Back to work

My apologies to readers for being for so long in "lazy mode". Actually I got interrupted largely by a request to provide a quality article on Basque, Sardinian and European origins for a soon to be published collective book in Basque language. This took me a lot of time and energies in late March and early April, so basically I put everything else on hold. The last weeks I've been resting indeed, what may be aggravated by a declining health that makes me sleep irregularly and often for much longer than most of you do. Being fed up with Internet information feeds and a quite active political reality also drain my energies to other endeavors, not to mention paperwork.

In this sense I want to announce that I have begun recently a new multi-purpose blog in Spanish language: Bagauda. Most of it is politics, I warn you, but I have also included the unedited raw article for that book I mention in the previous paragraph (prior to translation to Basque and corrections). I'm reasonably sure that those of you who have Spanish as primary or even secondary language will be interested in having a look (→ here).

Another relevant entry was the announcement of the upcoming congress on Iruña-Veleia to be held on May 7 in Vitoria-Gasteiz. You can still register but hurry up.

I will now proceed to comment in a separate entry on the news of the week, the Fu et al. study of a large array of Paleoeuropean ancient DNA. But, before I get to that, I must mention some interesting studies that I have not been able to get time to even properly read, let alone discuss:

• K. Voskarides, S. Mazières et al., Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements. Investigative Genetics 2016. Open access → LINK [doi:10.1186/s13323-016-0032-8]
• B. Vernot et al., Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science 2016. Freely accessible (with registration?) → LINK [doi:10.1126/science.aad9416]
• Y.Y. Waldman, A. Biddanda et al., The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry. PLoS ONE 2016. Open access → LINK [doi: 10.1371/journal.pone.0152056]

Another intriguing new independent paper by a regular visitor and commenter to this blog, Olympus Mons, that I have not yet read is:

→ R1b from Sulaweri-Shomu to Bell Beaker, available as PDF or in blog format.

He seems to argue for a Caucasus origin of both the lineage and Bell Beaker phenomenon. I have no opinion as of yet, because, simply put, I have not been able to read it in full.

Another regular visitor here to have put an independent paper online, also on the issue of R1b origins, is Paul Conroy:

→ Anatole A. Klyosov and Paul M. Conroy, Origins of the Irish, Scottish, Welsh and English R1b-M222 population. Available at Paul's Academia.edu account.

Again I have not yet got the opportunity to read it, so no opinion. 

Feel free to use this entry to comment on any of the aforementioned studies or articles or to provide info about stuff I may have missed.

PPNB ancient mtDNA and its legacy

There are several interesting studies in my "to do" list and I will be commenting them in the following days (I am quite busy these weeks and therefore I concentrate my efforts on weekends).

In this entry we have a rather interesting analysis of ancient mtDNA from the Pre-Pottery Neolithic B of Syria (NE and South) and its legacy on modern populations of West Asia and SE Europe, as well as on ancient European Neolithic ones.

Eva Fernández et al., Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands. PLoS Genetics 2014. Open access → LINK [doi:10.1371/journal.pgen.1004401]

I understand that the sequences are not really new but that they were first discussed in Fernández 2005 (thesis in Spanish) and 2008. What is new is the comparison with ancient and modern populations in search of their possible legacy.

Early PPNB (from CONTEXT C14 database)

In spite of the relevance of this analysis, it must be cautioned that the Tell Ramad and Tell Halula sites may not be fully representative of the actual genetic diversity of PPNB as a whole, a cultural area that spanned all the Levant, from the Kurdish mountains to the Sinai and Cyprus.

If, as the authors argue and I have already suggested in relation to the NE African affinities of European Neolithic ancestry, the arrival of Neolithic to Thessaly happened via a coastal route, inland PPNB sites may well not be as informative as Palestinian or Cypriot ones.

But this is what we have for now, so let's see what these ancient Syrian farmers tell us, while we await further Neolithic sequences from potentially more relevant sites.

Table 1. Mitochondrial DNA typing of 15 Near Eastern PPNB skeletons.

40% of the sequences belong to haplogroup K, a U8-derived lineage unknown in Europe before the Neolithic. Most of the other lineages (40%) belong to R0 but half of them belong to R0(xHV), extremely rare in Europe (common in Arabia instead) and the H sequences cannot be identified either with anything common nowadays. The remaining 20% of lineages (U*, N* and L3*) are not too helpful either.

So when the authors compare them with modern and ancient populations most of the affinity corresponds to a single basal haplotype of K (16224C,16311C) as described in supplementary table 5.

Figure 2. Contour map displaying the percentage of individuals of the database carrying PPNB haplotypes.
Only populations with clear geographic distribution were included. Gradients indicate the degree of similarity between PPNB and modern populations (dark: high; clear: small).

