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Humanist
12-26-2013, 11:08 PM
In terms of autosomal DNA, Iranian Jews are most similar to Eastern Mizrahim Jews, Iraqi Mandaeans and Assyrians. However, based on the physical appearance of Iranian Jews I am acquainted with, and examples from television, a significant number of Iranian Jews, in my opinion, could pass for Iranians of native Indo-Iranian speaking stock (albeit of central/southern origin). Perhaps DMXX can provide some insight into this phenomenon.

Two examples, below. Of course, we do not know their precise autosomal DNA, but if what they say about their ancestry is accurate, then I imagine they would not differ significantly from the Behar et al. Iranian Jews.

The actor who portrays the Iranian Deputy Intelligence Chief, Majid Javadi on Homeland:

http://www.haaretz.com/polopoly_fs/1.560242.1385465606!/image/3323172273.jpg_gen/derivatives/landscape_640/3323172273.jpg


One of the cast members of Shahs of Sunset, Mike Shouhed:

http://cdn3-www.realitytea.com/assets/uploads/2012/12/shahs-of-sunset-mike-shouhed.jpg

ZephyrousMandaru
12-27-2013, 01:11 AM
I agree, not only are Iranian Jews swarthy and look almost indistinguishable from Persians. Iraqi Mandaeans in particular are very swarthy. A good number of them are quite dark. On average, Iraqi Mandaeans evince phenotypes that look like a mixture of Arabian and Iranian.

Some examples below.

https://scontent-b.xx.fbcdn.net/hphotos-frc1/579338_734886023206611_736640232_n.jpg

https://scontent-a.xx.fbcdn.net/hphotos-frc3/970268_10200492226453808_235513384_n.jpg

https://scontent-b.xx.fbcdn.net/hphotos-prn1/1521701_643084002404736_1296471425_n.jpg

AJL
12-27-2013, 02:45 AM
I am not sure but I suspect there is probably a subtle but real preference for people in diaspora populations to favour mating with those whose appearance is more similar to the host population.

ZephyrousMandaru
12-27-2013, 04:04 AM
I think it's important to note that intra-variation level phenotypic diversity can be attributed to alleles found in the coding region, comprising about 1-10% of the genome. So in effect, what you're seeing in someone's appearance is an exhibition of a specific subset of alleles. So even if your principal component is West Asian, while your minority ancestral components are Mediterranean, Gedrosia or Southwest Asian. If by chance those minority alleles are randomly selected and codified into your phenotype.

Then those portions of your ancestry will dominate your phenotype, regardless of what your principal component is. I have a friend who is mostly Northern European with some Southern European ancestry, and yet looks very Southern European despite her high scores in Northern and Western European components. That's why I don't disregard minority components, even as little as 10% can have an impact.

A prime example of this would be myself and Humanist. We're both Assyrians yet, in terms of appearance Humanist and I couldn't look anymore different. He is a Brachycephalic, I am Dolichocephalic or Mesocephalic. He has green eyes, I have brown eyes. He has light brown hair, my hair is as black as coal.

He looks Southern European, I look like an Arab.

If you saw us both, and knew absolutely nothing about either of us. You would think we were unrelated, but you'd be wrong. Not only are we both Assyrians. But Humanist and I are 2nd to 4th cousins.

Sein
12-27-2013, 04:15 AM
On a related note, some genetically similar populations can differ consistently on a phenotypic level. In South-Central Asia, one only has to note the differences between Punjabis and Pashtuns. Both of these populations are pretty close in terms of autosomal ancestry. In fact, I think Punjabi people are the closest population to us (genetically), besides Tajiks. But even people without actual experience in the region can differentiate "us". An example of the phenotypic differences:

http://centralasiaonline.com/shared/images/2011/04/22/paksurrender.jpg

A closer view of the Punjabi individuals
1108

Closer views of the Pashtun individuals
1109

1110

My guess is that genetically diverged populations looking rather similar, and genetically similar populations looking somewhat diverged, must have something to do with "epigenetics", and environmental conditions?

Also, I think Zephyrous makes a great point here.

DMXX
12-27-2013, 07:33 AM
My immediate thoughts are in line with what Zephyrous has succinctly described, but perhaps with a little twist.

The inference concerning the physical manifestation of a population's genotypes being non-uniform is a rational one that is readily supported by all manner of anecdotes. For instance, I recall one user on another forum who self-identified as an African-American and had a phenotype consistent with this, only to discover that the majority (>75%) of their ancestry was West Eurasian rather than Sub-Saharan African. Extending this to multiple individuals gives us similar mismatches; how many of us who belong to a single ethnicity or regional group can observe great variation in features within our families, when the overall genetic composition likely varies little across the board?

Regarding the case of the Iranian Jews, I entertain the idea that some limited mixture with the local non-Jewish (Gentile) population of Iran had taken place since the time of the deportations in ancient times. We know that, although Ashkenazim folk in East Europe have largely retained their Near-Eastern genetic heritage, there is some local European admixture. It is therefore reasonable to postulate something similar happened with the Jewish population that eventually found Iran to be their homeland.

As described above (including Zephyrous' post), I think it's quite likely the typically Iranian features of some Iranian Jews is due to chance inheritance and expression of said features due to that Gentile admixture that happened over two millennia. There certainly is overlap in features across the region to begin with, but certain phenotypes are definitely more localised in certain places. I wouldn't mistake the first gentleman Humanist posted for anything other than an Iranian, or perhaps an Afghan.

