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August 12, 2012

The Jewish Diaspora: not an empire of the mind


Berber queen?

In light of the previous post you know that I was going to post on the new paper in PNAS, North African Jewish and non-Jewish populations form distinctive, orthogonal clusters. Additionally, the press people at Albert Einstein did reach out to me. That doesn’t mean I’ll blog a paper, but it does mean that I’ll give it an extra look. If the authors or people associated with the paper care to have their work publicized, and reach out to humble bloggers, then that’s all good in my book. Also, I suppose over the past two years I’ve become a locus of “Jewnetics” commentary.

In some ways this is the Golden Age of Jewnetics, though we are approaching the epoch of silver. There has to be diminishing marginal returns at some point, and I think the 2010 papers which I reviewed earlier really established the broad outlines of the scientific genealogy of the Jewish people. But just because the broad outlines are established doesn’t mean that there isn’t something to say on specific aspects which haven’t been deeply explored. Some of the commentary on this weblog ...

An exegesis of Robert Pollack?

Filed under: Genetics,Genomics,Jewish Genetics — Razib Khan @ 1:17 pm

I was going to review North African Jewish and non-Jewish populations form distinctive, orthogonal clusters at some point soon, but I’m going to have to move that up. Someone on Twitter pointed me to this really weird article, Being Jewish Is More Mind Than Matter: It’s Not Just Genes That Makes Us a People or Nation, by one Robert Pollack. Let me be frank: I have a hard time even commenting on material which I can’t really understand. For example:

Ancestors are a very large population: Each of us can be sure we had more than 1,000 ancestors in only the last 10 generations, or a few centuries. And genetically speaking, a lot can happen over the generations. After all, each of us inherits only one of the two versions of DNA that each parent had previously inherited from his or her parents. A particular version of DNA information may be discarded and lost at any point in time; new DNA may be introduced; or an ancient line of genetic information may be conserved — carried and passed on from generation to generation even as it accumulates different genetic changes that are also passed down.

This stuff ...

July 21, 2012

Ashkenazi Jews are not inbred – 2

I know I excoriate readers of this weblog for being stupid, ignorant, or lazy. But this constant badgering does result in genuinely insightful and important comments precisely and carefully stated on occasion. I put up my previous post in haste, and when I published it I wasn’t totally happy with the evidence from which the authors adduced that Ashkenazi Jews were not inbred. Here’s why, from the comments: Doesn’t identity-by-state permutations test reflect a counterbalance of admixture vs. inbredness + drift? Rather than just the degree of inbreeding? Since the population has strong admixture effects, a low IBS doesn’t exclude strong inbreeding, does it?

From my little personal experience IBS is not the best statistic from which to generalize widely, and can be highly misleading in admixed individuals, as implied by the commenter. First, since I’ve stated above that the Ashkenazi Jews are admixed, let me go into a tangent as to why Ashkenazi are admixed between a Middle Eastern and Western European population, as opposed to being a relatively unadmixed ancient Eastern Mediterranean group with affinities to both regions. The previous previous paper found evidence of linkage ...

February 8, 2011

Jacob’s Legacy: A Genetic View of Jewish History

Link to review: Jacob’s Legacy: A Genetic View of Jewish History.

August 27, 2010

Chosen genes of the Chosen People

ashjewheadshotLast spring two very thorough papers came out which surveyed the genetic landscape of the Jewish people (my posts, Genetics & the Jews it’s still complicated, Genetics & the Jews). The novelty of the results was due to the fact that the research groups actually looked across the very diverse populations of the Diaspora, from Morocco, Eastern Europe, Ethiopia, to Iran. They constructed a broader framework in which we can understand how these populations came to be, and how they relate to each other. Additionally, they allow us to have more perspective as to the generalizability of medical genetics findings in the area of “Jewish diseases,” which for various reasons usually are actually findings for Ashkenazi Jews (the overwhelming majority of Jews outside of Israel, but only about half of Israeli Jews).

Just as the two aforementioned papers were deep explorations of the genetic history of the Jewish people, and allowed for a systematic understanding of their current relationships, a new paper in PNAS takes a slightly different tack. First, it zooms in on Ashkenazi Jews. The Jews whose ancestors are from the broad swath of Central Europe, and later expanded into Poland-Lithuania and Russia. The descendants of Litvaks, Galicians, and the assimilated Jewish minorities such as the Germans Jews. Second, though constrained to a narrower population set, the researchers put more of an emphasis on the evolutionary parameter of natural selection. Like any population Jews have been impacted by drift, selection, migration (and its variant admixture), and mutation. Teasing apart these disparate parameters may aid in understanding the origin of Jewish diseases.

ResearchBlogging.orgThe paper is open access, so you don’t have to take my interpretation as the last word. Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population:

The Ashkenazi Jewish (AJ) population has long been viewed as a genetic isolate, yet it is still unclear how population bottlenecks, admixture, or positive selection contribute to its genetic structure. Here we analyzed a large AJ cohort and found higher linkage disequilibrium (LD) and identity-by-descent relative to Europeans, as expected for an isolate. However, paradoxically we also found higher genetic diversity, a sign of an older or more admixed population but not of a long-term isolate. Recent reports have reaffirmed that the AJ population has a common Middle Eastern origin with other Jewish Diaspora populations, but also suggest that the AJ population, compared with other Jews, has had the most European admixture. Our analysis indeed revealed higher European admixture than predicted from previous Y-chromosome analyses. Moreover, we also show that admixture directly correlates with high LD, suggesting that admixture has increased both genetic diversity and LD in the AJ population. Additionally, we applied extended haplotype tests to determine whether positive selection can account for the level of AJ-prevalent diseases. We identified genomic regions under selection that account for lactose and alcohol tolerance, and although we found evidence for positive selection at some AJ-prevalent disease loci, the higher incidence of the majority of these diseases is likely the result of genetic drift following a bottleneck. Thus, the AJ population shows evidence of past founding events; however, admixture and selection have also strongly influenced its current genetic makeup.

