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Thread: The Ashkenazi Jewish Genome

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    The Ashkenazi Jewish Genome

    S. Carmi et al., The Ashkenazi Jewish Genome.

    Ashkenazi Jews (AJ) number ≈10 million individuals worldwide, mostly in the US and Israel. In accordance with historical records, recent studies showed that AJ are genetically homogeneous with mixed European and Middle-Eastern ancestry and that the AJ population had undergone a severe bottleneck around 800ya followed by an extremely rapid expansion. These characteristics make the AJ population highly attractive for genetic studies. Here, we report the sequencing of 128 complete genomes of healthy AJ individuals. Sequencing was carried out by Complete Genomics to coverage >50x, and achieved 97% call rate, Ti/Tv=2.14, and 99.7% concordance with SNP arrays. Additional cleaning further reduced the number of false positives to just ≈5000, as determined by examining runs-of-homozygosity. We show that our AJ sequencing panel is 3- fold more effective in filtering out benign variants in clinical AJ genomes than a European, non-Jewish panel. Similarly, our AJ panel reduced the inaccuracy of AJ array imputation, for both rare and common alleles, by 10-20%. Inspection of specific genes related to AJ genetic disorders identified known disease mutations as well as dozens of additional risk alleles. Population-genetic comparison of the AJ genomes to 26 Flemish genomes sequenced using the same technology revealed increased heterozygosity and less allele sharing in AJ, in accordance with the AJ admixed nature and partial Middle-Eastern origin. On the other hand, AJ showed more population-specific allele sharing, higher load of deleterious alleles, and a smaller overall projected number of variants, potentially due to the recent bottleneck. Analysis of identical-by-descent segments, which are abundant in AJ and highly informative on recent history, confirmed a recent severe bottleneck of merely ≈300-400 individuals. Using the allele frequency spectrum, which is informative on ancient history, we inferred the time of the Out-of-Africa founder event to be ≈52,000±4000ya, and the fraction of European ancestry in AJ to be ≈55±2%. We also inferred the split between the ancestral Middle-Eastern population and contemporary Europeans to be as recent as ≈11,000±500ya, suggesting the genetic origin of modern-day Europeans is predominantly Neolithic, and much later than the first dated Homo sapiens migration into Europe. This result, made possible by our pioneering sequencing of individuals with Middle-Eastern ancestry, resolves a long-standing debate over European origins.
    http://abstracts.ashg.org

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    A recent severe bottleneck of 300-400 individuals is consistent with Gil Atzmon's 2011 thinking as quoted in:

    http://nymag.com/news/features/ashke...11/index2.html

    "Ashkenazim branched off from other Jews around the time of the destruction of the First Temple, 2,500 years ago. They flourished during the Roman Empire but then went through a “severe bottleneck” as they dispersed, reducing a population of several million to just 400 families who left Northern Italy around the year 1000 for Central and eventually Eastern Europe."

    Do the authors of this paper derive the same size bottleneck independently through their IBD analysis? It would seem so based on the abstract. No wonder I have 2200 Family Finder cousins, with some sticky DNA segments (presumably IBD) as small as 1-2 cM shared by up to 100 different matches.

    [Edit: OK, after locating the abstract on-line I can see that Ostrer and Atzmon are co-authors, so they are pretty much confirming their own earlier bottleneck estimates.]
    Last edited by seferhabahir; 09-07-2013 at 12:12 AM.

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    Quote Originally Posted by seferhabahir View Post
    A recent severe bottleneck of 300-400 individuals is consistent with Gil Atzmon's 2011 thinking as quoted in:

    http://nymag.com/news/features/ashke...11/index2.html

    "Ashkenazim branched off from other Jews around the time of the destruction of the First Temple, 2,500 years ago. They flourished during the Roman Empire but then went through a “severe bottleneck” as they dispersed, reducing a population of several million to just 400 families who left Northern Italy around the year 1000 for Central and eventually Eastern Europe."
    I don't believe 2 things
    1) i don't believe they were several millions Jews at the time of the Roman Empire. One million in the Jewish religion is a great maximum.

    2) I don't believe there was a bottleneck after Charlemagne : The political and economical state from Charlemagne 's time was favourable enough to have a more imprtant jewish population, even in the misfortunes of the 14e century, the Great Plague and the slaughters.

