theory. We do have philistines that were dug up last week, just last week and I would definitely use them if we ever want to figure out the reason why jews plot in Europe. They are an ancient population from Mediterranean Europe who have quite a history with ancient jews.

Neolithic levantines don't plot in Europe, nor do Palestinians, Druze, or other levantines. Far from it.

Ancient genomes will teach us more than anything else. We have them. We must use them. The days of using modern levantines and italians/greeks should come to an end.

Angela
22-07-16, 15:07
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?

I think it's a pretty well understood term; it means "a bit more". It comes from the financial sector. Obviously, he can't quantify it without ancient genomes.

https://answers.yahoo.com/question/index?qid=20110928124639AA2tFEH

As for your second question, let's take the example of just the SSA contribution to modern Levantine genomes. By some analyses, the Palestinians are 7-8% SSA, Jordanians about 7%, Lebanese 3 1/2%, but the Samaritans are 2%, the Druse 2%. If the Jews of the first centuries of the Common Era were more like the Druze than the Palestinians, then they would need less Southern European admixture to pull them to their present position.
https://docs.google.com/spreadsheets/d/1Me2vweYJN2mNtnDaypabv31sy2-kSWVhNJvanIsWtJU/edit?pref=2&pli=1#gid=0

So, as I suggested above, perhaps there was a change from the Levant Bronze Age to the Iron Age and then a change back to a more Bronze Age profile with the Muslim invasions and the Arab slave trade. Or maybe not. We just don't know yet.

We could try to look at what we know about the ethnogenesis of the Samaritans and the Druze, but we don't know a whole lot. The Samaritans claim descent from the tribes of Ephraim and Manasseh, but the "Jews" of the period said they were half Jews descended from the Jews who remained in Palestine when most Jews were taken into captivity in Babylonia, and the "foreigners" settled on the land by the Assyrians.
https://en.wikipedia.org/wiki/Samaritans

You might find this blogpost by Razib Khan interesting.
http://blogs.discovermagazine.com/gnxp/2011/01/the-assyrians-and-jews-3000-years-of-common-history/#.V5IX_rgrLNM

As to the Druze, I don't think anyone really understands their ethnogensis. They speak Arabic, their religion grew out of Ismailism, but a lot of Muslims don't consider them Muslim. Was there input into their genome from Iran? We don't know. They incorporated a lot of Plato's ideas, and they could be considered Gnostics on one level, but does that mean they absorbed "Greek" ancestry? I doubt it, but who knows. Or, were they perhaps just relatively isolated highlanders whose adoption of this religion and subsequent endogamy meant that they were not as affected by yet another flow north from Arabia? Again, I don't know, and I don't think anyone else does either.

I'm content to wait for some more clarity from ancient DNA, but then I don't have any "theory" or "agenda" to push.

davef
22-07-16, 16:59
Thanks angela! That makes perfect sense, and that's pretty much in line with what popped in my mind when razib said that if they were more like Druze who are closer to eiropeans than most other levantines, then less european would've gotten them where they are. That's easy.

And regarding another comment, someone mentioned that 297k isn't enough for ibd, but I don't quite know why he's complaining about the ibd results. They seem pretty consistent with other papers and make historical sense.


I'm not agenda driven either. What I like to do is put ideas on the table and ask educated people of their opinions about those ideas. I wouldn't come to this forum if I was agenda driven because agendas are frowned upon, and I would get nowhere because (thankfully) someone like you would intervene and point out the holes.

Angela
22-07-16, 18:25
The IBD results don't make sense because there is not enough IBD sharing with any Europeans to pull the Ashkenazim away from even the Druze, much less Palestinians.

It's not precisely a function of the Druze being more "European"; it's more a question of the Druze being more "West Eurasian" than the modern Palestinians. The Druze have very little "European", per se.

I don't know if it was you, but I think someone also said that the Early Farmers plot in the Middle East. Actually, they don't at all. You can see it with this plot from Lazaridis, where the EN, who only picked up about 7% new gene flow after leaving the Near East, are not near the modern Near Easterners at all.