The SE European and West Asian populations with the greatest legacy of this haplotype are: the Csángó of Moldavia (22%), Cypriots (13%), Ashkenazi Jews (11%), Crimean Tatars (10%) and Georgians (9%). Cardium Pottery farmers from Catalonia (23%) and a pooled Central European Danubian Neolithic sample (10%) also score high for this lineage.

Some other PPNB matrilineages also show some lesser modern prevalence:

• 16223T (L3) → Qatar, Yemen (not necessarily the same L3(xM,N) lineage, it must be said)
• 16224C,16311C,16366T (K) → Druze
• 16256T (H) → Bedouin

The other haplotypes have not been detected in modern nor European Neolithic populations.

The obvious conclusion is that only the 16224C+16311C K haplotype was, of all the Euphrates PPNB lineages active in the Neolithic European founder effect. This haplotype was present only in 1/15 individuals from the Euphrates PPNB, so rather marginal over there, although a close relative found today among the Druze was more common (3/15).

Another conclusion is that the Csángó probably have a quite direct line of ancestry to the early European farmers, shedding some light on the origin of this mysterious population at risk of extinction.

The coastal route to Thessaly proposed here makes all sense to me because, on one side, early Anatolian Neolithic cultures do not seem to have any obvious cultural affinity with the first European Neolithic of Sesklo (Painted Pottery) and Otzaki (Cardium Pottery), and, on the other side, there is clear evidence of some NE African genetic legacy mediated by Palestine: Y-DNA E1b-V13 naturally but also the "Basal Eurasian" speculation of Lazaridis that ended up being revealed as Dinka affinity in fig. S7 of Skoglund & Malström.

This theory can only be strongly confirmed if Palestinian and Cypriot ancient DNA is sequenced and fits well in it. Similarly ancient Balcanic DNA would be most interesting to have as well for a more direct reference. But, in any case, the theory seems at the very least plausible and supported by some important evidence.

My hypothetical reconstruction of a plausible coastal route of Neolithic towards Thessaly (dashed red line)
on a base map of Middle PPNB from the CONTEXT database.

It is also important to notice that the Syrian PPNB sequences are different from the modern mtDNA pool of West Asia, dominated by lineages like J, T1 and U3. This suggests that, at the very least in this region of the Syrian Euphrates, there have been important demographic changes since Neolithic, something confirmed by data from the same are but of later dates (which anyhow is not yet modern either). 

Fernández et al. discuss this issue in some detail:

Our PPNB population includes a high percentage (80%) of lineages with a Palaeolithic coalescence age (K, R0 and U*) and differs from the current populations from the same area, which exhibit a high frequency of mitochondrial haplogroups J, T1 and U3 (Table S7). The latter have been traditionally linked with the Neolithic expansion due to their younger coalescence age, diversity and geographic distribution [11], [12], [49]. In addition to the PPNB population, haplogroup T1 is also absent in other Early Neolithic populations analyzed so far [17], [22], [26], [30]. Haplogroup U3 has been found only in one LBK individual and it has been suggested that it could have been already part of the pre-Neolithic Central European mitochondrial background [19].

Haplogroup J is present in moderate frequencies in Central European LBK-AVK populations (11.75%) and it has been proposed as part of the Central European “mitochondrial Neolithic package” [19]. However, it has also been described in one late hunter-gatherer specimen of Germany, raising the possibility of a pre-Neolithic origin [23]. Haplogroup J is present in low frequency (4%) in Cardial/Epicardial Neolithic samples of North Eastern Spain [27], [28], [31]. Absence of Mesolithic samples from the same region prevents making any inference about its emergence during the Mesolithic or the Neolithic. However, its absence in the PPNB genetic background reinforces the first hypothesis.

These findings suggest that (1) late Neolithic or post-Neolithic demographic processes rather than the original Neolithic expansion might have been responsible for the current distribution of mitochondrial haplogroups J, T1 and U3 in Europe and the Near East and (2) lineages with Late Paleolithic coalescent times might have played an important role in the Neolithic expansive process. The first suggestion alerts against the use of modern Near Eastern populations as representative of the genetic stock of the first Neolithic farmers while the second will be explored in depth in the following section.

From the viewpoint of material Prehistory, it is of course correct, that PPNB was overwhelmed by later cultural processes, which may have implied demic expansions and replacements of some sort, even if many of them seem to originate within West Asia.

First of all, there is the Halafian cultural expansion, originating in Upper Mesopotamia; then we also have to consider the Semitic cultural and linguistic expansion, originating in Palestine; finally we have to consider the Indoeuropean waves: first the Anatolian group (Hittites, etc.) via the Caucasus, later the Balcanic group of Phrygians (and probably Armenians as derived branch) and finally the Iranian one from Central Asia. Even within the Semitic expansion there were probably several waves as well. All together must have significantly reshuffled the genetic landscape of the region. 

