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Thread: Modelling Admixture with D-stats

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    Assuming that the Bronze Age Levants are representative of how ancient Jews were genetically, I'm still open to the possibilities that modern European Jews either are true descendants of these people but absorbed a ton of South Euro like ancestry up to the point where they don't resemble their Biblical forefathers, or they started out from a South Euro like population. The former idea draws from the fact that they are extremely far from Bronze Age Levant (far as in the genetic distance between them and the British) and a half far South Euro (Sicily, Malta) half Bronze age Levantine wouldn't plot nearly as far into Europe where Euro Jews are now. 3-5 percent additional north/east euro won't do much to assist. The D-stats that Fire-Haired did an excellent job on show only 14 percent Bronze Age Jordan (don't know if that's the same as BA Levant, I'll have to see).

    I'm sure these opinions would make me the bad guy on most other anthro forums, as they aren't very "politically correct" but I don't set out to offend. I'll still be happy if someone is willing to spot out the holes and offer something that sides with the idea that Euro Jews resemble the Jews of the Bible genetically. I'm not counting on my opinions to be accurate.
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    The last results I posted for Ashkenazi Jews were of the form (Chimp, Row)(Mbuti, Colmn) this is of (Chimp, Colmn)(Mbuti, Row) and as far as I've seen the later creates better fits than the former.

    @davef,

    This is the best fit I've had for Ashkenazi Jew. It might be realistic. First admixture in the Balkans, then immigration to Eastern Europe and admixture there.

    BTW, Jordan_EBA is very similar to modern SW Asians but not the same. SW Asians have extra African ancestry and many have an extra load of Iran_Neo-like ancestry. Ashkenazi_Jews and Druze are ones with this extra load of Iran_Neo.

    I doubt Jordan_EBA is a good reference for ancient Jews. IMO, Modern Levanties are, like Druze, Palestinans, Samartians, etc. The Jews tell of migration in the Bible. They arrived in Israel only by the Late Bronze age about 1,500 years after Mr. Jordan_EBA was born. Who knows what type of admixture they picked up along the way and who knows what admixture arrived in the Levant in general after Jordan_EBA.

    distance=0.005375"
    Ashkenazi_Jew
    "Druze" 50.05
    "Greek" 34.5
    "Belarusian" 11.05
    "Jordan_EBA" 4.4
    "Satsurblia" 0
    "Iran_Neolithic" 0

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    OK, my patience is at an end, Tomenable. Now I'm going to have to waste time removing all these off topic posts to new threads. I don't appreciate it, and on a holiday no less.

    Cut it out, and I mean it!


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    Quote Originally Posted by Fire Haired14 View Post
    The last results I posted for Ashkenazi Jews were of the form (Chimp, Row)(Mbuti, Colmn) this is of (Chimp, Colmn)(Mbuti, Row) and as far as I've seen the later creates better fits than the former.

    @davef,

    This is the best fit I've had for Ashkenazi Jew. It might be realistic. First admixture in the Balkans, then immigration to Eastern Europe and admixture there.

    BTW, Jordan_EBA is very similar to modern SW Asians but not the same. SW Asians have extra African ancestry and many have an extra load of Iran_Neo-like ancestry. Ashkenazi_Jews and Druze are ones with this extra load of Iran_Neo.

    I doubt Jordan_EBA is a good reference for ancient Jews. IMO, Modern Levanties are, like Druze, Palestinans, Samartians, etc. The Jews tell of migration in the Bible. They arrived in Israel only by the Late Bronze age about 1,500 years after Mr. Jordan_EBA was born. Who knows what type of admixture they picked up along the way and who knows what admixture arrived in the Levant in general after Jordan_EBA.

    distance=0.005375"
    Ashkenazi_Jew
    "Druze" 50.05
    "Greek" 34.5
    "Belarusian" 11.05
    "Jordan_EBA" 4.4
    "Satsurblia" 0
    "Iran_Neolithic" 0
    Is a distance of .005 good? Also if you use south italy in place of greek, would the distance increase? That would be interesting

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    Quote Originally Posted by davef View Post
    Is a distance of .005 good? Also if you use south italy in place of greek, would the distance increase? That would be interesting
    Doesn't matter, although it might be about the same given that South Italians/Sicilians and Greeks aren't all that different autosomally; there's no IBD sharing with South Italians. There is with Greeks.