Also, in terms of the Druze, they don't plot anywhere near those farmers either. The Druze are not a remnant population of Anatolian farmers. The closest we have to that is the Sardinians.
http://1.bp.blogspot.com/-QJs5tV0H3t4/VIwY7BlNxyI/AAAAAAAAByQ/LakjgsBYRNc/s1600/2dkweaw.jpg

The Druze have also been pulled toward Africans as well as towards ANE.

davef
22-07-16, 19:08
Wait, do you even need ibd to pull away? I thought that ashkenazi pull away in admixture tests which don't account for ibd and I understand those tests can't be taken literally and don't say enough.

I guess what you meant by that statement is that in order to plot closer to europeans, one must have genetic input from an actual european population which would result in ibd sharing with that population.... . Don't worry, that's not news to me :)!!

I bet ibd with certain ancient europeans and levantines (especially levantines) would be much higher. Willing to bet money on that. I'm not hand picking modern ones. Why can't it be? It would be crazy to score that much south european (35 percent) and middle eastern (about half) and not ibd with any european or middle eastern group that existed back then.
Why would it not be crazy? That question was not rhetorical.

Ok yeah general west Eurasian that can be found from British to Saudis replacing ssa would definitely move someone more towards certain purer Eurasians.

davef
22-07-16, 19:36
I see you changed your post. I don't think I said that, but I did once suggest that parts of the Middle East used to be more european or Anatolian farmer related even after most of the Anatolian farmers left, but with Bronze Age levantines we know how that's wrong,
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.

oreo_cookie
22-07-16, 23:24
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.


This right here is why people assume that Ashkenazim have Italian DNA. Because Sicilians and Ashkenazim on PCA plots, are both roughly halfway between North Italians and modern day Levantines, people say "well, Ashkenazim are Levantine on the male side, North Italian on the female side, and thus plot like Sicilians when you mix it all up." But Sicilians have very low IBD sharing with the Levant, which implies that West Asian input into Sicily occurred in the Bronze Age rather than from Phoenicians or anything more recent, and that the Sikels, Sicanians, and Elymians at the time of contact with Phoenicians had already been genetically shifted toward West Asia.

At this point, Ashkenazim would not have existed... they'd still be Israelites. My guess is that ancient Israelites were probably closer to Druze than to Lebanese Arabs or Palestinians, and thus we should look at Druze or Cypriots as a good proxy, which means that you'd need closer to 1/3 South European admixture, not 1/2, to explain European Jews' plotting today. They only land in Sicily because Sicilians have enough West Asian affinity that they drift away from the core European cluster, it's not due to any directly shared ancestry. The same would be true of Cretans, who also are very close to Ashkenazim autosomally.

IBD sharing, above all, reflects how recent the exchange took place. Sicilians DO have high IBD sharing with Maghrebi people, implying that the North African input into the population is more recent. I am unclear if Ashkenazim have the same.

Not that this is scientific, but I have seen a few Druze results on GEDmatch and compared to Lebanese Arabs, they shift toward Iberia, Sardinia, etc. and their overall closest population is Cyprus.

davef
23-07-16, 14:18
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.

oreo_cookie
23-07-16, 16:38
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.

Angela
23-07-16, 18:02
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.

Point number 1: This is not a thread on Italian DNA, although I'm sure you would prefer that it were...

Point number 2: Even if it were, here on this Board we don't give much credence to pronouncements for which proof has not been offered.

Point number 3: Proof consists of academic papers, not "personal" admixture calculator results of unknown people, whose ancestry and results are impossible to verify, and which even if verifiable do not come from a random statistical sample.

Now, this thead is about Xue et al. Feel free to post about it if you have something new to add. We really don't need to hear the same point made over and over again, especially on a summer Saturday some of us might actually want to go out and enjoy.

oreo_cookie
23-07-16, 18:15
davef brought up Sicily, not me, and he should be informed that Cypriots are not genetically typical Southern European, they are significantly Levantine themselves so it would never make sense to use them as a reference sample for "European" DNA in Jews. Anyway, I do not have anything to add in here other than what I said, so I won't post in this thread again.

davef
23-07-16, 21:23
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.

oreo_cookie
23-07-16, 21:36
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.