But unless we get more ancient West Asian DNA it will be most difficult to discern clearly how all that played out. After all the Syrian Euphrates can be exceptional in many aspects, being right in the middle of all: a true pivot of the Fertile Crescent, subject to pressure from all directions. 

Ample analysis of the genetics of European (Ashkenazi) Jews

A new paper on European (Ashkenazi) Jewish genetics is available:

Ehran Elhaik, The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses. arXiv 2012. Open access. [arXiv:1208.1092v1 [q-bio.PE]]

(Supplemental material available HERE). 

The author prefers to use the term European Jews to that of Ashkenazi, because Ashkenaz is traditionally Germany and this may imply certain assumptions about the origins of this population, i.e. the Rhineland model, which he intends to contrast with the Khazar model and what he calls the Judean model. 

No intention exists in all the paper of investigating the Anatolian model, by which Western Jews would be descendants, in essence, not so much of Iron Age Jews from Palestine (Judean model) but neither from Europeans, be them Western (Rhineland model) or Eastern (Khazar model), but rather of Hellenistic converts from areas like Cilicia or Cyprus.

This alternative model is clearly supported by autosomal genetics, in this and previous papers. However haploid genetics seems to point to different sources.

In the paper, European Jews were roughly subdivided into Eastern (Belorussia, Latvia, Poland, and Romania) and Central (Germany, Netherland, and Austria) European Jews: EEJ and CEJ respectively in the graphs. They show some but not well defined structure however.

I'd say that the core of the paper's interest is in the following graphs:

1. Autosomal PCA:

Fig. 3 PCA scatterplot of West Eurasians (click to enlarge)

Again, as in previous analysis, including mine, Western Jews, in this case the European or Ashkenazi subgroup appears to cluster near Cypriots, suggesting a Southern Anatolian main origin (Tarsus area) very likely. However this region (ancient Cilicia) is still to be directly compared with Jews (I know it's just it's fine tuning but still when you have a theory, you'd like to see it reality-checked).

Another possibility would be hat this clustering is an artifact, assuming diverse origins homogenized by Jewish endogamy since the Middle Ages. But the fact that all three Western European subpopulations (Ashkenazi, Sephardi and Moroccan) tend to cluster over there (when they do not behave as fully distinct, as happened to me with all but Sephardites earlier this year).

Not shown here is fig. 7 that lists proportions of shared IBDs with West Asian and Caucasus populations (only): Caucasians are highest (roughly 9%), followed by Palestinians (c. 7%), while most groups are at c. 5% (except Lebanese who are at c. 3%).

In general this data supports some but limited Palestinian connection and a much more northernly origin of Western (or at least Ashkenazi) Jews. This is consistent with previous data (see below).

2. Haploid or uniparental relations:

Fig. 7 Relative affinity of (A) mtDNA and (B) Y-DNA of European Jews

Note please that the map is awfully drawn in some key details, for example the dark areas in Kurdistan correspond in fact to Lezgian (from Daghestan, in the NE Caucasus) and another one I don't discern well but that begins with I and hence must be an Iranian or Indian group, not Kurdish. The center of the "Kurdistan" affinity hotspot must be hence much farther NE, in Daghestan or Azerbaijan.

So by uniparental lineages, European Jews do appear as a mixture of Western (strongest in Y-DNA) and Caucasian lineages (strongest in mtDNA), supporting both the Rhineland and the Khazar hypothesis in a combined way. However no comparison with Cypriots nor Southern Turks was made, and these are the populations to whom Western Jews show most direct affinity by autosomal DNA, being Cilicia one, if not the largest, hotspot of the Jewish Diaspora in the Roman Era, a most likely realistic origin for

See also previous analysis:

• My own amateur analysis: (Sephardi) Jews in the context of the Levant and Anatolia
• Discussion on Behar 2010 at Leherensuge (my old discontinued blog)
• Discussion on Atzmon 2010 at Leherensuge

 

(Sephardi) Jews in the context of the Levant and Anatolia

In June 2010, in rapid succession, we had the opportunity of learning from two papers which studied Jewish genetics in the context of wider samples.

The first one (Atzmon 2010 - PPV, discussed by me here) showed us, even if hidden in the supplementary material only, that the main Jewish cluster was extremely close to their "Turks and Cypriots" sample, specially to some of them (Cypriots apparently):

This central or pivotal group of Jews, marked as GRK+TUR and SYR, are the so-called Sephardi, which, in spite of their name (Sepharad means Spain) do not necessarily originate in the Iberian peninsula but rather share historically a pan-Mediterranean type of ritual, distinct from that of Ashkenazim and other Jewish populations (see also this article if you wish to understand better the complexity of Jewish ethnic divisions).