The sample size of Ashkenazi Jews was ~400, and they looked at ~700,000 SNPs. As I said, how Jews relate to other populations really isn’t at the core of this paper as it was in the earlier ones from the spring, but there were the PCA plots (sorry Mike), a frappe bar plot, and a phylogenetic tree derived from Fst statistic. Again, remember that PCA is showing you the largest independent components of genetic variation within the data. The bar plot has a set of ancestral populations of which individuals are composites of. And finally, Fst measures between population component of genetic variation. The larger the Fst across two populations the bigger the genetic distance.

Using the Druze & Palestinians as the ancestral Middle Eastern reference the authors estimated that the European admixture into Ashkenazi Jews is on the order of 30-55%. This is in the same ballpark as the previous studies, so no great surprise. As I stated in earlier posts the authors can spin the same results in very different ways. From what I can tell these authors are inclined to emphasize the strong possibility that in terms of genetic distance Ashkenazi Jews are somewhat closer to Europeans than they are to Levantine Arabs. Of course these sorts of assertions need to be handled with care. The genetic distance between Ashkenazi Jews and Tuscans is less than half that between Ashenazi Jews and Russians, while the Jewish-Russian value is about 50% larger than the Jewish-Palestinian one. Remember that there’s a fair amount of circumstantial evidence that Tuscans may themselves be a relatively recent hybrid population between indigenous residents of the Italian peninsula and Near Easterners.

ashjtab1One thing that this paper does do is rebut any strong assertion that Ashkenazi Jews are a genetically homogeneous population which went through a powerful bottleneck. Basically, the idea that Jewish diseases are just an outcome of the operational inbreeding that occurs when genetic variation is expunged from a population through low effective population size. The clincher seems to be comparison of heterozygosity of Ashkenazi Jews and gentile Europeans. The former are actually somewhat more heterozygous than the latter. There’s been a bit of evidence from previous research that the long term effective population size of Ashkenazi Jews was not necessarily very small, so this isn’t a total surprise. Remember that heterozygosity simply means the fraction of individuals heterozygous at a locus.

One way you can become heterozygous is naturally admixture. Remember that populations differ across many genes. As an example, there’s a pigmentation gene, SLC24A5, where all Europeans are at one state, and all West Africans in another. Naturally African Americans exhibit much more heterozygosity on this locus than the ancestral populations. The Ashkenazi Jewish case is less extreme because the two parental populations are genetically closer, but the principle still holds.

A consequence of recent admixture between genetically different populations are high levels of linkage disequilibrium, non-random associations of alleles at different loci across the genome. Why? There are many genes where two populations may be very different. Offspring inherit half their genome from one parent, and half from the other, and the parents pass along to their offspring particular associations of alleles. There may be a set of European distinctive alleles on a chromosome, and an African distinctive set of alleles, so that in a hybrid individual the alleles are strongly correlated across loci. These associations are broken down over time by recombination. The regularity of this process can serve as a clock with which to measure the period since admixture. African Americans were used to calibrate the time since admixture for the Uyghur people of western China, who are mixed from West and East Eurasian populations. The authors did not do this in this paper, I assume because the ancestral populations were genetically rather close in comparison to the two above examples, so there’d be less linkage disequilibrium to break down in the first place.

In the Ashkenazi Jewish population they found more linkage disequilibrium than in Europeans as well as longer haplotypes. This could be the result of a population bottleneck where drift could drive up the frequency of blocks of the genome, but as they note in the paper that should probably reduce heterozygosity. The natural inference then is that admixture between distinct populations can explain both data points.

ashslselectBut let’s cut to the chase. What genes exhibit signatures of natural selection in Ashkenazi Jews? More precisely, what distinctive regions of the genome exhibit signatures of natural selection? They used the standard haplotype type based methods. Basically you’re looking for regions of the genome where there are long blocks of correlated alleles, signs of a selective sweep due to a favored variant which dragged along flanking genomic regions as it rose rapidly in frequency, more rapidly than recombination could break apart the associations. Because recombination does breaks up associations over time, you need the selective sweeps to be relatively recent to detect them with these methods. Since the Jewish people, and Ashkenazi Jews more particularly, are relatively recent historically timing shouldn’t be an issue for Jewish specific sweeps. But another factor is that the two primary tests they used, EHH and iHS, are not good at picking up sweeps which are just starting. EHH is geared toward sweeps which are almost complete, so the frequency of the selected allele is near 100%. iHS is better are mid-range values. Using a combination of these two techniques they found that six genes which are implicated in diseases characteristic of Ashkenazi Jews have the hallmarks of natural selection. Natural selection is self-evident, so what seems to have been going here is that the disease was simply a side effect or byproduct of adaptation.

The strongest signal they found was in ALDH2. The strongest signal in Europeans, LCT, was not found in Ashkenazi Jews. But is LCT a strong signal in Europeans? Many Southern European populations have low frequencies of the derived LCT allele, indicating that they haven’t been subject to strong selection for lactase persistence. These are the same populations genetically close to the Ashkenazi Jews. The authors suggest that the Jewish-European admixture occurred before the sweep of the derived LCT allele, but it seems more plausible that the Ashkenazim simply admixed with a European population, such as Italians, which do not exhibit much lactase persistence. As for ALDH2, the association between genetic variation on this locus and alcoholism is well known, and has been used to explain the low Jewish rates of the disease. In this case, the authors posit that protection from alcoholism is a positive side effect of natural selection:

The mechanism driving selection of the ALDH2 locus is unknown, but a plausible target of selection also within this selected region is the TRAFD1/FLN29 gene, which is a negative regulator of the innate immune system, important for controlling the response to bacterial and viral infection (49). TRAFD1/FLN29 may have conferred a selective advantage in the immune response to a pathogen, perhaps near the time that the Jews returned to Israel from their Babylonian captivity. Despite the unclear selective mechanism, this remains a remarkable example of a putatively selected region accounting for a known population phenotype.

Many of the other loci naturally did not show signatures of natural selection. But this sort of work is exploratory, and there are limits to the power of their techniques. As it is, it seems that we’re very far along on understanding the phylogenetic tree of the Jewish people, and we’re finally getting a grip on the exogenous parameters which might prune the branches.

Citation: Steven M. Bray, Jennifer G. Mulle, Anne F. Dodd, Ann E. Pulver, Stephen Wooding, & Stephen T. Warren (2010). Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population PNAS : 10.1073/pnas.1004381107

Related: John Hawks, New data on Ashkenazi population history.