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    Quote Originally Posted by Angela View Post
    OK, my patience is at an end, Tomenable. Now I'm going to have to waste time removing all these off topic posts to new threads. I don't appreciate it, and on a holiday no less.

    Cut it out, and I mean it!
    Well... you only forgot to remove your own Off-Topic posts, Angela.

    Anyway, I wish you a wonderful vacation.

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    Quote Originally Posted by Tomenable View Post
    Well... you only forgot to remove your own Off-Topic posts, Angela.

    Anyway, I wish you a wonderful vacation.
    Tomenable, you know very well that we are more liberal about posting off topic material than a lot of other sites. However, more than eight posts in a row about something that's off topic? That's a bit different. Just watch it.

    Anyway, let's not quarrel. Thanks for the good wishes, but our three day Fourth of July week end is almost over. One more barbecue, for which I am leaving now! :)

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    Quote Originally Posted by davef View Post
    Is a distance of .005 good? Also if you use south italy in place of greek, would the distance increase? That would be interesting
    Anything under 0.02 is a good fit. So 0.005 is very very good. Southern Italy is a bit of an outlier but maybe the Balkans were like Southern Italy(minus NW African ancestry) before Slavic migrations.

    Ashkenazi Jews get an equally good fit with South Italy.

    distance=0.005037"
    Ashkenazi_Jew
    "Italian_South" 51.1
    "Druze" 34.95
    "Belarusian" 13.95

    Now assuming Ashkeanzi Jews came to Central/East Europe with no Southern European admixture. This fit works as well. It's not consistent with Y DNA. I haven't looked at Ashkenazi mtDNA though.

    distance=0.007639"


    Ashkenazi_Jew
    "Druze" 68.9
    "Belarusian" 31.1

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    Angela has a temper lol.

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    South Asia

    HighLights:

    >Iran_Chalcolithic: West Eurasian side is a mixture of Steppe and something high in CHG and EEF. Iran_Neo doesn't fit this profile. Iran_Chl fits well, but most South Asian's still need extra CHG.
    >Yamnaya: Yamnaya is a better proxy for Steppe ancestry than Srubnaya. It doesn't look like South Asians have WHG ancestry which excludes the possibility of Srubnaya-like people.

    This is the best model I've found for South Asians. Iran_Neo is not a good ancestor proxy for them suprisingly. When I modeled them with Iran_Neo they usually scored 0, and instead scored equal amounts in CHG(Satsurblia) and Anatolia_N. According to these D-stats their non-ASI and Steppe ancestor was a CHG/EEF mix, and Iran_Neo doesn't fit that profile. It has too low CHG affinity not just too low EEF affinity.

    Iran_Late_Neo had some EEF_like admixture, but doesn't work either. Iran_Chl though had lots of EEF and CHG admixture and fits well as the none ASI and Steppe ancestor of South Asians, but most still need some extra CHG.

    Yamnaya_Samara Srubnaya Satsurblia Anatolia_Neolithic Levant_Neolithic Iran_Chalcolithic Hungary_HG India_South Han Nganasan Yoruba
    Kalash 30.25 0 10.4 0 0 21.55 0 37.8 ----- ----- ----- 0.010657
    GujaratiA 15.3 10.7 2.9 0 0 17.85 0 53.25 ----- ----- ----- 0.00596
    Tajik_Ishkashim 27.75 17.1 6.55 6.35 0 14.55 0 17.8 4.35 5.55 ----- 0.013662
    Sindhi 16.8 0 5.65 0 0 27.5 0 50.05 ----- ----- ----- 0.006482
    Pathan 22.7 5.65 6.4 3.3 0 19.15 0 42.8 ----- ----- ----- 0.009229

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    Comparing Bronze age Jordan to Modern SW Asia/N Africa

    This model works well for SW Asia/North Africa.


    Highlights.


    >Extra load of ancient Iranian admixture in SW Asia and Egypt and Ashkenazi Jews(meaning admixture is at least 2,000 years old).


    >Extra African admixture in most of SW Asia and a big load in North Africa.