On that note, it would actually be interesting to determine whether or not that idea (Iranian Jews have some level of non-Jewish Iranian ancestry) has any merit through the Oracle program. This can be done by using the Iranian Jewish reference as the target population and any Iranian reference as a fixed source. If it works, I'd expect other Jewish populations (Samaritans?) to come out as the majority donor with Iranian a minority. That would be quite something to see; might try it later if I have time!

ZephyrousMandaru
12-27-2013, 08:09 AM
Just as a quick side note. One should also consider, that the percentages of each component is represented as a total estimate for that respective component. So just because you're 50% of one component as an average of the total components, doesn't necessarily mean that each of your autosomal segments will be the majority of that component. For example, here are my By Chromosome results for the Globe13 calculator.

The minor components are highlighted in bold.


Chromosome 1

0.00% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
22.73% Southwest_Asian
0.00% East_Asian
30.39% Mediterranean
0.03% Australasian
0.31% Arctic
46.51% West_Asian
0.00% North_European
0.03% South_Asian
0.00% East_African

Chromosome 2

0.01% Siberian
0.00% Amerindian
0.00% West_African
0.78% Palaeo_African
20.18% Southwest_Asian
1.06% East_Asian
24.06% Mediterranean
0.23% Australasian
0.00% Arctic
50.27% West_Asian
0.32% North_European
3.07% South_Asian
0.00% East_African

Chromosome 3

0.62% Siberian
0.00% Amerindian
0.00% West_African
2.30% Palaeo_African
25.10% Southwest_Asian
0.00% East_Asian
26.79% Mediterranean
0.00% Australasian
0.00% Arctic
42.26% West_Asian
0.57% North_European
1.30% South_Asian
1.06% East_African

Chromosome 4

0.00% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
20.41% Southwest_Asian
0.27% East_Asian
29.23% Mediterranean
0.00% Australasian
0.00% Arctic
42.43% West_Asian
0.02% North_European
7.65% South_Asian
0.00% East_African

Chromosome 5

0.00% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
26.68% Southwest_Asian
0.00% East_Asian
31.97% Mediterranean
0.00% Australasian
1.15% Arctic
39.39% West_Asian
0.81% North_European
0.00% South_Asian
0.00% East_African

Chromosome 6

0.00% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
20.15% Southwest_Asian
0.00% East_Asian
24.54% Mediterranean
0.86% Australasian
0.00% Arctic
53.80% West_Asian
0.00% North_European
0.00% South_Asian
0.64% East_African

Chromosome 7

0.53% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
22.12% Southwest_Asian
0.00% East_Asian
21.12% Mediterranean
0.00% Australasian
2.03% Arctic
38.43% West_Asian
15.75% North_European
0.02% South_Asian
0.00% East_African

Chromosome 8

0.00% Siberian
0.00% Amerindian
0.01% West_African
0.30% Palaeo_African
31.41% Southwest_Asian
2.74% East_Asian
14.92% Mediterranean
0.00% Australasian
0.46% Arctic
50.15% West_Asian
0.00% North_European
0.00% South_Asian
0.00% East_African

Chromosome 9

2.21% Siberian
0.33% Amerindian
0.00% West_African
0.00% Palaeo_African
18.89% Southwest_Asian
0.00% East_Asian
28.74% Mediterranean
1.23% Australasian
0.00% Arctic
43.66% West_Asian
4.94% North_European
0.00% South_Asian
0.00% East_African

Chromosome 10

0.00% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
28.37% Southwest_Asian
0.00% East_Asian
32.90% Mediterranean
0.00% Australasian
0.00% Arctic
38.72% West_Asian
0.01% North_European
0.00% South_Asian
0.00% East_African

Chromosome 11


0.00% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
21.65% Southwest_Asian
0.00% East_Asian
38.76% Mediterranean
2.78% Australasian
0.97% Arctic
35.83% West_Asian
0.00% North_European
0.00% South_Asian
0.00% East_African

Chromosome 12


0.67% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
28.48% Southwest_Asian
0.00% East_Asian
31.13% Mediterranean
0.00% Australasian
0.00% Arctic
39.71% West_Asian
0.01% North_European
0.00% South_Asian
0.00% East_African

Chromosome 13

0.00% Siberian
0.00% Amerindian
0.00% West_African
1.91% Palaeo_African
17.53% Southwest_Asian
0.00% East_Asian
35.78% Mediterranean
3.16% Australasian
0.64% Arctic
40.52% West_Asian
0.00% North_European
0.00% South_Asian
0.46% East_African

Chromosome 14

0.00% Siberian
0.77% Amerindian
0.00% West_African
0.00% Palaeo_African
20.26% Southwest_Asian
0.00% East_Asian
20.88% Mediterranean
2.34% Australasian
0.00% Arctic
55.75% West_Asian
0.00% North_European
0.00% South_Asian
0.00% East_African

Chromosome 15

3.06% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
26.87% Southwest_Asian
0.00% East_Asian
24.10% Mediterranean
0.00% Australasian
0.00% Arctic
45.96% West_Asian
0.00% North_European
0.00% South_Asian
0.00% East_African