    If there was a bottleneck, it was certainly about 600AD after the episodes of Justinian Plagues with the general reduction of European population in a defavourable climate and the towns reduced to a village size. The reprisal of demography was in the second half of the 7th century progressive until Charlemagne reign, some difficulties between 840 and 940 by not catastrophic.
    Anyway in the Middle Age, fast population growing as in modern times, is not possible because the sanitory state and famines.

    If bottleneck, the only possible date is 1400 years ago, and not 800 years ago. Error is probably due to the surestimation of mutation rate..
    Last edited by palamede; 09-07-2013 at 07:01 PM.

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    Quote Originally Posted by palamede View Post
    I don't believe 2 things
    1) i don't believe they were several millions Jews at the time of the Roman Empire. One million in the Jewish religion is a great maximum.

    2) I don't believe there was a bottleneck after Charlemagne : The political and economical state from Charlemagne 's time was favourable enough to have a more imprtant jewish population, even in the misfortunes of the 14e century, the Great Plague and the slaughters.

    If there was a bottleneck, it was certainly about 600AD after the episodes of Justinian Plagues with the general reduction of European population in a defavourable climate and the towns reduced to a village size. The reprisal of demography was in the second half of the 7th century progressive until Charlemagne reign, some difficulties between 840 and 940 by not catastrophic.
    Anyway in the Middle Age, fast population growing as in modern times, is not possible because the sanitory state and famines.

    If bottleneck, the only possible date is 1400 years ago, and not 800 years ago. Error is probably due to the surestimation of mutation rate..
    I don't see how you can be so sure of this. The Justinian Plagues primarily affected the Eastern Roman Empire, and are not documented to have prompted the prejudicial climate that is documented to have occurred after the Black Death

    http://www.fordham.edu/halsall/jewis...blackdeath.asp

    and moreover do not match the dating the geneticists have arrived at.
     

    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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    Quote Originally Posted by AJL View Post
    I don't see how you can be so sure of this. The Justinian Plagues primarily affected the Eastern Roman Empire, and are not documented to have prompted the prejudicial climate that is documented to have occurred after the Black Death

    http://www.fordham.edu/halsall/jewis...blackdeath.asp

    and moreover do not match the dating the geneticists have arrived at.
    In Gaul in the second half of 6th century, terrible episodes of Justinian plagues are related by Gregory, bishop of Tours.
    In http://en.wikipedia.org/wiki/Plague_of_Justinian , you can read the following text

    Some scholars[8] have suggested that the plague facilitated the Anglo-Saxon conquest of Britain, since its aftermath coincided with the renewed Saxon offensives in the 550s, after a period during which the Saxons were contained. British sources from this period report plague, but Saxon ones are silent (as there are no sixth-century English documents). The Romano-British may have been disproportionately affected because of trade contacts with Gaul and other factors,[9] such as British settlement patterns being more dispersive than English ones, which "could have served to facilitate plague transmission by the rat".[10] The differential effects may have been exaggerated. In this era, British sources are more likely to report natural disasters than Saxon ones.[citation needed] In addition, "the evidence for artifact trade between the British and the English" implies significant interaction and "just minimal interaction would surely have involved a high risk of plague transmission".[10]


    800 years ago, the 12th century was a properous time for the European inhabitants, including the very numerous Jewish settlements in hundreds l towns of Western Europe and an important time for the Jewish Culture with a lot of exemples. There are a lot of testimonies.

    In http://en.wikipedia.org/wiki/History...Jews_in_France

    Merovingian Period
    It is known that the Christian clergy participated in their feasts; intermarriage between Jews and Christians sometimes occurred; the Jews made proselytes, and their religious customs were so freely adopted that at the third Council of Orléans (539) it was found necessary to warn the faithful against Jewish "superstitions", and to order them to abstain from traveling on Sunday and from adorning their persons or dwellings on that day. In the 6th century, a Jewish community thrived in Paris.[8] A synagogue was built on the Ile de la Cite, but was later torn down and a church was erected instead.[8]

    In 629 King Dagobert proposed to drive from his domains all Jews who would not accept Christianity, from his reign to that of Pepin the Short no further mention of the Jews is found. But in the south of France, which was then known as "Septimania" and was a dependency of the Visigothic kings of Spain, the Jews continued to dwell and to prosper. From this epoch (689) dates the earliest known Jewish inscription relating to France, that of Narbonne. The Jews of Narbonne, chiefly merchants, were popular among the people, who often rebelled against the Visigothic kings.