    >WHG admixture in Morocco. Could recently be from Spain or represent older admixture from Spain.


    >Similar amount of ancient Iranian admixture in Morocco as in Bronze age Jordan. Moroccans ancestors mostly arrived sometime between 9000 BC and 3000 BC from Levant, mixed with Africans(Yoruba) and Europeans(WHG), and have been isolated since then?



    Eastern_HG Satsurblia Levant_Neolithic Iran_Chalcolithic Hungary_HG India_South Nganasan Yoruba
    Jordan_EBA 2.9 0 62.35 34.75 0 ----- ----- 0 0.00756
    Druze 5.3 2.7 36.3 54.5 0.8 ----- ----- 0.4 0.014096
    BedouinB 2.85 0 43.25 48.5 0 ----- ----- 5.4 0.01321
    Egyptian 2.55 0 41.4 43.3 1.05 ----- ----- 11.7 0.014943
    Lebanese_Christian 2.7 0 35.25 58.65 3.4 ----- ----- 0 0.015177
    Lebanese_Muslim 5.4 0.5 32 59.55 0.85 ----- ----- 1.7 0.013334
    Moroccan 2.2 1.1 49.25 21.6 5.3 ----- ----- 20.55 0.014024


    So you can see modern SW Asia has significantly more ancient Iran-related admixture. Ashkenazi Jews show the same extra amount of Iran-related admixture. Since their ancestors left the Levant some 2,000 years ago, it means this admixture can't be too recent. When Iran_Chl is replaced by Iran_Neo, modern and Bronze age SW Asia/North Africa still prefer ancient Iran(Iran_Neo) over ancient Caucasus(Satsurblia) which is interesting. It could mean admixture came directly from Iran.


    Iran_Chl had lots of Levant_N/Anatolia_N-related and CHG-related admixture. It's very differnt from Iran_Neo. So SW Asia/North Africa is definitely mostly descended of Levant_N/Anatolia_N-like people.


    Levant_N had some African admixture, but there's definitely more African admixture in modern SW Asia/North Africa. More African admixture than was in the Bronze age individual from Jordan. It looks like there might also be Steppe/Eastern_HG admixture.

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    Quote Originally Posted by Fire Haired14 View Post
    The last results I posted for Ashkenazi Jews were of the form (Chimp, Row)(Mbuti, Colmn) this is of (Chimp, Colmn)(Mbuti, Row) and as far as I've seen the later creates better fits than the former.

    @davef,

    This is the best fit I've had for Ashkenazi Jew. It might be realistic. First admixture in the Balkans, then immigration to Eastern Europe and admixture there.

    BTW, Jordan_EBA is very similar to modern SW Asians but not the same. SW Asians have extra African ancestry and many have an extra load of Iran_Neo-like ancestry. Ashkenazi_Jews and Druze are ones with this extra load of Iran_Neo.

    I doubt Jordan_EBA is a good reference for ancient Jews. IMO, Modern Levanties are, like Druze, Palestinans, Samartians, etc. The Jews tell of migration in the Bible. They arrived in Israel only by the Late Bronze age about 1,500 years after Mr. Jordan_EBA was born. Who knows what type of admixture they picked up along the way and who knows what admixture arrived in the Levant in general after Jordan_EBA.

    distance=0.005375"
    Ashkenazi_Jew
    "Druze" 50.05
    "Greek" 34.5
    "Belarusian" 11.05
    "Jordan_EBA" 4.4
    "Satsurblia" 0
    "Iran_Neolithic" 0
    I agree, and that looks pretty good. Have you tried it with Samaritans instead of Druze?

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    [QUOTE]
    Quote Originally Posted by Fire Haired14 View Post
    This model works well for SW Asia/North Africa.


    Highlights.


    >Extra load of ancient Iranian admixture in SW Asia and Egypt and Ashkenazi Jews(meaning admixture is at least 2,000 years old).


    >Extra African admixture in most of SW Asia and a big load in North Africa.
    This confirms what we know from history and from prior analyses. There's been a steady flow of African admixture moving north. The Arab slave trade after the Muslim invasions is often the explanation given, and I think that's part of it, with most of it coming from women slaves. However, I think there's always been some gene flow, and a good chunk of it came with the movement of tribes from Arabia, before, and especially after, Islam. They themselves mostly got it from women as well. It shows mostly in the mtDna, not the yDna.