Chromosome 16

0.00% Siberian
0.00% Amerindian
0.00% West_African
1.37% Palaeo_African
21.92% Southwest_Asian
0.63% East_Asian
13.38% Mediterranean
2.87% Australasian
1.92% Arctic
44.52% West_Asian
10.90% North_European
2.48% South_Asian
0.00% East_African

Chromosome 17


0.83% Siberian
0.00% Amerindian
0.00% West_African
1.28% Palaeo_African
21.28% Southwest_Asian
0.00% East_Asian
33.71% Mediterranean
0.00% Australasian
1.80% Arctic
41.11% West_Asian
0.00% North_European
0.00% South_Asian
0.00% East_African

Chromosome 18

0.00% Siberian
0.00% Amerindian
0.00% West_African
0.01% Palaeo_African
23.58% Southwest_Asian
1.09% East_Asian
29.84% Mediterranean
0.00% Australasian
0.20% Arctic
41.40% West_Asian
0.01% North_European
3.86% South_Asian
0.00% East_African

Chromosome 19


0.00% Siberian
4.53% Amerindian
0.01% West_African
1.17% Palaeo_African
20.00% Southwest_Asian
1.13% East_Asian
15.84% Mediterranean
0.00% Australasian
0.00% Arctic
56.76% West_Asian
0.00% North_European
0.00% South_Asian
0.57% East_African

Chromosome 20

0.00% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
30.17% Southwest_Asian
0.00% East_Asian
20.13% Mediterranean
0.00% Australasian
0.00% Arctic
49.69% West_Asian
0.01% North_European
0.00% South_Asian
0.00% East_African

Chromosome 21


0.00% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
43.13% Southwest_Asian
0.00% East_Asian
11.56% Mediterranean
0.00% Australasian
0.00% Arctic
45.30% West_Asian
0.01% North_European
0.00% South_Asian
0.00% East_African

Chromosome 22

0.00% Siberian
0.00% Amerindian
0.00% West_African
0.00% Palaeo_African
29.94% Southwest_Asian
0.00% East_Asian
13.51% Mediterranean
5.84% Australasian
0.01% Arctic
44.61% West_Asian
6.09% North_European
0.00% South_Asian
0.00% East_African

As you can see, on some of my chromosomes, the frequency of the minor components is greater than the frequency of my principal component (West Asian).

ZephyrousMandaru
12-27-2013, 08:12 AM
On that note, it would actually be interesting to determine whether or not that idea (Iranian Jews have some level of non-Jewish Iranian ancestry) has any merit through the Oracle program. This can be done by using the Iranian Jewish reference as the target population and any Iranian reference as a fixed source. If it works, I'd expect other Jewish populations (Samaritans?) to come out as the majority donor with Iranian a minority. That would be quite something to see; might try it later if I have time!

That would be an extremely tedious undertaking, there's hundreds of populations you'd have to remove from the Oracle.

Palisto
12-27-2013, 08:33 AM
My immediate thoughts are in line with what Zephyrous has succinctly described, but perhaps with a little twist.

The inference concerning the physical manifestation of a population's genotypes being non-uniform is a rational one that is readily supported by all manner of anecdotes. For instance, I recall one user on another forum who self-identified as an African-American and had a phenotype consistent with this, only to discover that the majority (>75%) of their ancestry was West Eurasian rather than Sub-Saharan African. Extending this to multiple individuals gives us similar mismatches; how many of us who belong to a single ethnicity or regional group can observe great variation in features within our families, when the overall genetic composition likely varies little across the board?

Regarding the case of the Iranian Jews, I entertain the idea that some limited mixture with the local non-Jewish (Gentile) population of Iran had taken place since the time of the deportations in ancient times. We know that, although Ashkenazim folk in East Europe have largely retained their Near-Eastern genetic heritage, there is some local European admixture. It is therefore reasonable to postulate something similar happened with the Jewish population that eventually found Iran to be their homeland.

As described above (including Zephyrous' post), I think it's quite likely the typically Iranian features of some Iranian Jews is due to chance inheritance and expression of said features due to that Gentile admixture that happened over two millennia. There certainly is overlap in features across the region to begin with, but certain phenotypes are definitely more localised in certain places. I wouldn't mistake the first gentleman Humanist posted for anything other than an Iranian, or perhaps an Afghan.

On that note, it would actually be interesting to determine whether or not that idea (Iranian Jews have some level of non-Jewish Iranian ancestry) has any merit through the Oracle program. This can be done by using the Iranian Jewish reference as the target population and any Iranian reference as a fixed source. If it works, I'd expect other Jewish populations (Samaritans?) to come out as the majority donor with Iranian a minority. That would be quite something to see; might try it later if I have time!

I am an Iraqi Kurd and most of the distant cousins I found at 23andme are from Iran without any clear trend in terms of religion. These relatives are Sunnis, Shiites, Christians, and Jews from Iran. Therefore I think the reason why Iranian Jews look a little bit like non-Jewish Iranians is because they are admixed with non-Jewish Iranians and thus related to non-Jewish Iranians. This admixture must have occurred not only in ancient times but also quiet recently.