Image Credit: Wikimedia

July 16, 2010

More Jews, fewer markers

Filed under: Genetics,Genomics,Jewish Genetics,Jews — Razib Khan @ 10:43 am

At around the same time that the two big Jewish genetics papers came out, there was another one in BMC Genetics which I had overlooked. It’s open access so you can read the whole thing, but seems like they used 32 STR’s as markers. Their primary finding about Jewish populations was that there was a north vs. south distinction, illustrated in this map:

1471-2156-11-48-2

June 14, 2010

Science is sufficient for any inference

Filed under: Culture,Genetics,Jewish Genetics — Razib Khan @ 3:15 pm

Because I’m a generally somewhat more anthropocentric in regards to my interest in the “squishy science” I am often amused by the wide range of inferences that people make when presented with a set of scientific results. Naturally, when I talk about the genetics of Jews it gets a lot more heated. You did not see most of the extremely bizarre comments which kept coming in as I simply marked them as spam. But I thought I would point to how different individuals can derive totally contradictory inferences from the same posts in two weblog reactions. These two bloggers link to my posts as summaries of the research. First:

…A recent study suggests that Jews are tied by more than common religion, we have the same genetics.

While even some Jews have fought the notion that there is a Jewish race, it is something I am happy to embrace. I am no scientist or geneticist, but it is clearly obvious through recent research that we do, in fact, have a common genetic link. This has been discussed in a second article as well.

While it is complex research, the data speaks for itself. Alan Dershowtiz has said it. Martin Luther King Jr. has said it. And I have said it again and again. If you hate Jews, you do not hate a set of beliefs. You do not hate a country. You are a racist. Period.

Conversely:

I knew Mr. Razib Khan will show his true self eventually, and he did. Despite his protestations to the contrary, he objectively is working for the goal of de-legitimatizing Israel by falsifying scientific data to prove that Jews are not a distinct people with shared identity but a collection of descendants of various South-European ethnic groups. Naturally, this theory is welcomed by various Arab scoundrels with their claim that Israelis are newcomers from Europe, and that Palestinians (Arabs, that is) are closer to original ancestors than “occupiers”-Jews, therefore they have legitimate right to kick Israelis from their homeland and take it for themselves….

I probably disagree with the details of the conclusion of the first post (I think there is something a bit weird personally about the importance of an anti-Israel stance in many circles if one isn’t a Palestinian or a Muslim, but I don’t think it has to do with racism). But the second post is plainly false in its assertions about my post. The individual probably didn’t read the post linked in the criticism, as I state that “Jewish groups share a lot of the genome identical by descent.” I doubt you have to be super well versed in scientific terminology to get the drift of what I’m talking about. But another issue in the second post is that the poster doesn’t seem to care much about Mizrahi Jews; it’s clear that this group has little European ancestry, and they obviously weren’t European colonizers. I know that Leftist and Arab/Muslim critics of Israel do focus on the state’s Ashkenazi Jewish secular Zionist origins, and many Leftists have applied to the white/non-white dichotomy onto Israeli society somewhat inappropriately (Jews being white, Arabs being non-white). One tendency which crops up in comments & questions about Jewish genetics which I’ve noticed is the implicit  substitution Ashkenazi Jew for Jew. Again, as if non-European Jews are a triviality which can be dismissed out of the rhetorical equation (this is certainly not the case in Israel where about half the Jewish population is of non-European origin).

This is the sort of thing which makes me generally skeptical that any given scientific result necessarily entails a set of policy or value positions. Over and over I’ve seen the same scientific data leveraged into supporting diametrically opposing normative stances. Clearly then the science isn’t driving the logic of the core argument; rather, science is a handmaid which is brought on after the fact to lend an air of authority, and the glamor of its cultural prestige.

June 10, 2010

Genetics & the Jews (it’s still complicated)

Filed under: Genetics,Genomics,Jewish Genetics,Jews — Razib Khan @ 5:05 am

After the post on Jewish genetics from a few days ago I was going to do a follow up clarifying a few issues. It was a big paper and I skipped over material which I thought might have benefited from further elaboration, but would have taken up too much time. But Dienekes alerts me to another paper which just came out in Nature of interest, The genome-wide structure of the Jewish people:

Contemporary Jews comprise an aggregate of ethno-religious communities whose worldwide members identify with each other through various shared religious, historical and cultural traditions…Historical evidence suggests common origins in the Middle East, followed by migrations leading to the establishment of communities of Jews in Europe, Africa and Asia, in what is termed the Jewish Diaspora…This complex demographic history imposes special challenges in attempting to address the genetic structure of the Jewish people…Although many genetic studies have shed light on Jewish origins and on diseases prevalent among Jewish communities, including studies focusing on uniparentally and biparentally inherited markers…genome-wide patterns of variation across the vast geographic span of Jewish Diaspora communities and their respective neighbours have yet to be addressed. Here we use high-density bead arrays to genotype individuals from 14 Jewish Diaspora communities and compare these patterns of genome-wide diversity with those from 69 Old World non-Jewish populations, of which 25 have not previously been reported. These samples were carefully chosen to provide comprehensive comparisons between Jewish and non-Jewish populations in the Diaspora, as well as with non-Jewish populations from the Middle East and north Africa. Principal component and structure-like analyses identify previously unrecognized genetic substructure within the Middle East. Most Jewish samples form a remarkably tight subcluster that overlies Druze and Cypriot samples but not samples from other Levantine populations or paired Diaspora host populations. In contrast, Ethiopian Jews (Beta Israel) and Indian Jews (Bene Israel and Cochini) cluster with neighbouring autochthonous populations in Ethiopia and western India, respectively, despite a clear paternal link between the Bene Israel and the Levant. These results cast light on the variegated genetic architecture of the Middle East, and trace the origins of most Jewish Diaspora communities to the Levant.

I doubt it’s a coincidence that this paper came out right on the heels of the previous one; papers are presented at conferences and word gets around, and I assume that the two groups were rushing to get their work published soon enough so as not to be totally overshadowed by the first past the post. The text of both papers is also an interesting window into the role of interpretation in science, as this one seems to emphasize the common Middle Eastern ancestry of Jews (excluding outliers such as the Ethiopian Jews), while the previous one highlighted structure within the Jewish community. Despite the similarities, this second paper is worth exploring for one major reason: it includes two populations of Jews, Moroccans and Yemenis, which were not in the previous research.