    WHG admixture in Morocco. Could recently be from Spain or represent older admixture from Spain.
    Mostly older, in my opinion.

    >Similar amount of ancient Iranian admixture in Morocco as in Bronze age Jordan. Moroccans ancestors mostly arrived sometime between 9000 BC and 3000 BC from Levant, mixed with Africans(Yoruba) and Europeans(WHG), and have been isolated since then?
    Not totally isolated, but not enough admixture to really change the autosomal signature.

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    Quote Originally Posted by Angela View Post
    I agree, and that looks pretty good. Have you tried it with Samaritans instead of Druze?
    I can't because Samartians aren't included in any D-stat spreadsheet I know of. The below models work. The extra African admixture in Palestinian and Lebanses_Muslim inflate Greek admixture. The model works but I'm pretty sure most of that African admixture came in the Middle Ages.

    This one is basically a repeat of the Druze+Greek+BelaRussian one. Druze is broken up into Jordan_EBA and Iran_Chl.

    distance=0.010013"
    Ashkenazi_Jew
    "Greek" 42.3
    "Jordan_EBA" 34.05
    "Iran_Chalcolithic" 13.1
    "Belarusian" 10.55

    These models also work.
    distance=0.00537"
    Ashkenazi_Jew
    "Greek" 74.45
    "Palestinian" 25.55
    "Belarusian" 0

    distance=0.004519"
    Ashkenazi_Jew
    "Greek" 60.15
    "Lebanese_Muslim" 39.8
    "Belarusian" 0.0

    distance=0.005583"
    Ashkenazi_Jew
    "Lebanese_Christian" 66.1
    "Belarusian" 19.75
    "Greek" 14.15

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    Quote Originally Posted by Fire Haired14 View Post
    Anything under 0.02 is a good fit. So 0.005 is very very good. Southern Italy is a bit of an outlier but maybe the Balkans were like Southern Italy(minus NW African ancestry) before Slavic migrations.

    Ashkenazi Jews get an equally good fit with South Italy.

    distance=0.005037"
    Ashkenazi_Jew
    "Italian_South" 51.1
    "Druze" 34.95
    "Belarusian" 13.95

    Now assuming Ashkeanzi Jews came to Central/East Europe with no Southern European admixture. This fit works as well. It's not consistent with Y DNA. I haven't looked at Ashkenazi mtDNA though.

    distance=0.007639"


    Ashkenazi_Jew
    "Druze" 68.9
    "Belarusian" 31.1
    The top set of stats are most consistent with the amount of IBD sharing for the Ashkenazim with Slavs. That's certainly the admixture profile that various researchers, including Jewish researchers have posited in the past, so how come there's no evidence of IBD sharing?

    It's a puzzlement, to quote the King of Siam. :)

    As for "Italian South", I've been saying forever that they're a highly drifted population. I see people are finally agreeing.

    I've also been saying forever that it may very well turn out that they're the best proxy for what Greek populations were like in the Classical Era. Sicilians are a little different because of the influx of northern Italian and central Italian genes during the Middle Ages. I actually reconnected through 23andme with someone whose family went to Sicily from LaSpezia.

    https://en.wikipedia.org/wiki/Lombards_of_Sicily

    This explains it much better, including the location of the towns:
    https://books.google.com/books?id=5a...Sicily&f=false

    Here is a map:
    http://s2.postimg.org/ichtvypt5/vncxm1.gif

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    Quote Originally Posted by Angela View Post
    As for "Italian South", I've been saying forever that they're a highly drifted population. I see people are finally agreeing.
    Do you have links to papers showing they're drifted?

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    This looks pretty good given everything we know:
    Ashkenazi_Jew
    "Druze" 50.05
    "Greek" 34.5
    "Belarusian" 11.05
    "Jordan_EBA" 4.4
    "Satsurblia" 0
    "Iran_Neolithic" 0

    Now we'll see what the ancient dna shows.

    I think Jews may have picked up a little Egyptian, if not from ancient times, then from Alexandrian Jews, which might explain that Jordan EBA 4.4%, but that's sheer speculation.