From the Dodecad Globe13 run (https://docs.google.com/spreadsheet/ccc?key=0ArAJcY18g2GadF9CLUJnTUdSbkVJaDR2UkRtUE9ka UE#gid=2):

South Asian component in %:
South_Asian Population
0 Georgians
0 Georgian_D
0 Samaritan_All
0 Abhkasians_Y
0 Balkars_Y
0 Armenians
0 Sicilian_D
0 Ashkenazi_D
0 Turkish_Cypriot_D
0 S_Italian_Sicilian_D
0 Ashkenazy_Jews
0 Cypriots
0 Druze
0 Turkish_Aydin_Ho
0 North_Ossetians_Y
0.1 Sephardic_Jews
0.1 Adygei
0.2 Georgia_Jews
0.2 Armenian_D
0.4 Morocco_Jews
0.6 Turkish_Istanbul_Ho
0.7 Saudis
0.7 Chechens_Y
0.7 Turkish_D
0.9 Assyrian_D
0.9 Armenians_15_Y
1 Lebanese
1.1 Iraq_Jews
1.1 Turkish_Kayseri_Ho
1.1 Kumyks_Y
1.4 Azerbaijan_Jews
1.5 Turks
1.6 Syrians
1.6 Lezgins
1.7 Iranian_Jews
2.6 Uzbekistan_Jews
4.2 Kurds_Y
4.2 Kurd_D
6.3 Iranian_D
7.6 Iranians


That would be an extremely tedious undertaking, there's hundreds of populations you'd have to remove from the Oracle.
I just did it:
Using Dodecad K12b data of Iranians and Samartians to describe Iranian Jews (Oracle):
52.7% Samaritians + 47.3% Iranians = 7.5363 not a good match

Humanist
12-27-2013, 09:54 AM
I am an Iraqi Kurd and most of the distant cousins I found at 23andme are from Iran without any clear trend in terms of religion. These relatives are Sunnis, Shiites, Christians, and Jews from Iran. Therefore I think the reason why Iranian Jews look a little bit like non-Jewish Iranians is because they are admixed with non-Jewish Iranians and thus related to non-Jewish Iranians. This admixture must have occurred not only in ancient times but also quiet recently.

From the Dodecad Globe13 run (https://docs.google.com/spreadsheet/ccc?key=0ArAJcY18g2GadF9CLUJnTUdSbkVJaDR2UkRtUE9ka UE#gid=2):

South Asian component in %:
South_Asian Population
0 Georgians
0 Georgian_D
0 Samaritan_All
0 Abhkasians_Y
0 Balkars_Y
0 Armenians
0 Sicilian_D
0 Ashkenazi_D
0 Turkish_Cypriot_D
0 S_Italian_Sicilian_D
0 Ashkenazy_Jews
0 Cypriots
0 Druze
0 Turkish_Aydin_Ho
0 North_Ossetians_Y
0.1 Sephardic_Jews
0.1 Adygei
0.2 Georgia_Jews
0.2 Armenian_D
0.4 Morocco_Jews
0.6 Turkish_Istanbul_Ho
0.7 Saudis
0.7 Chechens_Y
0.7 Turkish_D
0.9 Assyrian_D
0.9 Armenians_15_Y
1 Lebanese
1.1 Iraq_Jews
1.1 Turkish_Kayseri_Ho
1.1 Kumyks_Y
1.4 Azerbaijan_Jews
1.5 Turks
1.6 Syrians
1.6 Lezgins
1.7 Iranian_Jews
2.6 Uzbekistan_Jews
4.2 Kurds_Y
4.2 Kurd_D
6.3 Iranian_D
7.6 Iranians


But, if it was Iranian/Kurdish admixture entering the Iranian Jewish gene pool quite recently, would we not expect at least some "North European" in Globe 13? Iraqi Jews, Iranian Jews, and Azerbaijan Jews register 0.0 "North European" in Globe 13.

"North European"


5.8 -- Kurds_Y
5.3 -- Iranian_D
5.3 -- Makrani
5.2 -- Turkish_Cypriot_D
5.1 -- Cypriots
4.9 -- Lebanese
4.7 -- Kurd_D
4.5 -- Iranians
4.1 -- Abhkasians_Y
3.5 -- Uzbekistan_Jews
3.2 -- Cochin_Jews
2.9 -- Georgian_D
2.7 -- Bedouin
2.6 -- Syrians
2.3 -- Moroccans
2.1 -- Saudis
1.8 -- Georgia_Jews
1.5 -- Armenians
1.1 -- Armenian_D
1.1 -- Georgians
1 -- Jordanians
1 -- Armenians_15_Y
0.9 -- Bnei_Menashe_Jews
0.8 -- Yemenese
0.7 -- Palestinian
0.6 -- Druze
0.1 -- ARICULTIVATOR_Pa
0 -- Samaritan_All
0 -- Ethiopians
0 -- Ethiopian_Jews
0 -- Egyptians
0 -- Iraq_Jews
0 -- Iranian_Jews
0 -- Assyrian_D
0 -- Azerbaijan_Jews

Palisto
12-27-2013, 10:50 AM
But, if it was Iranian/Kurdish admixture entering the Iranian Jewish gene pool quite recently, would we not expect at least some "North European" in Globe 13? Iraqi Jews, Iranian Jews, and Azerbaijan Jews register 0.0 "North European" in Globe 13.