The methodology of both groups was similar. Take Jewish and non-Jewish populations of interest, and sequence them with a SNP-chip, and then try and extract out some useful patterns for the purposes of analytics. Here’s an important issue I want to reemphasize: the different methods of extracting out useful patterns give somewhat different results, and these results themselves are to a great extent human constructions which map only approximately onto the shape of reality. Measures of “genetic distance” are really just useful reifications and their biological reality as the differences amongst billions of base pairs is a somewhat different thing. This is why it is difficult to be more than trivial sometimes when it comes to what the “bottom line” on these studies are; the bottom lines represent human attempts to generate intuitive categories and representations on natural processes which are in some ways deeply alien to us. So with the cautions out of the way, let’s look at what the figures in this paper might indicate to our puny human intuitions.

First, here is a slice of a PCA where various Jewish groups have been mixed with a range of populations from the HGDP data set as well as a few extra ones. Specifically, I’ve focused on panel B which expands the region of the plot which contains populations of European and West Asian origin. Additionally, I’ve added a few extra labels and expanded the legend for clarity of viewing.

jewsnat1

The second figure constrains the variation to European and West Eurasian populations for the purposes of extracting out the two largest dimensions of variation. Observe that the general configurations of the relationships remains the same (if rotated a bit), but the magnitudes are now shifted. In the first plot the unadmixed African populations were the most diverse group, while in the second the Arab groups with appreciable African ancestry such as the Bedouin are. So eigenvector 1 seems to roughly rank order West Asian groups by their African ancestry, while the second eigenvector is a rough east-west axis within the various regional groups.

jewsnat2

The PCA aligns well with the previous paper. Ashkenazi Jews are roughly between European and Middle Eastern populations, as one would expect if they were in some sense an admixture between the groups. In the first paper the “Italian” group was from northern Italy. In this paper it is from Tuscany (Tus/T respectively for figure 1 and 2). The more interesting aspect are the non-Ashkenazi groups. This paper seems to confirm the east-west division evident in the earlier paper, whereby Ashkenazi & Sephardic groups form a natural cluster, as do the Mizrahi Jews of Iraq and Iran. Additionally, the Jews of Morocco seem to fall close to the Ashkenazi-Sephardic cluster (Moroccan Jews are Sephardic, but separated out a bit for the purposes of this paper). In the HGDP sample the closest thing to a “host” population for the Moroccan Jews are the Mozabites of Algeria, who are a Saharan Berber group. Unfortunately I don’t think this is the best proxy for the Berber groups because the Mozabites have a substantial proportion of Sub-Saharan African ancestry, more than is typical from what I can gather for populations from the Maghreb. But they added in their own group of Moroccans as well, though I didn’t track down the notation in the supplementary table 1 to ascertain the provenance of this sample.

The Yemeni Jews on the other hand are easier to understand. They seem to shake out as just another Middle Eastern population. They’re a subset of the Saudis in both plots. Since they’re regionally constrained to the southwest of the Arabian peninsula this makes sense, as the Saudi sample seems more regionally diverse in its recent ancestry (the next figure makes this clear to me). So the Yemeni Jews are roughly a third major cluster of “mainline” Jewish groups. Though their history is not as antique as that of the Jews of Iraq and Iran, who presumably go back to the period of the Persian Empire of the Achaemenids (earlier in the case of the Babylonian Jewry naturally), it does pre-date Islam. Additionally the genetic data suggest that this Jewish community has been relatively endogamous since the rise of Islam, as the next plot highlights.

It uses the ADMIXTURE method, with eight ancestral populations represented by each particular color. I’ve truncated the plot to populations of interest, in particular the Middle Eastern ones.

The inference that Middle Eastern Jews have been relatively endogamous since the rise of Islam is supported by this figure, the red-brown segment is pretty close to Sub-Saharan African ancestry in an individual’s genome. The Arab and North African Muslim groups tend to have some appreciable Sub-Saharan African ancestry, but the Jewish groups do not. This is probably due to the fact that the arrival of Sub-Saharan Africans as slaves was more a feature of the Islamic era states, which had far more pervasive trade links with Africa south of the Sahara than any of the societies of antiquity. The Jews within the lands of Islam who did not convert were marginalized and did not participate fully in the commercial and cultural life of these societies. It seems plausible to assume then that there were few avenues for persons of slave ancestry and origin to enter into the Jewish community, as was common within Muslim society, where the offspring of slave women were recognized as free if the father was free. The Druze, a post-Muslim sect traditionally restricted to the mountains of Lebanon exhibit the same lack of Sub-Saharan African ancestry as Middle Eastern Jews, and this presumably is a pointer to their marginalization over the past one thousand years from the world of Arab Islam generally.

From this figure it looks as if the Moroccan Jews are fundamentally distinctive in some way from the non-Jewish population of Morocco. The green segment within the plot seems lacking in groups from the far western edge of the World Island of Africa-Eurasia. The full figure shows it is also lacking from populations on the eastern edge, as well as Sub-Saharan Africa, excluding those which have admixture. This component then point to origins within the center of the World Island, focused on the Mashriq and regions somewhat to the east. The magnitude of contribution of this segment to Moroccan Jews to me clinches the earlier observation of a close association between Ashkenazi, Sephardic and Moroccan Sephardic Jews, and a tie back to the Middle East in part for all these groups (though some of this may be of deeper origin, as the contrast between French and French Basques shows that different groups within the same nation can have different contributions, and the Moroccan non-Jewish samples may not be representative).

Finally, let’s look at the table which attempts to summarize genetic distances using allele sharing. The lower values indicate more genetic closeness.

jewsnat3

Throwing all the variation together in a grab bag doesn’t seem to really inform that much from what I can tell. Here are the authors:

Genetic relationships between our population samples were then explored with the measure of allele sharing distances (ASDs)…Table 1 provides genetic distances between each Jewish community and its corresponding host population, all Jewish communities, west Eurasian Jewish communities, their respective Jewish group inferred from the PCA, and non-Jewish Levantine populations. The Ashkenazi, Sephardi, Moroccan, Iranian, Iraqi, Azerbaijani and Uzbekistani Jewish communities have the lowest ASD values when compared with their PCA-based inferred Jewish sub-cluster…In all except the Sephardi Jewish community, this ASD difference is statistically significant … ASD values between Ashkenazi, Sephardi and Caucasus Jewish populations and their respective hosts are lower than those between each Jewish population and non-Jewish populations from the Levant. This might be the result of a bias inherent in our calculations as a result of the genetically more diverse non-Jewish populations of the Levant. The Ethiopian and Indian Jewish communities show the lowest ASD values when compared with their host population….