If I find it I'll send it -- if you have other questions message me. I don't want to derail the thread any more than I have, my apologies to other users here.

Hauteville
24-07-16, 09:38
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.
Yes some islander Greeks have some Slavic Y-Chromosome at the same time Sicily is one of the most germanized regions by Y-Chromosome of Italy that make equal all.
Maps by the same author.
https://s32.postimg.org/fdh1qa251/13709823_690252044462447_8329495196490145252_n.jpg (https://postimg.org/image/jzd5ymno1/)


https://s32.postimg.org/txy4l3x3p/13770535_690365121117806_5102015285444749814_n.jpg (https://postimg.org/image/b5m9hj0pd/)


Sicilians DO have high IBD sharing with Maghrebi people, implying that the North African input into the population is more recent.
On the same study also Calabrians and Lucanians have similar amount of IBD sharing with North Africans and those two regions never had Muslims occupations, and IBD is reciprocal. Which can means that there is a significant Italian input on Maghrebi region since Roman times or in the times of Norman conquest when most of the muslims (in large part were local converts) settled to North Africa.


Phoenicians or anything more recent, and that the Sikels, Sicanians, and Elymians at the time of contact with Phoenicians had already been genetically shifted toward West Asia.
The estimating TMRCA of J1 and J2 in Southern Italy and Sicily is indeed in the early bronze age said Stefania Sarno. If there is some Punic DNA you can find it around Marsala or maybe Palermo but the rest of Sicily hadn't Phoenician settlements unlike North Africa and Iberian peninsula for example, but again we don't really know who were the Phoenicians and what is their DNA, a Phoenician man from Carthage had European mtDNA for example.

davef
25-07-16, 04:30
Italian genetics are awesome, but we need to stick to Ashkenazim genetics and stay on topic.

davef
05-08-16, 01:56
This was interesting:
http://www.ashg.org/2013meeting/abstracts/fulltext/f130123362.htm

My memory of the exact percentages is fuzzy, but what's striking about it is that the percentages of each component in this study are close to those in the study conducted by Xue.

Middle Eastern: .38
Italian: .305
French: .11
Russian: .04
Caucasian: .165

I'll just add up Caucasian and meddle eastern to make it a "Levantine" category akin to the Middle East category in the Xue study making it roughly .54 in comparison to Xue's .50 value. I'll admit its a bit of a stretch to do this.

Also the 16 percent Northern European found by Xue (west plus east Europe) is similar to the 15 percent Northern European found in this study (french plus Russian). I'm not quite sure whether they used french from the north or south as the former are north euros similar to the British and the latter are more like the Spaniards.

The .305 italian is also somewhat close to the .35 italian found by Xue. I'm again uncertain of the region from where the italian samples were taken from. Like france, italy is far from being a homogenous country, genetically speaking.

The researchers used a larger proportion of the genomes (almost 700k SNPs) which by my limited knowledge should give a better estimate.

The fact that a separate study produced similar values is somewhat intriguing. I'll have to look into the regions from where the italians and the french were taken.

davef
08-08-16, 18:20
According to this image, Ashkenazim are pretty close to Sardinians, Balkars (I looked them up just now, they're a Caucasian group) and Cypriots! And far from everyone else it seems. They only seem to cluster with other euros in how related they are to ancient groups. I have no idea where this was originally pulled from, but i got it from the Razib thread
Angela posted.

Interesting how close they are to another endogamous population with old middle eastern roots.does it explain why Ashkenazim score more neolithic european farmer than levantines?

Here's the link. Chances are I may have no idea what I'm talking about, so beware readers (unless you're someone like Angela or LeBrok who knows a lot about this topic).

http://m.imgur.com/xBV90aP

Angela
08-08-16, 18:45
According to this image, Ashkenazim are pretty close to Sardinians, Balkars (I looked them up just now, they're a Caucasian group) and Cypriots! And far from everyone else it seems. They only seem to cluster with other euros in how related they are to ancient groups. I have no idea where this was originally pulled from, but i got it from the Razib thread
Angela posted.

