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.