So what’s the bottom line here? I think the bottom line is that there isn’t a bottom line, and that we need to proceed on a case by case basis. I’ve focused on Middle Eastern Jews in this post, but let’s put the spotlight on the Indian Jews, the Bene Israel of Bombay, who were separated from the Jewish Diaspora, and the Cochin Jews, who were more well integrated (the Bene Israel did not have the Talmud, the Cochin Jews did). Both these groups resemble their Indian host populations genetically. Yet, Y chromosomal markers strongly imply that the Bene Israel are descended from male Middle Eastern Jews (many carry the Cohen Modal Haplotype). What likely occurred in India was that generations of admixture between Jews and non-Jews resulted in the elision of differences between the two groups, despite the persistence of a cultural distinction. Why the difference with other Jewish groups? I suspect that it has to do with the relative lack of a special relationship between Jews and the host culture in India as opposed to the world of Islam or Christendom. In India Jews were just another group, not subject to particular exclusion or marginalization. Non-Jews could, and did, move into the Indian Jewish community, while this was taboo in the Islamic or Christian world. A similar process seems to have occurred to the Jews of Kaifeng, who intermarried and eventually lost their identity because of their greater eventual isolation from the Jewish Diaspora in comparison to the Indian Jews, especially those of Cochin. The last generations of the Jews of Kaifeng, who likely descended from Middle Eastern traders, witnessed the sons of this community enter into the Chinese bureaucracy through cultivation of that culture’s classics, as well as the farce of Han wives of Jewish notables tending to pigs in their yards.

Citation: Behar, D., Yunusbayev, B., Metspalu, M., Metspalu, E., Rosset, S., Parik, J., Rootsi, S., Chaubey, G., Kutuev, I., Yudkovsky, G., Khusnutdinova, E., Balanovsky, O., Semino, O., Pereira, L., Comas, D., Gurwitz, D., Bonne-Tamir, B., Parfitt, T., Hammer, M., Skorecki, K., & Villems, R. (2010). The genome-wide structure of the Jewish people Nature DOI: 10.1038/nature09103

June 6, 2010

Genetics & the Jews

The 2,000 year dance between the Jewish people and Western civilization has spawned many questions of scholarly interest. A relatively minor point, though not trivial, has been the issue of the biological relatedness of the Jewish people, and their relatedness to the nations among whom they were resident. This particular point became more starkly relevant with a scientific understanding of human genealogy and genetic relationship in the 18th and especially 19th centuries, but its root can be traced back to antiquity. Jews are not simply a set of individuals who espouse a belief in the God of the Jews, or hold to the laws of the God of the Jews. Rather, one aspect of Jewish identity is its collective component whereby the adherents of the Jewish religion also conceive of themselves as a particular nation or tribe, and therefore bound together by a chain of biological descent. Ergo, the traditional assertion that one is a Jew if one’s mother is a Jew.

Of course these issues can not be understood except in light of a complex historically contingent sequence of events. Our understanding of what it means to be Jewish today, or the understanding of Jews themselves as to their own identity, is the outcome of a long process where self-identified Jews interacted with the broader milieu, as well as evolving in situ. In other words, the Jewish people and the seeds of the Jewish Diaspora were shaped by developments within and without the Jewish culture, and these developments left an impact on the genes of the Jewish people. Contemporary groups outside the “Jewish mainstream,” such as the Beta Israel, Bene Israel and the Karaites, but with an acknowledged connection to Judaism, are windows into other faces of being Jewish besides that of Rabbinical Judaism.

And yet it is descents of the adherents of Rabbinical Judaism, the Judaism of the Pharisees, which we think of when we think of Jews (even the non-Orthodox traditions emerged out of a cultural milieu where Orthodox Judaism was normative). The vast majority of the Jews of the world trace their lineage back to the groups who organized their lives around not just the Bible, but also the Talmud, and subsequently commentaries and rulings by rabbis who were trained in the Talmud. Today these Jews fall into three broad groups, the Ashkenazim, Sephardim and Mizrahim. The Ashkenazim are rather easy to define, as they are the Jews of Central Europe who have been so prominent over the past few centuries. Though it seems likely that in the first millennium their ancestors were to be found along the Rhine, more recently their center of gravity has been in Central & Eastern Europe, in particular Poland and Lithuania. The Sephardim were originally the Jews of Spain, but after their expulsion in 1492 they settled in the Ottoman Empire, and to a lesser extent in other regions of Europe such as the Netherlands. A major confounding issue with the modern Sephardim is that in the Ottoman lands they encountered and interacted with preexistent Jewish communities, who often maintained a distinctive identity subsequent to the influx of the Sephardim. Though in most cases, such as in Morocco and Syria, the Sephardim became culturally dominant and assimilated the indigenous Jewish community into their identity (though they often abandoned Ladino, the language they brought from Spain, for the local lingua franca), in other cases two distinct Jewish communities were coexistent down down to the modern era (e.g. Greece). Finally, the Mizrahim are Jews of the East or Oriental Jews, those Jews whose ancestors hail from Muslim lands where the Sephardim were never a presence. To a great extent the Mizrahim identity is a recent catchall constructed to identify a real dividing line between those groups which are the products of the Sephardic-indigenous synthesis, such as the Moroccan Jews, and those which are not, such as the Yemeni Jews. Often all non-Ashkenazi Jews are referred to as Sephardic because of a common religious liturgy which binds them.

