June 6, 2014

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 accessLINK [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. 


  1. Maybe the bulk of west-asian moved into Europe and left nearly nothing behind.........everyone has it in Europe except NE Europeans.

    1. ... "everyone has it in Europe except NE Europeans."

      Early European Neolithic ancestry is not the same as {West Asian + NE African} ancestry but at only partly so - or so it seems.

      Between the West Asian Neolithic and the European Neolithic there is:

      1. A bottleneck or founder effect.
      2. Important admixture with European aborigines from the Balcans.

      It's not just masses of Anatolians, so far undocumented in the archaeological record but something more subtle and complicated. Farming arrived from West Asia for sure, as did some of the ancestry (even if some of it is ultimately original from NE Africa, what points rather to Palestine than to Asia Minor) but what about pottery? Thessalian farmers were making pottery in troves, just a few centuries after farming arrival, when in West Asia it was a total novelty yet. This pottery concept may have arrived from NE Europe, where it arrived (fist in all West Eurasia) from China via the Taiga carried by the proto-Uralic migration.

      It's complex.

      "Maybe the bulk of west-asian moved into Europe and left nearly nothing behind..."

      I can't but take this as a joke, although I suspect you mean it seriously, right?

      Well, that's against all the logic of demic migrations and founder effects. Millions of Europeans migrating to America have not depopulated the Old Continent at all: people only migrate because they really need it, usually because of overpopulation, land robbery or persecution. Most of their relatives remain behind in any case.

      Of course it is theoretically possible that the the founder population could be totally exterminated but seems very unlikely on first sight. Much more likely is that the few migrants carry certain characteristics that are randomly non-representative of the original population. This is known as founder effect: http://en.wikipedia.org/wiki/Founder_effect. Sometimes it's also said to be a "bottleneck", although the meaning of this concept is much wider and "senso stricto" implies mass mortality and no migrations. The effect is similar however.

  2. You are confused in thinking the populace is the same as today. movement in ancient times exhausted the populace in an area and the replacement people quickly took over the old markers.

    next issue is - all the people in anatolia except the assyrians are non-Semitic people, these hittities, phyrigians, lycians, luwians etc are non-semitic people.

    Who are your west-asians?

    what is the % of semitic and non-semitic for west-asians?

    1. "all the people in anatolia except the assyrians are non-Semitic people, these hittities, phyrigians, lycians, luwians etc are non-semitic people.

      Who are your west-asians?"

      All those you mentioned are Indoeuropeans of the Anatolian branch. But you (purposely?) ignored all the pre-Indoeuropean peoples of West Asia: Hattic, Hurrians, Sumerians and Elamites at the very least.

      You also ignored that ancient Cretans, who arrived from Anatolia by all accounts, were not Indoeuropean speakers either. Nor were probably the ancient Cypriots nor the Etruscans who again seem to stem from Anatolia, nor their historical relatives from Lemnos, just in front of Troy.

      The Anatolian Indoeuropeans arrived from beyond the Caucasus with the Kura-Araxes culture only after 3500 BCE, the Phrygians and their probable easternmost offshot, the Armenians, arrived from the Balcans much later (and their language seems closely connected to Greek, and their origin seem to be in the Bryges of Paeonia).

      Between ancient and modern times we can document the following (pre-IE) linguistic families or languages of unknown affiliation in West Asia and derived colonization areas:
      → Semitic (only Asian representative of the wider Afroasiatic family)
      → Elamite (possibly related with Dravidian)
      → Sumerian
      → Hurrian (arguably related to NE Caucasian
      → Hattic (arguably related to NW Caucasian)
      → Kartvelian
      → Eteocypriot
      → Eteocretan
      → Tyrsenian (at the very least Lemnian must be considered)

      As the Levant and Central Iraq (and probably all Arabia) were incorporated to the Semitic area at the dawn of History, the greatest linguistic diversity was probably in the Anatolia/Caucasus/Kurdistan area, because further South only Sumerian and Elamite survived to the historical period.

      Hurrian, Hattic, Kartvelian, Eteocypriot, Eteocretan and Tyrsenian (Pelasgian?) are enough non-IE linguistic diversity to not allow any room for IE existing in Anatolia and expanding from there in the Neolithic as suggested by Renfrew and such. It does not make any sense that IE expanded from Anatolia to nearly everywhere but was unable to consolidate its alleged homeland against such a diversity of competitors.