    Carolingian Period
    It is certain that the Jews were numerous in France under Charlemagne, their position being regulated by law. Exchanges with the Orient strongly declined with the advent of the Saracens in the Mediterranean sea , while oriental products such as gold, silk, black pepper or papyrus almost disappeared under the Carolingians. The only real link between the Orient and Occident was insured by the Radhanites Jewish traders.[9]

    A formula for the Jewish oath was fixed by Charlemagne. They were allowed to enter into lawsuits with Christians, and in their relations with the latter were restrained only from making them work on Sunday. They were not allowed to trade in currency, wine, or grain. Of more importance is the fact that they were tried by the emperor himself, to whom they belonged. It is a curious fact that among the numerous provincial councils which met during Charlemagne's reign not one concerned itself with the Jews, although these had increased in number. Louis le Débonnaire (814–833), faithful to the principles of his father, granted strict protection to the Jews, to whom he gave special attention in their position as merchants.


    11th and 12th centuries

    Franco-Jewish literature
    During this period, which continues until the First Crusade, also saw the awakening of Jewish culture in the south and north of France. The initial interest included poetry, which was at times purely liturgical, but which more often was a simple scholastic exercise without aspiration, destined rather to amuse and instruct than to move. Following this came Biblical exegesis, the simple interpretation of the text, with neither daring nor depth, reflecting a complete faith in traditional interpretation, and based by preference upon the Midrashim, despite their fantastic character. Finally, and above all, their attention was occupied with the Talmud and its commentaries. The text of this work, together with that of the writings of the Geonim, particularly their responsa, was first revised and copied; then these writings were treated as a corpus juris, and were commented upon and studied both as a pious exercise in dialectics and from the practical point of view. There was no philosophy, no natural science, no belles-lettres, among the French Jews of this period.[citation needed]

    The great Jewish figure which dominated the second half of the 11th century, as well as the whole rabbinical history of France, was the Ashkenazi Rabbi Rashi (Rabbi Shlomo Yitzchaki) of Troyes (1040–1106). He personified the genius of northern French Judaism: its devoted attachment to tradition; its untroubled faith; its piety, ardent but free from mysticism. His works are distinguished by their clarity, directness, and are written in a simple, concise, unaffected style, suited to his subject. His commentary on the Talmud, which was the product of colossal labor, and which eclipsed the similar works of all his predecessors, by its clarity and soundness made easy the study of that vast compilation, and soon become its indispensable complement. Every edition of the Talmud that was ever published has this commentary printed on the same page of the Talmud itself. His commentary on the Bible (particularly on the Pentateuch), a sort of repertory of the Midrash, served for edification, but also advanced the taste for seeking the plain and true meaning of the bible. The school which he founded at Troyes, his birthplace, after having followed the teachings of those of Worms and Mainz, immediately became famous.

    .....

    Expulsion from France, 1182


    A miniature from Grandes Chroniques de France depicting the expulsion
    The First Crusade led to nearly a century of accusations (blood libel) against the Jews, many of whom were burned or attacked in France. Immediately after the coronation of Philip Augustus on 14 March 1181, the King ordered the Jews arrested on a Saturday, in all their synagogues, and despoiled of their money and their investments. In the following April 1182, he published an edict of expulsion, but according the Jews a delay of three months for the sale of their personal property. Immovable property, however, such as houses, fields, vines, barns, and wine-presses, he confiscated. The Jews attempted to win over the nobles to their side, but in vain. In July they were compelled to leave the royal domains of France (and not the whole kingdom); their synagogues were converted into churches. These successive measures were simply expedients to fill the royal coffers. The goods confiscated by the king were at once converted into cash.
    During the century which terminated so disastrously for the Jews their condition was not altogether bad, especially if compared with that of their brethren in Germany. Thus may be explained the remarkable intellectual activity which existed among them, the attraction which it exercised over the Jews of other countries, and the numerous works produced in those days. The impulse given by Rashi to study did not cease with his death; his successors—the members of his family first among them—brilliantly continued his work. Research moved within the same limits as in the preceding century, and dealt mainly with the Talmud, rabbinical jurisprudence, and Biblical exegesis.[citation needed]

    Recalled by Philip Augustus, 1198


    For the desastrous climate of the 6th century

    http://en.wikipedia.org/wiki/Extreme...35%E2%80%93536
    http://medievalhistorygeek.wordpress...limate-change/

    For France and Europe in general, about 600AD was a low point very sinister in all domains: very few archeological remains, Point zero for culture, arts and even for religious culture reanimated by Irish monks.

    History is more exact than genetic extimation .Mutation rates are still very imprecise and would deserve you keep some prudence in the believings .
    Last edited by palamede; 09-07-2013 at 09:50 PM.