But naturally it gets more complicated than this. Between the rise of Islam and Christianity as the dominant religious civilizations in which Jews were embedded and the Enlightenment Rabbinical Judaism had established a modus vivendi. Jews were a corporate entity, a minority subordinate to the majority, whose relationship with the majority was mediated through eminent individuals who spoke for and had power over the community. Though often fraught in the execution in the abstract the position of Jews within pre-modern political units was not controversial; Jews were subjects with obligations, often a useful minority for potentates. They were not citizens with rights and responsibilities. Over the past few centuries that has obviously changed. The French Revolution and the emergence of the idea of a nation-state where all citizens have equal rights and responsibilities before the law, along with a scientific concept of race, complicated the Jewish relationship with the societies in which they were resident, particularly in Europe (though pan-Turk and pan-Arab nationalism were analogous and resulted in similar problems of identity). Despite phenomena such the Spanish fixation on “cleanliness of blood”, as well the Jews self-conception as the descendants of Israel, it was in the 19th century that the idea of a Jewish race with very specific and determined biological qualities which were heritable came to the fore. The Nazi total extermination program stood in contrast to previous assaults on the existence of Jewish community, where conversion to Christianity, and assimilation more broadly, were plausible goals. The Nazis aimed to eliminate not just the culture of the Jews, but their very biological existence. Ironically assimilated European Jews themselves internalized this sense of their racial/national distinctiveness, evident even in those with no religious aspect of Jewish identity at all such as Sigmund Freud. This explains the secular nature of the original Zionist project, whose aim was to create a national homeland for the Jews as a people, and so normalize them as a nation among nations, rather than being among the nations (this was a project which religious and assimilationist Jews initially opposed).

With the Holocaust, and the post-World War II rejection of racial nationhood, the often pseudo-scientific practice of measuring and categorizing people according to skull metrics, and more legitimately blood groups, fell into disrepute. Some scholars began to reconfigure the Jews not as a biological descent group, but as a religious ideology or confession which eventually became an ethnic identity. The most extreme proponents of the cultural model presumed that Jewish groups emerged through cultural diffusion and religious proselytization. The Jews of Poland were Poles who adopted Rabbinical Judaism. The Jews of Morocco were Arabs or Berbers who adopted Rabbinical Judaism. And so forth. In other words this school transformed Jewishness into what the German Reform movement had attempted, making of Jews just another religious confession with no ethnic connotations (and therefore entailing a reinterpretation of some aspects of Chosen Peoplehood).

But the pendulum has swung back, in part thanks to the rise of genetic science, and in part broader currents in the Jewish world. In regards to the second I will note that the American Reform movement has pulled back from its more aggressive accommodations with the sensibilities of gentiles. Of particular relevance for the topic at hand, Reform Judaism has reversed its rejections of the idea of Jewish nationhood. I suspect this is in large part because American Jews, and Jews in Western nations more generally, feel less need to prove that they belong by aligning themselves self-consciously to mainstream conceptions of religious identity as anti-Semitism has declined.

And now we come to genetics. The genetics of Jews are a large set of related fields. Much of it is motivated by medical considerations, in particular “Jewish diseases” such as Tay-Sachs. Though the ultimate aim of much research is to clarify population stratification in association studies, over the past few years there has been a great deal of light shed on the possible origins of and the relationships of Jews to each other and other populations. Originally the focus was on uniparental lineages, male and female markers passed through the Y chromosome and mtDNA respectively. The general results of these were that both the extreme scenarios of total replacement and pure cultural diffusion are false. On the one hand Jews across the world by and large share unexpected genetic affinity which one would not predict from geography, but only from their common religious-ethnic identity as Jews. But Jews also cluster geographically in a way that is reminiscent of the gentile populations among whom they have settled, suggesting either independent evolution after an initial separation and/or admixture with the local populations.

jewpc2One of the most popular posts on this weblog focuses on the differences between Ashkenazi Jews and gentiles, in particular peoples of European descent. The figure to the left illustrates that white Americans who are gentile or Jewish are rather easy to distinguish genetically from each other. That Jews exhibit a particularly distinctive genetic signature may not be all that surprising, considering that medical geneticists have long known that there are diseases which are biologically rooted and heavily overrepresented among this population. Distinctive traits imply distinctive genes. And the demographic history of the Jewish people as attested to in the literary records can be fitted rather easily within the framework of many of the results coming out of the genetic studies.

But what about the issues I mooted above in regards to the divisions among the Diasporic Jewish community? A new paper in The American Journal of Human Genetics takes a stab at attempting establish a set of relations between different Jewish communities, as well as other populations which they may have admixed with. Abraham’s Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry:

For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, Greek, and Ashkenazi) and comparison with non-Jewish groups demonstrated distinctive Jewish population clusters, each with shared Middle Eastern ancestry, proximity to contemporary Middle Eastern populations, and variable degrees of European and North African admixture. Two major groups were identified by principal component, phylogenetic, and identity by descent (IBD) analysis: Middle Eastern Jews and European/Syrian Jews. The IBD segment sharing and the proximity of European Jews to each other and to southern European populations suggested similar origins for European Jewry and refuted large-scale genetic contributions of Central and Eastern European and Slavic populations to the formation of Ashkenazi Jewry. Rapid decay of IBD in Ashkenazi Jewish genomes was consistent with a severe bottleneck followed by large expansion, such as occurred with the so-called demographic miracle of population expansion from 50,000 people at the beginning of the 15th century to 5,000,000 people at the beginning of the 19th century. Thus, this study demonstrates that European/Syrian and Middle Eastern Jews represent a series of geographical isolates or clusters woven together by shared IBD genetic threads.

The major limitation of this study that I can see is that two very numerous and interesting groups of non-Ashkenazi Jews, Moroccan and Yemenis, were not included. Yemenis in particular are of interest because there is some historical reference to kings of Yemen who adhered to the Jewish religion, and so implicitly may have brought over substantial numbers of South Arabians to the religion. The studies I have seen about the genetics of Yemeni Jews are mixed in regards to whether they exhibit more affinity with other Jews, or with non-Jewish Yemenis. But set next to the treasure trove of results that’s a minor complaint. Quick review of the groups in the study:

Ashkenazi – easy, Jews of Central Europe

Iraqi Jews – Mizrahi, presumably Jews who descend from the Babylonian community which dates back to the First Exile

Iranian Jews – Mizrahi, should be derived from the Babylonian Jewish community. For most of history after the conquest of Babylon by the Persians Mesopotamia and the Iranian heartland were integrated into one political unit. The the division between Mesopotamia and Iran was fixed after the Ottomans managed to hold what became Iraq against the attempts by the Safavid dynasty of Persia to reclaim it in the 16th century.