Interesting how close they are to another endogamous population with old middle eastern roots.does it explain why Ashkenazim score more neolithic european farmer than levantines?

Here's the link. Chances are I may have no idea what I'm talking about, so beware readers (unless you're someone like Angela or LeBrok who knows a lot about this topic).

http://m.imgur.com/xBV90aP

Davef, if my memory serves, you tend to put an extraordinary amount of emphasis on certain results, like PCAs, or Admixture calculator scores from gedmatch. You have to look at the results from all the tools to try to figure out some of these relationships.

In terms of PCA, I take heed of them too, but they're only one tool, and by far not the best, as they sometimes account for only rather low amounts of total genetic variation, maybe 25% in some cases.

As for these Admixture gedmatch scores floating around, you should be aware that we have no way of independently verifying whether result X, supposedly from person Y from some specific city in Sicily, or Calabria, for example, are even Italian, much less from that particular province and city city. The same goes for any results. That's why I really only take account of academic admixture results.

As for this particular chart, it's based on fst, and measures total genetic distance. It doesn't tell you what ancient groups at what times admixed to form any of those populations, if that's your interest.

At the same time, Ashkenazim plot close to Cypriots on most PCAs, so that's more confirmation of a similarity. Once again, though, we can't tell the population genetics history of the Ashkenazim, or the Cypriots, for that matter, from those results.

davef
08-08-16, 20:13
Thanks for the response!

I did put a lot of stock into those gedmatch programs when I shouldn't have because they don't pinpoint where those similarities came from since different populations shared some of the same genes.

I know that fst chart doesn't give the full story but I'm struck by how close Ashkenazim are to Sardinians in that fst chart which might explain much of their affinity with Europe and this might just minimize the amount of extra european admixture. But yet again Sardinians aren't anything like Bronze Age Canaanites at all.

And I question the reliability of the IBD test used in Xue and Carmi. 50 percent Levantine and the IBD amounts to nothing? Unless I'm unaware as to how the program was able to arrive at the 50 percent Levantine figure. That's half the genome. certainly one would expect IBD with the levant beyond someone who is 1/128 th palestinian 127/128 th Finnish (I pulled those values out of my nose).

I know using modern populations is iffy but with these same modern populations a gigantic 50 percent of the genome is related to them according to the admixture run.

Basic question.,..what triggered the admixture calculator to say "50 percent Levantine?" To me 50 percent Levantine by this calculator means you share half your genes with Levantines (not to necessarily say you have a Levantine parent from modern Syria or Lebanon etc). Feel free to point out the flaws in what I said btw.

John Doe
08-08-16, 20:30
At the same time, Ashkenazim plot close to Cypriots on most PCAs, so that's more confirmation of a similarity. Once again, though, we can't tell the population genetics history of the Ashkenazim, or the Cypriots, for that matter, from those results.

Exactly, for example Ashkenazim plot closer to Maltese and Sicilians on most PCAs, however that doesn't mean one derived from the other or even that they derive from the same founder populations.

davef
09-08-16, 21:33
True, and based on the fst chart Ashkenazim are more like Sardinians and Cypriots. Difference could be just due to drift and the supposed intermarriage with northerners. I don't know where the chart came from so I can't do much more than guess.

davef
11-08-16, 20:03
According to another forum, the neolithic k13 results for one of the Bronze Age levantines are:
Natufian-47
Anatolia Neolithic -25
Iran Neolithic-21
EHG-4
SHG-WHG-.5

Approximations since I don't remember them off the top of my head but only should be off by less than one percent which means nothing here.

As shaky as it is to rely on calculators, this is still rather interesting. It's a long way to an Ashkenazim from here, genetically speaking.