"North European"


5.8 -- Kurds_Y
5.3 -- Iranian_D
5.3 -- Makrani
5.2 -- Turkish_Cypriot_D
5.1 -- Cypriots
4.9 -- Lebanese
4.7 -- Kurd_D
4.5 -- Iranians
4.1 -- Abhkasians_Y
3.5 -- Uzbekistan_Jews
3.2 -- Cochin_Jews
2.9 -- Georgian_D
2.7 -- Bedouin
2.6 -- Syrians
2.3 -- Moroccans
2.1 -- Saudis
1.8 -- Georgia_Jews
1.5 -- Armenians
1.1 -- Armenian_D
1.1 -- Georgians
1 -- Jordanians
1 -- Armenians_15_Y
0.9 -- Bnei_Menashe_Jews
0.8 -- Yemenese
0.7 -- Palestinian
0.6 -- Druze
0.1 -- ARICULTIVATOR_Pa
0 -- Samaritan_All
0 -- Ethiopians
0 -- Ethiopian_Jews
0 -- Egyptians
0 -- Iraq_Jews
0 -- Iranian_Jews
0 -- Assyrian_D
0 -- Azerbaijan_Jews

Good point.

ZephyrousMandaru
12-27-2013, 11:51 AM
If there was an introgression of alleles that originated from an Iranian population. It must have been an ancient one, perhaps the Elamites or Kassites? Whatever population it was, it must have occurred prior to any influx of the Indo-European populations that influenced Iran.

DMXX
12-27-2013, 05:36 PM
If there was an introgression of alleles that originated from an Iranian population. It must have been an ancient one, perhaps the Elamites or Kassites? Whatever population it was, it must have occurred prior to any influx of the Indo-European populations that influenced Iran.

The progression of thought that's developed in this thread is, I'm pleased to say, quite stimulating intellectually.

If the North European component is literally absent among Near-Eastern Jewish groups, the only possibility as you've stated was for a common genetic contribution from a native Iranian group into both modern Iranians and Iranian Jews that wasn't Indo-European speaking in origin pretty early on.

The problem with this scenario is accentuated by the result of the Oracle run - Modern Iranians just don't make a good donor population for Iranian Jews. That brings us to at least two possible explanations;

1) Modern Iranians have experienced a significant genetic shift away from the common genetic contributor with Iranian Jews since the latter arrived in Achaemanid Persia around 600 B.C. Could it be possible the Achaemanid Persians in fact had a minimal impact on Iran, whereas other Iranic-speakers such as the Parthians, Scythians and Medians did, resulting in a later elevation of North European among Iranians? We should also recall the East Eurasian contribution brought by Turkish tribes from Medieval times onwards.

2) There is in fact no direct genetic explanation for the apparent phenotype shift towards Iran in Iranian Jews, which brings AJL's earlier thought about phenotype selection within a group to a new homeland.

Humanist
12-27-2013, 06:14 PM
2) There is in fact no direct genetic explanation for the apparent phenotype shift towards Iran in Iranian Jews, which brings AJL's earlier thought about phenotype selection within a group to a new homeland.

It may be worthwhile to keep uniparental markers in mind as well. Although, in my opinion, this points to antiquity as a possible source, rather than more recent times.


Based on the coding region analysis, we extended the initial number of 49 putative lineages (Table S4) to 53 potentially founding lineages, because the coding region analysis suggested that four putative founding lineages (J1b'e/J1e, H4a1a, H30 and R0a1c) were each comprised of 2 daughter sub-lineages. For 52 of the 53 lineages, confidence intervals covered 2,000 years as a potential coalescence age, and are therefore concordant with the founder event occurring during the last 2,000 years. The only lineage for which the confidence interval did not cover 2,000 years is the Iranian Jewish U7a1. However, two additional lineages, L0a2c and T2f, gave a coalescence estimate larger than 4000 years, with their confidence intervals greatly exceeding 2,000 years. Thus, we can state that in general, while almost the entire set of founder lineages identified herein is consistent with the constraint of a coalescence age within the last 2,000 years, it is likely that some may have started to expand earlier. It should be recalled that the imposed 2,000 year constraint adds a degree of stringency–and relaxing this to values greater than 2,000 years would be expected to result in the inclusion of more lineages within the time from expansion.

Behar DM, Metspalu E, Kivisild T, Rosset S, Tzur S, et al. (2008) Counting the Founders: The Matrilineal Genetic Ancestry of the Jewish Diaspora. PLoS ONE 3(4): e2062. doi:10.1371/journal.pone.0002062


U7 Frequencies From Some Sources (U7 ≥ .5%)