Syrian Jews – Sephardic, but a compound of ancient Levantine Jews who date back to Roman antiquity and post-1492 Sephardim. The native Syrian liturgical tradition apparently persisted down into the modern period before its recent extinction

Turkish Jews – Sephardic, but a compound of Anatolian Jews who date back to Roman antiquity and post-1492 Sephardim

Greek Jews – Mostly Sephardic, a compound of Greek Jews who date back to Roman antiquity and post-1492 Sephardim (note that Greece was part of the Ottoman Empire until the 19th century)

Italian Jews – I believe this study classes them as Sephardic, but the origin and nature of this group is ambiguous. The Jewish community of Italy may date back to Roman antiquity, and so lay outside of the Ashkenazi-Sephardic dichotomy, but operationally it has been influenced by the pan-Mediterranean peregrinations of the Sephardic Diaspora

In fact the last point, that different Jewish communities have interacted and influenced each other, is a general truth. Persecutions of Jews during the medieval period as far away as Germany and Spain resulted in infusions of new migrants into the Jewish community of Kerala in South India as an extreme case. Just as there was an Islamic world which stretched from the Atlantic to the borders of China, and a Christian world which spanned Spain and Russia, so the Jewish world stretched from its heart in Central Europe and the Middle East, all the way to far flung outposts such as Kaifeng in North China and Kerala in South India. But powerful streams of cultural interconnectedness do not necessarily entail a great deal of gene flow.

Let’s go to the results as illustrated in the figures. First a table which shows pairwise genetic distances between the Jewish populations enumerated above and selected groups from the HGDP database. The numbers above the diagonal represent Fst, in other words the proportion of genetic variation within the total population as defined by the row-column pair which is between population. The bigger the number, the greater the genetic distance between the two populations.

jewsFST1

Since I had to shrink the figure some, here’s the text which describes the gist of these results:

These findings demonstrated that the most distant and differentiated of the Jewish populations were Iranian Jews followed by Iraqi Jews (average FST to all other Jewish populations 0.016 and 0.011, respectively). The closest genetic distance was between Greek and Turkish Sephardic Jews (FST = 0.001) who, in turn, were close to Italian, Syrian, and Ashkenazi Jews. Thus, two major groups were identifiable that could be characterized as Middle Eastern Jews and European/Syrian Jews, an observation that was supported by pairwise FST and by phylogenetic tree analysis….

The Turkish and Greek communities were operationally nearly unified until the independence of Greece 150 years ago, so the small distance makes sense. It is notable that the distinction in terms of genetic distances maps onto that between the Roman and Persian Empires, where two Jewish communities emerged with different loci, Mesopotamia and the Palestine-Alexandria axis, respectively. Syrian Jews, who were within the boundaries of the Roman Empire, are more similar to European Jews than Iraqi Jews to their east. Though this may be due in part to the influx of Sephardim from Spain within the past few hundred years.

But Fst numbers can be hard to interpret in a gestalt fashion. So let’s look at PCA plots. They filtered the SNPs for the most ancestrally informative ones; i.e., ones which exhibit lots of between population difference. With these SNPs they extracted the largest independent components of variation. Note that the difference between PC 2 and 3 is small in magnitude, and so both are of interest. First, here are the Jewish groups in aggregate as they relate to other HGDP populations:

jewfig2a

No surprise. Jews span Europeans and Middle Easterners. But let’s drill down to a finer grain. They also used the PopRes data set, which from what I recall is a bit more cosmopolitan than the HGDP one. I’ve added some clarifying labels.

jewfig2b

The above changes nothing really in how we understand the relationships of Jews, in particular Ashkenazi Jews, to Europeans. Roughly, Jewish genetic relatedness to European groups tracks how strongly influenced by Rome a region was. Jews are closest to Italians, least close to Finns and Russians. Also, remember to be careful about PCA plots; from what I can gather these dimensions fall out of the set of SNPs designed to maximize between population differences between the Jewish groups so as to increase the power to distinguish Jewish clusters.

Going back to the HGDP sample, you see similar patterns.

jewfig2c

jewfig2d

Iranian and Iraqi Jews, Jews who were not touched by the Sephardic Diaspora, or, the Roman Empire, are distinct from the Jewish groups to their west. In fact it is interesting to observe that the various Levantine Arab groups are rather close to Syrian Jews when set next to the Iraqi and Iranian Jews, at least in total genome content.

Another way to look at the variation is through Structure, where there are K ancestral groups, and individual genomes are conceived of as a synthesis of K groups.

jewstruct

The Structure plot confirms that Ashkenazi Jews are more European than other Jewish groups, and Iranian Jews the least European. This influence of geography, or isolation by distance, shows up in other studies. But it should be weaker or non-existent in a perfectly cosmopolitan Jewish Diaspora where distance is no consideration. This model seems false. The most plausible explanation for the patterns here, supported by uniparental lineages, is that local Jewish populations have admixed with surrounding populations. Of course it could be that Ashkenazi Jews went through a population bottleneck and became a highly endogamous inbred community, so that genetic drift resulted in their uniqueness. But in that case they should show up as distinctive as the Kalash of Pakistan, who may be thought to have formed their own “micro-race” through genetic isolation.

Switching back to a big-picture summary of the genetic relationships, here’s a phylogenetic tree which was generated with the Fst numbers above. I think these should be viewed with caution, as trees like this are sharp and discontinuous by their nature. Even the authors observe that these Jewish groups, as well as human populations in general, have been characterized by gene flow and admixture over time, so that the assumptions which underly some of these representations are idealizations. Trees are invariably claimed to be robust, and yet somehow I’ve seen a really wide range of trees across different studies contingent upon the marker set or technique for the same set of populations quite often.

phylotree

Finally, the authors examined the degree of identity by descent (IBD) across the genome of the Jewish groups. IBDjust refers to the fact that a region of the genome is identical with another because they’re descended from the same original copy. Siblings for example have huge regions of the genome identical by descent because each parent contributes one half of the offsprings’ genome. Over the generations the correlations of genetic variants across a physical strand are broken up by recombination. If two individuals who are putatively not related have long regions of the genome which are identical by descent that suggests that they share a recent common ancestor whose genomic contribution hasn’t been diluted by too much time and recombination.