    It would be nice if someone could model them with Samaritans at some point.

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    Quote Originally Posted by Fire Haired14 View Post
    Do you have links to papers showing they're drifted?
    Not recent genetics papers, no, but Cavalli-Sforza maintained in all his writings about Italy that we're a very drifted population. It's not just true of the Sardinians. It's a function of geography, given that Italy is so mountainous.

    However, it's also a function of politics. With the end of the Empire, Italy was torn into lots of little pieces which were ruled by different foreign countries and which had very little to do with one another. Intermarriage was only within the valley, or the mountain, or the political unit.
    "Campanilismo" or attachment to one's own town bell is still important in Italy today, although less so than in the past.

    That's part of why there is such a difference between north and south Italy. It's not just different migrations south of Rome versus north of Rome, although those are very important. It's that until the 1960s there was virtually no gene flow between the two areas. Almost all of my matches at 23andme are with people from Liguria, Emilia, Toscana and Piemonte. I don't have one "cousin" with southern Italian ancestry. I don't even have any from the Veneto. (Bizarrely, I have quite a few, although small, with people from Denmark, and some from the "Celtic" fringe in the British Isles.) Southern Italy, even more than Sicily, with its Lombard migrations, has been very isolated. The only attested gene flows in the last 1000 years, other than some short lived Muslim incursions and a well known resettlement, are from Albania, and some from the Byzantines, especially after the Muslim ascendancy. That's it, to my knowledge. Maybe if any of our Southern Italian members read this they can chime in, but that's my reading of the history. The only exception might be around Naples and Palermo, but as I already said, Sicily is a little different.

    Oh, the Cavalli-Sforza book is called "Consanguinity, Inbreeding, and Genetic Drift in Italy". I've got a copy in my bookshelves. I think it's time I re-read it.

    http://press.princeton.edu/titles/7800.html

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    Ok I trust that. Italy in Roman times might have been a differnt story though.

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    distance=0.004519"
    Ashkenazi_Jew
    "Greek" 60.15
    "Lebanese_Muslim" 39.8

    This horse is in the lead ^
    (Iphone won't let me copy Belarussisn but its 0 in this case.)

    I also have South Italian ancestry as well, though I don't know exactly from where but it's definitely not sicilian. With the stats posted above and that whole South Italians are like Ancient Greek thig Angela was harping about ; I wonder what size toga fits me .

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    And you know the big neolithic paper (genetic structure of worlds first farmers) that was just recently released a few weeks ago? South Italians are leagues away from anyone on the fst chart, then again how reliable is that measurement? I think they have the English as closer to Greeks in comparison to South Italians which blows my mind given that these two populations have such a history with each other.

    I may be unaware of how fst can be misleading or misinterpreted. Is it a reliable measure of genetic closeness?

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    Back on Jews :). I have to say again they do look Northern European. Like I've said there's a historically large Ashekanzi Jewish community about a mile from my house. I've seen groups of them. Many have Light Brown or Blonde hair. I always see at least one with Red hair when there's a group. I had a Jewish teamate in Little League with bleach Blonde hair and everyone in his family had Blue eyes. Few or none have olive or Brown skin. Look at the few pictures on this thread there's always at least one Red beard in there.

    Bosnians look much more exotic and are darker, and you'll never see one with Red hair. I do trust DNA test results but I'm not gonna buy garbage about them actually looking like Palestinains or Druze. They simply do not. I walked by a baseball field today where there were a bunch of Ashkenazi kids with some traditional clothing on playing. My Dad said "See they must have gone to Scandinavia or something and mixed with people there" and explained they're not "He said no they're Northern European right?". He can't believe. He thought his whole life they were converts from Northern Europe.

    It doesn't make sense. Maybe Pigmentation does make a bigger difference than we think. Maybe Turkish would look white with paler features and Swedes would look Middle Eastern with darker ones.

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    Here is data on hair colours collected by pre-war anthropologists:

    Land - % light hair (Jews / Gentiles) | % very dark hair (Jews / Gentiles):

    Prussia - 11.23 / 39.75 | 43.34 / 14.05
    Hesse - 11.17 / 31.53 | 41.50 / 13.22
    Baden - 10.32 / 24.34 | 41.95 / 21.18
    Bavaria - 10.38 / 20.36 | 39.45 21.10
    Alsace-Lorraine - 13.51 / 18.44 | 34.59 / 25.21

    Jews were statistically speaking much darker-haired than Gentiles.