31.3% Samaritan Shen et al. 2004
10.5% Brahui Quintana-Murci et al. 2004
9.8% IraniJw Behar et al. 2008
8.7% Sindhi Quintana-Murci et al. 2004
8.2% Iran Quintana-Murci et al. 2004, Metspalu et al. 2004
8.0% Assyr Public and Private Data
6.9% Kurds Comas et al. 2000
6.8% Burusho Quintana-Murci et al. 2004
5.2% AzeriJw Behar et al. 2008
4.8% MrshAB Al-Zahery et al. 2011 (Iraqi Marsh Arab)
4.3% Hazara Quintana-Murci et al. 2004
3.4% Bedouin Behar et al. 2008
3.0% Jordan Behar et al. 2010
3.0% Makrani Quintana-Murci et al. 2004
3.0% Uzbek Quintana-Murci et al. 2004
2.8% Iraqi Al-Zahery et al. 2011
2.6% Balochi Quintana-Murci et al. 2004
2.5% Tuscan Pala et al. 2009
2.2% IraqiJw Behar et al. 2008
2.1% Uygur Yao et al. 2004
2.1% Bulgaria Richards et al. 2000
1.6% Egypt Behar et al. 2010
1.6% Turkey Tambets et al. 2000
1.4% AshkJw Behar et al. 2006
1.2% LibyaJw Behar et al. 2008
1.2% UAE Alshamali et al. 2008
1.1% S.India Behar et al. 2010
1.1% Cyprus Behar et al. 2010
1.0% Georgia Quintana-Murci et al. 2004, Comas et al. 2000
0.9% Saudi Abu-Amero et al. 2007
0.9% Syria Behar et al. 2010
0.8% Yemen Kivisild et al. 2004
0.7% Armeni Richards et al. 2000
0.6% Romania Behar et al. 2010
0.5% Russia Malyarchuk et al. 2002
0.5% Adyghe Richards et al. 2000

AJL
12-27-2013, 07:40 PM
If the North European component is literally absent among Near-Eastern Jewish groups, the only possibility as you've stated was for a common genetic contribution from a native Iranian group into both modern Iranians and Iranian Jews that wasn't Indo-European speaking in origin pretty early on.

Perhaps Sumerians and/or Elamites could be potential candidates for a common non-IE contributor in historical times.

DMXX
12-27-2013, 07:48 PM
Perhaps Sumerians and/or Elamites could be potential candidates for a common non-IE contributor in historical times.

An important caveat just came to mind...

The acquired Iranian samples used in these programs are mixed but are largely from the top half of the country. We don't have autosomal data of Iranians from across the country, but the Behar et al. Iranian reference set is probably from the south/south-central parts.

As the Elamites particularly were only present in the south of the country, establishing a non-IE/Elamite/Sumerian common background between Iranian Jews and Gentiles would make the Behar Iranians a more appropriate choice for the Oracle than the project Iranians.

If Palisto could carry out the Oracle run again but replace the Iranians used, that would give us a better indication.

Palisto
12-27-2013, 11:38 PM
The progression of thought that's developed in this thread is, I'm pleased to say, quite stimulating intellectually.

If the North European component is literally absent among Near-Eastern Jewish groups, the only possibility as you've stated was for a common genetic contribution from a native Iranian group into both modern Iranians and Iranian Jews that wasn't Indo-European speaking in origin pretty early on.

The problem with this scenario is accentuated by the result of the Oracle run - Modern Iranians just don't make a good donor population for Iranian Jews. That brings us to at least two possible explanations;

1) Modern Iranians have experienced a significant genetic shift away from the common genetic contributor with Iranian Jews since the latter arrived in Achaemanid Persia around 600 B.C. Could it be possible the Achaemanid Persians in fact had a minimal impact on Iran, whereas other Iranic-speakers such as the Parthians, Scythians and Medians did, resulting in a later elevation of North European among Iranians? We should also recall the East Eurasian contribution brought by Turkish tribes from Medieval times onwards.

2) There is in fact no direct genetic explanation for the apparent phenotype shift towards Iran in Iranian Jews, which brings AJL's earlier thought about phenotype selection within a group to a new homeland.

You assume that Indo-Europeans must have the North European component but we don't know that. We don't have autosomal DNA of ancient Indo-Europeans.

Does the North European component correlate with the "Ancient North Eurasian" (ANE)?
http://dienekes.blogspot.com/2013/12/europeans-neolithic-farmers-mesolithic.html

I have the impression that the smaller the size of an endogamous population the less components can be detected by Admixture runs regardless of its origin. The level of endogamy can be estimated by shared IBD within a population compared to other populations. Dodecad analyzed Jews here (unfortunately, Iranian Jews are not included but I would guess there results would be similar to Iraqi Jews):
http://dienekes.blogspot.com/2012/08/fastibd-analysis-of-several-jewish-and.html
Iraqi Jews show extreme sharing within their population (=151 cM shared):
http://4.bp.blogspot.com/-aMUJs3QUQTs/UCJQyUVGyoI/AAAAAAAAFPg/DqxwVOs6GLI/s1600/Iraq_Jews.png

The threshold for 23andme- and gedmatch-"distant relatives" is a shared segment bigger than 7 cM
Based on Dodecad run "distant relative" >7cM:
Iraq_Jews
Iraq_Jews 151
North_African_Jews_D 18.6
Yemen_Jews 10.5
Saudis 9.9
Palestinian 9.3
Syrians 8.8
Sephardic_Jews 8.7
Assyrian_D 8.7
Bedouin 8.6
Kurd_D 8.5
Morocco_Jews 8.4
Iranians_19 8.3
Druze 8.2
Armenians_Y 8.1
Ashkenazi_D 8
Jordanians 7.8
Yemenese 7.7
Georgians 7.6
Ashkenazy_Jews 7.5
S_Italian_Sicilian_D 7.5
Cypriots 7.3
Lezgins 7.3
Greek_D 7.2
C_Italian_D 7.1
Abhkasians_Y 7.1
North_Ossetians_Y 7.1
Chechens_Y 7.1
Turks 7
Balkars_Y 7