Figure 3 of this paper summarizes the main IBD results. In panel A the red bars are Jewish-Jewish comparisons, yellow Jewish-non-Jewish, and blue non-Jewish-non-Jewish. Panel C plots the genetic relationships adduced from the IBD results on a 2-D plane.

figIDB2

Jewish groups share a lot of the genome identical by descent. Additionally, there’s a general agreement with the other results as to which groups are close to each other. They note in the text that the segments identical by descent among Jews are rather small, which implies  that recombination has broken up the large blocks. So that means that a high proportion of Jewish-Jewish IDB is a function more of many common ancestors deep in the past, rather than a few more recent common ancestors. Ashkenazi Jews in particular exhibit increased sharing of the genome across short blocks as opposed to longer ones, suggestive of a demographic expansion from a small population. Genic regions were was also moderately enriched around the loci which were IDB, a possible indication of functional commonalities across Jewish populations. If you’re interested in genes which Jews tend to share IDB, here they are a list:

tables6

After all that where are we? I think this section of the discussion addresses the broad brush findings:

The Middle Eastern populations were formed by Jews in the Babylonian and Persian empires who are thought to have remained geographically continuous in those locales. In contrast, the other Jewish populations were formed more recently from Jews who migrated or were expelled from Palestine and from individuals who were converted to Judaism during Hellenic-Hasmonean times, when proselytism was a common Jewish practice. During Greco-Roman times, recorded mass conversions led to 6 million people practicing Judaism in Roman times or up to 10% of the population of the Roman Empire. Thus, the genetic proximity of these European/Syrian Jewish populations, including Ashkenazi Jews, to each other and to French, Northern Italian, and Sardinian populations favors the idea of non-Semitic Mediterranean ancestry in the formation of the European/ Syrian Jewish groups and is incompatible with theories that Ashkenazi Jews are for the most part the direct lineal descendants of converted Khazars or Slavs. The genetic proximity of Ashkenazi Jews to southern European populations has been observed in several other recent studies.

Early history matters, and what these findings point to is that a division between western and eastern Jews which falls along the lines of Roman-Persian political division exists today even after 2,000 years. In terms of both culture and genetics there is “first mover” advantage. Even though only a minority of the population of the United States is of English origin, the vast majority of Americans speak English, and adhere to cultural traditions of English provenance. Similarly, admixture events early in the history of a group may have an outsized effect contingent upon later variations in population size.

Focusing more on specific cultural and historical parameters the authors note that what was Jewish in the time of Augustus was very different from what was Jewish in the time of Charlemagne. By the time of Charlemagne the Judaism of the Pharisees had marginalized other groups (excepting to some extent the Karaites). In the time of Augustus Jews were divided between different sects and persuasions, and there was a welter of diversity. Additionally, in the marketplace of Roman religion Jews were a moderately entrepreneurial group. The dynasty of Herod himself was of convert origin. There was a wide spectrum of Jewish religious practice and belief, from the near monastic isolation of the Essenes, to the engaged but separatist Pharisees, and finally to the wide range of more syncretistic practices which fall under the rubric of “Hellenistic Judaism.” Many scholars assert that it was from the last sector which Christianity finally arose as a Jewish sect, and that Christianity eventually absorbed all the other forms of Hellenistic Judaism. Judaism of the Pharisees, which became Rabbinical Judaism, and more recently Judaism qua Judaism, was shaped in large part by having to accommodate and placate the dominant Christian and Islamic religious cultures in which it was integrated by the early medieval period. Conversion to Judaism from Christianity or Islam was often a capital crime (though conversion from Christianity to Judaism was not forbidden in Muslim lands, while presumably conversion from Islam to Judaism in Christian lands would not have been, though few Muslims lived in Christian lands). So after 500 A.D. it seems that what may have occurred was that a Jewish Diaspora characterized by geographically determined genetic diversity, despite some common original Levantine origin, was genetically isolated from surrounding populations. This explains why there seems relatively little influx of Slavic genes into the Ashkenazim despite their long sojourn within Poland-Lithuania and later the Russian Empire. In contrast, the Roman Jewish community was already large in the days of Julius Caesar, and presumably intermarried with the urban proletariat of diverse origins.In an ironic twist these data suggest that modern Jews, in particular the Ashkenazim, but to a lesser extent the Sephardim as well, share common ancestry with gentile Europeans due to the unconstrained character of the pagan Greco-Roman world which Jews were to a great extent strident critics of. Contra Tertullian Athens had much to do with Jerusalem.

Image Credit: Wikipedia

Citation: Atzmon, G., Hao, L., Pe’er, I., Velez, C., Pearlman, A., Palamara, P., Morrow, B., Friedman, E., Oddoux, C., & Burns, E. (2010). Abraham’s Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2010.04.015

December 9, 2009

More Jewish Genetics

Filed under: Jewish Genetics — Razib @ 2:22 pm

Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations. I posted on it at ScienceBlogs. Nothing too new.

November 10, 2009

Spengler does it again!

Filed under: Genetics,Jewish Genetics — Razib @ 12:03 pm

Just Spengler (David Goldman) being Spengler, From “Zionism is Racism” to “Judaism is Racism”:

Judaism has nothing to do with race-there are Jews of every race-but it does have to do with family. Jews are members of Abraham’s family. Not only tradition, but a great deal of DNA evidence support this claim. To insist that Jews adopt the criterion of “belief” for membership is to rule that God must act in accordance with a human court’s notion of the permissible range of God’s behavior. No wonder the Reform Jews and the British Humanist Association support this.

1) Yes, Jews are genetically distinct.

2) But, they are also the product of genetic admixture.

3) And, it seems more likely that that admixture arrived via maternal lineages, that is, gentile female ancestors (the mtDNA results are somewhat confused, but the Y lineages seem to be relatively strongly Middle Eastern in provenance in comparison to total genome content).

In light of the fact that the debate is over the validity of the criterion of maternal descent as to “Who is a Jew,” it seems deceptive to appeal to genetics when that field opens up more questions in regards to Jewish tradition than it closes. Of course, this sort of shell-game is normal behavior for Spengler. Someone should really put a “For Entertainment Purposes Only” sticker on his blog.

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