Just a few days later we got Behar 2010 (also PPV, discussed here), which did not deepen enough in the component analysis, in my understanding, but determined at least that Western Jews (Sephardi, Ashkenazi and Moroccan Jews) were of West Asian origin apparently.

However how exactly they related with West Asians was mostly unresolved (excepting that Palestinians have a lot of genetic distinctiveness and this was not shared with modern Jews nor nearly any other population at any meaningful level).

So, as I began toying around with ADMIXTURE, using the very basic but functional instructions by Razib, one of the ideas I had to explore were Western Jews (other Jewish communities seem to be derived from their host populations but Western Jews appeared as West Asian in these studies).

Extreme distinctiveness of Ashkenazim and Moroccan Jews

I doubted whether to retain the Ashkenazi and Moroccan Jewish samples or just work with Sephardites. In the end I retained them... but then I had to correct and start all over. Why? Ashkenazim specially cluttered the analysis with their extreme specificity (possibly because of some extreme bottleneck in their origins and/or inbreeding, although I can't say for sure).

The results were hardly a satisfactory answer for the question I meant to ask: how do Western Jews relate with the diversity of Anatolia and the Levant, the area where they probably originated? But rather placed these two communities as extremes in the area studied, as unlikely references rather than being referred to the wider native populations. Example:

Instead Sephardi Jews showed up as less strikingly monolithic and had been found in previous studies to be, quite obviously, central to the Jewish diaspora. So I decided to start all over retaining only Sephardi Jews, which should be enough to give the key answers about Western Jewish origins.

Analysis using only Sephardites

This analysis was more productive. The whole run is as follows:

The deeper K levels are not really too informative, specially not for the matter at hand, the origin of Sephardi Jews (and by extension all Western Jews probably). Probably the greatest interest is between K=4 and K=6. I decided to retain the last one as main snapshot:

The labels of the components in the last two images (bottom and right respectively) are a mere conceptual reference. 

Kebaran (source)

Since K=2 there is an obvious distinction between Palestinians and the rest. This is coincident with what we find in Behar 2010 for example and what I have found in previous analysis: that Palestinians show a marked distinctiveness even in West Asia. My hypothesis is that they retain best a distinctiveness that may be as old as the Kebaran culture or even older. I understand that this means that, very possibly, Palestinians are the true descendants of historical Jews, Canaanites, etc.

Early PPNB (source)

However this analysis was not designed to discern Palestinian affinities but those of Jews, so I won't discuss this farther. Just to say that if the Palestinian pole is akin to Kebaran-Natufian-PPNA, then the other main detected cluster, shared abundantly by everyone in the region, could well be akin to PPNB.

In any case, the result is that, no matter how deep you go, Sephardi Jews are not clearly distinct from other West Asians, specially not from Cypriots and most often than not also not distinct from Turks. The main difference is certain very weak and slippery relation with Palestinian and other Levantines. 

Particularly, component K5 (pop4 in the Fst table, blue in the bar graph), which I labeled as Palestine1, stroke as quite interesting. This component is most common among Palestinians (15% at K=6) but second most common among Sephardi Jews (5%), being smaller among all other populations analyzed. It is possible, I speculate, that this component is a remnant of a genetic link between the Palestinian population, long ago of Jewish religion and identity most likely, and the Diaspora Jews, most of whose ancestry seems to have other origins.

It would be, in this regard, most interesting to analyze genuine Palestinian Jews, descendants of those c. 10% Palestinians of Jewish religion who existed before the Zionist colonial project began, sadly even this notion of Palestinian Jewish has vanished or been erased, even if it was once common enough.

Regardless, in almost everything else, Sephardi Jews are identical to Cypriots and Turks, what suggests that my idea of Western Jews having originated not in Palestine but in the Hellenistic Diaspora, which was largely product not of emigration but of proselytism (and in this context early Christianity was just a Jewish sect of messianic character). 

It remains to see how Ashkenazi and Moroccan Jews fit in this description. But while I had to renounce to analyze them, all the previous data strongly suggests that they are not too distinct from Sephardi Jews and should share at least partly that same origin, followed by intense bottlenecks.

_______________________________________

Update (Jan 11): before I forget, I must mention this other paper (that I did not know about) mentioned by PConroy in the discussion:

Avshalom Zoossmann-Diskin, The origin of Eastern European Jews revealed by autosomal, sex chromosomal and mtDNA polymorphisms. Biology Direct 2010. Open access.

The author finds Eastern European Jews (the bulk of Ashkenazim) to be of essentially European origin mtDNA-wise, with special mention to Italy.