      Also the only historical European languages that can reasonably be tracked to the First Neolithic wave via archaeology and genetics are Iberian and Basque (probably Ligurian too but this one is almost not documented). So even in the wake of the Neolithic wave we see not a single trace of IE.

      Renfrew is a fraud.

    2. Well, "fraud" is a bit too aggressive and maybe even unfair. But his hypothesis clearly finds all kind of obstacles at every corner. It is just popular because of modern "civilized" Indoeuropean Nationalism.

      But it does not work, it fails completely to explain the facts, while Gimbutas' Kurgan model instead fits perfectly with every detail. Gimbutas rocks!

    3. "Also the only historical European languages that can reasonably be tracked to the First Neolithic wave via archaeology and genetics are Iberian and Basque (probably Ligurian too but this one is almost not documented)."

      No love for Paleo-Sardinian?

      Re: the Anatolian Hypothesis - I think that recent study on the origins of R1a provides a good explanation. An early Zarzian input into both Anatolia and pre-Indoeuropean would explain there be some common features without necessarily being genetic relationship between the two languages.

    4. "No love for Paleo-Sardinian?"

      Also. Just that it is like Ligurian and many other candidates: not documented beyond toponimy and substrate legacy. Instead Basque and to some extent Iberian are much better documented.

      On the other issue: there's no obvious link of any kind between R1a and European Neolithic. I'd rather think it represents (at least in Europe) some sort of Epipaleolithic migration later amplified by the Kurgan expansion. The main R1a subclade in Europe is best associated with Corded Ware or something like that.

      In South Asia instead it might still be associated with Neolithic, at least considering the geography, but in Europe: what has the area around Kiev to do with Neolithic? Nothing obvious.

    5. Whatever the timing, it affected both Kiev and Anatolia so it seems logical that whatever process spread R1a could have brought a few linguistic links with it. If so, then Renfrew would be correct in seeing links between Anatolian languages and Indoeuropean, but wrong on the reasons why these links exist.

    6. It's not about the timing: I'm talking about R1a-Z282, which is the bulk of European R1a by far. This lineage is centered and probably expanded from somewhere near Kiev or Minsk, what is precisely where we should not see any significant Neolithic impact, much less become a center of it.

      The Anatolian family is a very old distinct branch of the IE family but that does not mean it originated in Anatolia. It is not necessarily the same as "Anatolian languages", which may include all languages spoken in Anatolia at any time of history or prehistory. Notably the Hattic, the Hurrian and the Tyrsenian are likely "Anatolian languages" that have no apparent relation with Indoeuropean. Eteocypriot and Eteocretan are often also related to the peninsula, although less clearly so (and again not IE).

      I am not aware about Renfrew seeing any linguistic "links" anyhow and in fact this diversity and non-indoeuropeanness of so many Mediterranean and West Asian, and specifically Anatolian languages, what has become one of the greatest obstacles for his hypothesis. Another one is that the First Neolithic peoples of some key areas of Europe, Central Europe particularly, were clearly replaced in the Chalcolithic. Another one is his dependence on the Kurgan model to explain the Tocharian and Indo-Aryan expansion. And finally the main one is that the Kurgan model just rocks: explaining all very well in terms archaeological and cultural.

      Another issue is whether there were massive IE migrations: almost certainly not. There were massive IE conquests and assimilation of new subjects into their cultural frame (with whatever modifications).

  3. Excellent analysis and I'm happy that you are blogging again. I looked for modern FMS samples of K 16224C,16311C,16366T, but did not find any. Also, there are no members in the FTDNA K project with 16366T, so it appears this lineage did not migrate to Europe.

    It would be very helpful to have a FMS test for the Druze sample to see where this lineage fits in the K mtDNA phylotree.

  4. Worth noting IMHO that the Druze aren't included on the heat map. If they were you'd probably see a greater signal for the Israel/Lebanon/Syria area. Pity there are no Lebanese samples in the study.

    1. There is a Lebanese sample, if you're talking of Behar 2010. At least they are present in the ADMIXTURE graph.

    2. No, referring to this paper. Would have been nice to see a Lebanese sample compared to PPNB mtDNA.


Please, be reasonably respectful when making comments. I do not tolerate in particular sexism, racism nor homophobia. Personal attacks, manipulation and trolling are also very much unwelcome here.The author reserves the right to delete any abusive comment.

Preliminary comment moderation is... ON (sorry, too many trolls).