    Land - % of light hair for Jews (I couldn't find for Gentiles in these lands):

    Silesia - 8.20
    Pommern - 8.85
    Brandenburg - 9.64
    East & West Prussia - 11.61
    Galicia - 13.97
    Posen - 12.39
    Congress Poland - 13.28
    Bohemia - 8.29
    Lower Austria - 8.69
    Moravia - 9.86
    Bukovina - 13.55

    Data cited from "JewishEncyclopedia.com" website.

    Henryk Szpidbaum (himself Jewish) in 1933 published data on pigmentation of Polish Jews:

    Light hair - 13.28%
    Light eyes - 20.59%

    This is much lower than among Gentiles (68% to 72.4% light eyes, depending on source).

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

    According to Hans F. K. Günther, "Rassenkunde des jüdischen Volkes", published in 1930 (and cited by Henryk Szpidbaum in "Jews in Reborn Poland", 1933), already Ancient Hebrews had about 10% - 15% of light-haired individuals among them.

    I'm not gonna buy garbage about them actually looking like Palestinains
    Palestinians are 15-20 percent Sub-Saharan, if I recall correctly.

    This is probably due to Muslim slave trade in the last 1400 years.

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    Quote Originally Posted by Tomenable View Post
    Here is data on hair colours collected by pre-war anthropologists:

    Land - % light hair (Jews / Gentiles) | % very dark hair (Jews / Gentiles):

    Prussia - 11.23 / 39.75 | 43.34 / 14.05
    Hesse - 11.17 / 31.53 | 41.50 / 13.22
    Baden - 10.32 / 24.34 | 41.95 / 21.18
    Bavaria - 10.38 / 20.36 | 39.45 21.10
    Alsace-Lorraine - 13.51 / 18.44 | 34.59 / 25.21

    Jews were statistically speaking much darker-haired than Gentiles.

    Land - % of light hair for Jews (I couldn't find for Gentiles in these lands):

    Silesia - 8.20
    Pommern - 8.85
    Brandenburg - 9.64
    East & West Prussia - 11.61
    Galicia - 13.97
    Posen - 12.39
    Congress Poland - 13.28
    Bohemia - 8.29
    Lower Austria - 8.69
    Moravia - 9.86
    Bukovina - 13.55

    Data cited from "JewishEncyclopedia.com" website.

    Henryk Szpidbaum (himself Jewish) in 1933 published data on pigmentation of Polish Jews:

    Light hair - 13.28%
    Light eyes - 20.59%

    This is much lower than among Gentiles (68% to 72.4% light eyes, depending on source).

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

    According to Hans F. K. Günther, "Rassenkunde des jüdischen Volkes", published in 1930 (and cited by Henryk Szpidbaum in "Jews in Reborn Poland", 1933), already Ancient Hebrews had about 10% - 15% of light-haired individuals among them.



    Palestinians are 15-20 percent Sub-Saharan, if I recall correctly.

    This is probably due to Muslim slave trade in the last 1400 years.
    The differences seem to be a lot smaller in the Alsace Loraine region, last time I checked I think there was also a higher frequency of J2 in that region, has there been any thorough sampling of the area?

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    Quote Originally Posted by Angela View Post
    Doesn't matter, although it might be about the same given that South Italians/Sicilians and Greeks aren't all that different autosomally.
    The key difference is the near absence of any North African affinity in Greeks (though it is higher in Iberia than in Sicily), and higher Steppe/Russian derived ancestry in Greece. Whether it is Indo-European from very ancient times, Middle Age Slavic, or something else entirely we will never know, just that such a difference exists.

    I have said this for some time and you may not agree but I think southern Italians and Greeks are related in the sense that they descend, in close proportions, from the same waves of migration, but they are not directly descended from one another for the most part. Sicily was full of Lombard settlements but that still doesn't seem to have shifted them as north as most Greeks do, possibly because the admixture is concentrated in part of the population and didn't spread.

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