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    Quote Originally Posted by palamede View Post
    History is more exact than genetic extimation
    Geneticists might make errors, but DNA does not manipulate facts, as historians sometimes do. (Though geneticists might manipulate numbers, as individuals.)

    What I think you might not know is that about 70% of Jews as of AD ~600-950 were in Babylon, with many of the rest elsewhere in West Asia/the Near East and North Africa, and only a minority in Europe.
     

    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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    Quote Originally Posted by AJL View Post
    What I think you might not know is that about 70% of Jews as of AD ~600-950 were in Babylon, with many of the rest elsewhere in West Asia/the Near East and North Africa, and only a minority in Europe.

    I have ignored the city of Babylon was still inhabited in AD ~600-950. Thanks a lot to learn me.


    It is a joke. I suppose you wanted to say about 70% of Jews as of AD ~600-950 were in Omeyad and Abassid Califates, and a lot in Bagdad, the capital of Abassids .

    From Babylon to Bagdad , the capitals of successive empires in Middle East were the neighbouring cities, Seleucia and then Ctesiphon.
    Last edited by palamede; 09-08-2013 at 06:23 AM.

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    It is still a fact that at the end of the 10th century, of the three broad groups of Jewish subcultures, the smallest were Ashkenazic Jews.The next biggest were Sephardim, and the largest group by far were Jews of Arab lands (North Africa and Middle East as AJL states), and remained so for centuries. That is reiterated in a book I just read about the Cairo Genizah. If you throw in the devastating effects of the wholesale slaughters of many Ashkenazi communities in France and Germany during the Plague, I can see how a very small bottleneck could occur for Ashkenazi Jewish populations.

    I made my post mostly because I was intrigued by the very small number (300-400) that was stated in the abstract. It's much smaller than other estimates I have seen (several thousands to maybe a few tens of thousands). The initial post of this thread by Jean M was about how the authors inferred the split between the ancestral Middle-Eastern population and contemporary Europeans to be as recent as ≈11,000±500ya, suggesting the genetic origin of modern-day Europeans is predominantly Neolithic. Maybe you might prefer to talk about that instead.
    Last edited by seferhabahir; 09-08-2013 at 07:08 AM.

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    Quote Originally Posted by seferhabahir View Post
    It is still a fact that at the end of the 10th century, of the three broad groups of Jewish subcultures, the smallest were Ashkenazic Jews.The next biggest were Sephardim, and the largest group by far were Jews of Arab lands (North Africa and Middle East as AJL states), and remained so for centuries. That is reiterated in a book I just read about the Cairo Genizah. If you throw in the devastating effects of the wholesale slaughters of many Ashkenazi communities in France and Germany during the Plague, I can see how a very small bottleneck could occur for Ashkenazi Jewish populations.

    I made my post mostly because I was intrigued by the very small number (300-400) that was stated in the abstract. It's much smaller than other estimates I have seen (several thousands to maybe a few tens of thousands). The initial post of this thread by Jean M was about how the authors inferred the split between the ancestral Middle-Eastern population and contemporary Europeans to be as recent as ≈11,000±500ya, suggesting the genetic origin of modern-day Europeans is predominantly Neolithic. Maybe you might prefer to talk about that instead.
    1) I don't believe "the time of the Out-of-Africa founder event to be ≈52,000±4000ya"
    2) I don't believe "the ancestral Middle-Eastern population and contemporary Europeans to be as recent as ≈11,000±500ya, "
    3) I dont' believe in a Askenaze bottleneck 800 years ago.
    I believe the real dates are a lot older.

    But I believe in the very quick scientific progresses for the new 5 years, specially for the datations of the SNPs and my global attitude is WAIT and SEE .

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    Quote Originally Posted by AJL View Post
    Geneticists might make errors, but DNA does not manipulate facts, as historians sometimes do. (Though geneticists might manipulate numbers, as individuals.)
    Integrity and honesty are vital in both fields.
    verb (used with object), ma·nip·u·lat·ed, ma·nip·u·lat·ing. 1. to manage or influence skillfully, especially in an unfair manner


    Quote Originally Posted by AJL View Post
    What I think you might not know is that about 70% of Jews as of AD ~600-950 were in Babylon, with many of the rest elsewhere in West Asia/the Near East and North Africa, and only a minority in Europe.
    Is this conjecture, as there is no known physical census taken, in the region/regions you are outlining? If fact, can you state your source?

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