Kurd_D
Kurd_D 20.6
Turks 10.7
Iranians_19 10.1
Lezgins 9.8
Assyrian_D 9.4
Georgians 9.4
Armenians_Y 9.3
Chechens_Y 9.3
Abhkasians_Y 9.1
North_Ossetians_Y 9
Adygei 8.8
Kumyks_Y 8.8
Balkars_Y 8.6
Iraq_Jews 8.5
German_D 8.1
North_African_Jews_D 8
Druze 7.9
Hungarians_19 7.9
Ukranians_Y 7.9
C_Italian_D 7.8
Syrians 7.8
Polish_D 7.7
Yemen_Jews 7.6
Greek_D 7.6
Russian 7.6
Cypriots 7.6
French 7.5
Bulgarians_Y 7.4
Lithuanians 7.2
Saudis 7.2
Sephardic_Jews 7
S_Italian_Sicilian_D 7

Iranians_19
Saudis 12.7
Iranians_19 11.9
Kurd_D 10.1
Yemenese 9.9
Bedouin 9.5
Yemen_Jews 8.8
Syrians 8.4
Iraq_Jews 8.3
Lezgins 8.3
Palestinian 8.2
Georgians 8.2
Jordanians 8.2
Armenians_Y 8.1
Turks 8
Balkars_Y 8
Druze 7.9
Assyrian_D 7.8
Adygei 7.8
Abhkasians_Y 7.8
North_Ossetians_Y 7.8
Kumyks_Y 7.7
Moroccans 7.5
Chechens_Y 7.5
C_Italian_D 7.2
Bulgarians_Y 7.1
Russian 7

Palisto
12-27-2013, 11:51 PM
An important caveat just came to mind...

The acquired Iranian samples used in these programs are mixed but are largely from the top half of the country. We don't have autosomal data of Iranians from across the country, but the Behar et al. Iranian reference set is probably from the south/south-central parts.

As the Elamites particularly were only present in the south of the country, establishing a non-IE/Elamite/Sumerian common background between Iranian Jews and Gentiles would make the Behar Iranians a more appropriate choice for the Oracle than the project Iranians.

If Palisto could carry out the Oracle run again but replace the Iranians used, that would give us a better indication.

I did another Oracle run, this time I used Globe13 data, here are the top match Oracle results:
Distance Population1 %Pop1 Population2 %Pop2
1.3537 Iraq_Jews 84.7% Iranians 15.3%
1.3920 Iraq_Jews 94.0% Brahui 6.0%
1.4041 Iraq_Jews 83.8% Kurd_D 16.2%
1.4184 Iraq_Jews 94.0% Balochi 6.0%
1.4479 Iraq_Jews 85.7% Iranian_D 14.3%
1.4859 Iraq_Jews 83.8% Kurds_Y 16.2%
1.4972 Iraq_Jews 95.2% Kalash 4.8%
1.7525 Iraq_Jews 91.4% Abhkasians_Y 8.6%
1.7576 Iraq_Jews 89.9% Georgian_D 10.1%
1.8719 Iraq_Jews 91.8% Georgians 8.2%

DMXX
12-28-2013, 12:02 AM
You assume that Indo-Europeans must have the North European component but we don't know that. We don't have autosomal DNA of ancient Indo-Europeans.


It is a fairly comfortable deduction to make at this point considering:
a) Its' elevation in Iranic-speaking West Asian populations compared to their immediate neighbours (e.g. Armenians, Assyrians, Jewish minorities)
b) Its' correlation with Y-DNA haplogroup R1a1a frequencies in the same region
c) The presence of a North European component frequency gradient increasing as one moves further east towards Central Asia
d) The coalescence of both high Y-DNA R1a1a and North European component frequencies in Central Asia, the favoured candidate as a migration hub for the Indo-Iranians

As a fellow genetic genealogist I am sure you are aware of a couple of these observations. With a myriad of genetic signatures* complementing the favoured Pontic-Caspian steppe theory, it isn't appropriate to use the absence of primary data as a means to dismiss the above. Any assertion that level playing field exists for the interpretation of these observations is avoiding the clear intertwining of the above within each other.

* I am not of the opinion that, for instance, all the Y-DNA R1a1a/North Euro etc. can be attributed to a single source. I prefer the position of it behaving as a marker of unspecified magnitude for the time being.



Does the North European component correlate with the "Ancient North Eurasian" (ANE)?
http://dienekes.blogspot.com/2013/12/europeans-neolithic-farmers-mesolithic.html


In West Asia, very well. Please refer to the supplementary data of the study and you will note that North Caucasian populations like the Lezgin, which have >20% North European in most runs (example (https://docs.google.com/spreadsheet/ccc?key=0ArJDEoCgzRKedEY4Y3lTUVBaaFp0bC1zZlBDcTZEY lE&hl=en_US#gid=0)) also happen to have >20% ANE. Conversely, populations like Cypriots who don't have nearly as much North European also lack ANE.