John Doe
11-08-16, 20:33
True, and based on the fst chart Ashkenazim are more like Sardinians and Cypriots. Difference could be just due to drift and the supposed intermarriage with northerners. I don't know where the chart came from so I can't do much more than guess.
Assuming the Gedmatch calculators are to be taken seriously, the difference of admixture between Cypriots and Sicilians/Maltese/AJs seems IMHO a little too big to be the result only of genetic drift.

P.S And that's of course assuming Cypriots represent a good proxy population to pre Exilic Jews, which is mere speculation. Who knows? Maybe, just maybe, as a result of Philistine settlement and what not pre exilic Jews were already Cretan/Aegean like? But again that's just speculation and one can entertain these blinds assumptions only so much...

davef
11-08-16, 21:01
Not to worry, I'm not to say that the calculators know all :).

And the fst chart on the left in that image (distance between eac other) Ashkenazim, cypriots, Balkars, and Sardinians seem to cluster with each other (cypriots more so with jews) and very very far from other europeans, including italians.

You're right, it was crazy for me to suggest drift with a little northern admixture contributed most if not all to the distance.

John Doe
11-08-16, 21:14
You're right, it was crazy for me to suggest drift with a little northern admixture contributed most if not all to the distance.
Save the sarcasm, you typed "Difference could be just due to drift and the supposed intermarriage with northerners." so I assumed that when you say "supposed intermarriage", you meant that this was unlikely and that it can be due to drift only. But you know what? It might just be only to drift, because WE DON'T KNOW! That's the point! All this speculation in the dark produces nothing, we have to wait for more ancient DNA from the Near East and the Eastern Mediterranean.

davef
11-08-16, 21:33
I apologize for sounding sarcastic; not to worry, I wasn't trying to be.

I do admit, we are hugging the walls with these calculators and nothing beats ancient genomes or being empirical.

Zionas
31-10-16, 03:28
I'm quite sure that the origins of Ashnekazi and Sephardic Jews dates back further than the so-called Khazar theory. Speaking of Ashnekazi DNA there's someone on WeGene who has .2% Ashknekazi and a woman on the same site from Gansu who has less than .1%. Guy had .2% European and woman had .7%.

Joey D
29-11-16, 11:40
This right here is why people assume that Ashkenazim have Italian DNA. Because Sicilians and Ashkenazim on PCA plots, are both roughly halfway between North Italians and modern day Levantines, people say "well, Ashkenazim are Levantine on the male side, North Italian on the female side, and thus plot like Sicilians when you mix it all up." But Sicilians have very low IBD sharing with the Levant, which implies that West Asian input into Sicily occurred in the Bronze Age rather than from Phoenicians or anything more recent, and that the Sikels, Sicanians, and Elymians at the time of contact with Phoenicians had already been genetically shifted toward West Asia.

At this point, Ashkenazim would not have existed... they'd still be Israelites. My guess is that ancient Israelites were probably closer to Druze than to Lebanese Arabs or Palestinians, and thus we should look at Druze or Cypriots as a good proxy, which means that you'd need closer to 1/3 South European admixture, not 1/2, to explain European Jews' plotting today. They only land in Sicily because Sicilians have enough West Asian affinity that they drift away from the core European cluster, it's not due to any directly shared ancestry. The same would be true of Cretans, who also are very close to Ashkenazim autosomally.

IBD sharing, above all, reflects how recent the exchange took place. Sicilians DO have high IBD sharing with Maghrebi people, implying that the North African input into the population is more recent. I am unclear if Ashkenazim have the same.

Not that this is scientific, but I have seen a few Druze results on GEDmatch and compared to Lebanese Arabs, they shift toward Iberia, Sardinia, etc. and their overall closest population is Cyprus.

I found this post really interesting. I get a relatively high Caucasus percentage in all the various DNA tests, such that in the various four population tests, I'm consistently getting placed in Armenia/Georgia; Greece; South Italy and Nth Italy or Tuscany.

It's been making me wonder: what is this Caucasus reading which consistently comes up? The only thing which might make sense to me is something pre-Greek, which means the Sicels (I'm East Sicilian going back four generations).

As it happens, Ashkenazi Jew pops up for me a fair bit.