ZephyrousMandaru
12-28-2013, 12:02 AM
I did another Oracle run, this time I used Globe13 data, here are the top match Oracle results:
Distance Population1 %Pop1 Population2 %Pop2
1.3537 Iraq_Jews 84.7% Iranians 15.3%
1.3920 Iraq_Jews 94.0% Brahui 6.0%
1.4041 Iraq_Jews 83.8% Kurd_D 16.2%
1.4184 Iraq_Jews 94.0% Balochi 6.0%
1.4479 Iraq_Jews 85.7% Iranian_D 14.3%
1.4859 Iraq_Jews 83.8% Kurds_Y 16.2%
1.4972 Iraq_Jews 95.2% Kalash 4.8%
1.7525 Iraq_Jews 91.4% Abhkasians_Y 8.6%
1.7576 Iraq_Jews 89.9% Georgian_D 10.1%
1.8719 Iraq_Jews 91.8% Georgians 8.2%

There's an Oracle for Globe13?

DMXX
12-28-2013, 12:13 AM
There's an Oracle for Globe13?

I believe Palisto is using the manual Oracle program for R. It can be obtained here (http://dodecad.blogspot.com/2012/10/globe13-calculator.html).

The very low GD (<2) and consistent pattern (predominantly Iraqi Jewish with minor West Asian, south Iranians and Brahui best) indicates, in my opinion, that the additional phenotype overlap between Iranian Jews and their non-Jewish neighbours is due to a common non-IE element from the south of the country. I suppose the Elamite suggestion takes first place.

Palisto
12-28-2013, 01:09 AM
There's an Oracle for Globe13?
I made one :)

ZephyrousMandaru
12-28-2013, 01:11 AM
I made one :)

That's great, where can I download it?

Sein
12-28-2013, 01:36 AM
I'd love it if you could make this Globe13 Oracle public. I'm sure we all would really appreciate this.

Palisto
12-29-2013, 09:18 AM
That's great, where can I download it?

Here:
http://kurdishdna.blogspot.com/2013/12/globe13-calculator-for-genetic-distance.html
I used the same calculator a while ago here:
http://kurdishdna.blogspot.com/2012/11/biogeographical-ancestry-using-dodecad.html

Using the Excel file for Iranian Jews:
11231124112511261127

Calculated location (https://maps.google.com/maps?q=35.47%0942.97&ie=UTF-8&hq=&hnear=0x15525755718320f1:0x7595b3aca6cfe8fa,35.47% 0942.97&gl=us&ei=hei_UrezF4vmoAS08oKgCw&ved=0CCwQ8gEwAA) for Iranian Jews

Humanist
12-29-2013, 09:43 AM
1127

Calculated location (https://maps.google.com/maps?q=35.47%0942.97&ie=UTF-8&hq=&hnear=0x15525755718320f1:0x7595b3aca6cfe8fa,35.47% 0942.97&gl=us&ei=hei_UrezF4vmoAS08oKgCw&ved=0CCwQ8gEwAA) for Iranian Jews

The location that you have calculated for Iranian Jews is practically Assur. About 16 miles away.

ZephyrousMandaru
12-29-2013, 11:41 AM
Here:
http://kurdishdna.blogspot.com/2013/12/globe13-calculator-for-genetic-distance.html
I used the same calculator a while ago here:
http://kurdishdna.blogspot.com/2012/11/biogeographical-ancestry-using-dodecad.html

Using the Excel file for Iranian Jews:
11231124112511261127

Calculated location (https://maps.google.com/maps?q=35.47%0942.97&ie=UTF-8&hq=&hnear=0x15525755718320f1:0x7595b3aca6cfe8fa,35.47% 0942.97&gl=us&ei=hei_UrezF4vmoAS08oKgCw&ved=0CCwQ8gEwAA) for Iranian Jews

Thank you very much Palisto.

Tsakhur
02-23-2016, 12:43 AM
On a related note, some genetically similar populations can differ consistently on a phenotypic level. In South-Central Asia, one only has to note the differences between Punjabis and Pashtuns. Both of these populations are pretty close in terms of autosomal ancestry. In fact, I think Punjabi people are the closest population to us (genetically), besides Tajiks. But even people without actual experience in the region can differentiate "us". An example of the phenotypic differences:

http://centralasiaonline.com/shared/images/2011/04/22/paksurrender.jpg

A closer view of the Punjabi individuals
1108

Closer views of the Pashtun individuals
1109

1110

My guess is that genetically diverged populations looking rather similar, and genetically similar populations looking somewhat diverged, must have something to do with "epigenetics", and environmental conditions?

Also, I think Zephyrous makes a great point here.

This case can be said with Balochis/Brahuis/Makranis and many other South Asian groups as well. Its very fascinating despite that Balochs/Brahuis/Makranis are genetically mostly West Asian with significant South Asian ancestry (around 25% from what I read from other forums), many of them look surprising very South Asian. Some even look like they can fit easily as locals in South India.

These two men for example (I got the pics from Khanabadoshi) I think look very South Indian

Baloch
http://www.crisisbalochistan.com/assets/images/Abdul-haq_2012.jpg

Brahui (not sure if he is Baloch)
https://upload.wikimedia.org/wikipedia/commons/d/d9/Pakistani_Baloch.JPG

For me it is very surprising how their South Asian ancestry despite not being their major ancestry dominate their phenotypes. In fact they look even more South Asian than certain Pashtuns despite the latter having more ASI/South Asian ancestry.

I think this is similar to Zephyrous's point regarding how a minor component despite not being majority can determine your phenotype.