May 7, 2015

Neolithic mtDNA from the Seine basin

Finally we get some ancient DNA from the French demarcation, which should be one of the focus of the research, because of the importance of the territory of the French state in European paleo-history since the depths of the Paleolithic.

This data set is, in spite of its limitations, most important because it seems to support the notion of Megalithism being an important factor in the formation of European populations as we know them.

I strongly recommend reading the whole paper because it does not only deal with the genetic aspects but also offers excellent background on the archaeological context of the region to which these (non-monumental) burials belong to.

Maïté Rivollat et al., When the Waves of European Neolithization Met: First Paleogenetic Evidence from Early Farmers in the Southern Paris Basin. PLoS ONE 2015. Open accessLINK [doi:10.1371/journal.pone.0125521]


An intense debate concerning the nature and mode of Neolithic transition in Europe has long received much attention. Recent publications of paleogenetic analyses focusing on ancient European farmers from Central Europe or the Iberian Peninsula have greatly contributed to this debate, providing arguments in favor of major migrations accompanying European Neolithization and highlighting noticeable genetic differentiation between farmers associated with two archaeologically defined migration routes: the Danube valley and the Mediterranean Sea. The aim of the present study was to fill a gap with the first paleogenetic data of Neolithic settlers from a region (France) where the two great currents came into both direct and indirect contact with each other. To this end, we analyzed the Gurgy 'Les Noisats' group, an Early/Middle Neolithic necropolis in the southern part of the Paris Basin. Interestingly, the archaeological record from this region highlighted a clear cultural influence from the Danubian cultural sphere but also notes exchanges with the Mediterranean cultural area. To unravel the processes implied in these cultural exchanges, we analyzed 102 individuals and obtained the largest Neolithic mitochondrial gene pool so far (39 HVS-I mitochondrial sequences and haplogroups for 55 individuals) from a single archaeological site from the Early/Middle Neolithic period. Pairwise FST values, haplogroup frequencies and shared informative haplotypes were calculated and compared with ancient and modern European and Near Eastern populations. These descriptive analyses provided patterns resulting from different evolutionary scenarios; however, the archaeological data available for the region suggest that the Gurgy group was formed through equivalent genetic contributions of farmer descendants from the Danubian and Mediterranean Neolithization waves. However, these results, that would constitute the most ancient genetic evidence of admixture between farmers from both Central and Mediterranean migration routes in the European Neolithization debate, are subject to confirmation through appropriate model-based approaches.

The studied sample comes from Gurgy (NW Burgundy, near Auxerre) and is very large: 55 successful SNP-defined haplogroups, 39 HVS-I sequences, including 27 distinct haplotypes. The burials are dated to the 6th millennium BCE, when the area was reached by Neolithic. The following haplogroups were found (table S1):

  • HV: 22, of which:
    • V - 2 (4%)
    • H - 20 (36%), of which:
      • H* - 6
      • H1 - 10
      • H3 - 4
  • U - 20, of which:
    • U* - 3 (5%)
    • U4 - 1 (2%)
    • U5 - 5 (9%)
    • K - 11 (20%)
  • JT - 8, of which:
    • J - 6 (11%)
      • J* - 4
      • J1 - 2
    • T - 2 (4%)
  • X - 2 (4%)
  • N1a - 3 (5%)

For some reason the total I get from table S1 is 51 individual haplogroups instead of the 55 expected ones. I have double and triple-checked and can't find the four missing sequences, sorry. Count corrected (May 9): there were indeed 55 sequences (my bad).

In any case the mtDNA pool is surprisingly "modern" with most haplogroups in very similar frequencies from what we would find in present day Western European populations. This is not at all like what was found in Germany's Neolithic, at least initially, characterized by low frequencies of H and high frequencies of presently rare haplogroups like N1a, being instead more similar in its "modernity" to what has been found in the Basque Country (see HERE for a quick reference).

This suggests that we have in Neolithic Europe the following regions, judging on the "modernity" of their mtDNA pools (only):
  1. Central Europe (Germany, Hungary): low H, clearly "pre-modern"
  2. Mid-Western Europe (France, Basque Country): normal H and roughly also other lineages, almost "modern"
  3. Portugal: seemingly very high H, "hyper-modern"

And this strongly hints again, along with the early presence of lactose tolerance among Chalcolithic Basques and the massive consumption of dairies among British farmers (of North French origin) to an Atlantic Neolithic origin of at least the bulk of the genetic pool of modern Western Europeans.

Sadly for the fans of patrilineal genetics, no single Y-DNA sequence could be produced.

Mostly Danubian origins?

Paradoxically these early farmers from Burgundy do not seem strongly related to the South, at least not judging by the North Iberian data used as reference but rather to the Danubian Neolithic peoples of Germany instead. This is most apparent in the haplotype graph of fig. S7:

Fig. S7 - Median-joining network

We can see that most Gurgy haplotypes (red) cluster with Danubian Neolithic ones (green) rather than with North Iberian (blue) or Paleolithic ones (purple). Basically there is only one clear exception: an H lineage that seems indeed more related to the South than to Central Europe but the red-green exclusive connections are much more common. 

However when analyzed statistically, the Gurgy population appears intermediate between the Central European and North Iberian ones. For example:

Fig 1. Principal Component Analysis (PCA) on the ancient mtDNA dataset.

Not sure if this is yet another warning about the limitations of statistical analysis or instead suggests that there is more importance of the southern ancestry but that it has a different origin in Occitania (SE France) that is not being taken into account. 

My best hunch is that the statistical result is product of the relative affinity to Basque Neolithic (the "modernity" of the overall pool as discussed above, Basque samples are by far the most numerous of Northern Iberia) combined by a more direct affinity with the German Neolithic in the detail of the sequences. 

Closer to Chalcolithic than to Early Neolithic populations

There is no haplotype structure to consider here but the statistical analysis that the authors perform does find that the Gurgy population was, oddly enough, closer to later populations in both Germany and Iberia than to their contemporaries. If this could be confirmed, we would have a candidate population for the origin of the changes that affected Europe (at least Central Europe) in the early Chalcolithic (prior to the Indoeuropean invasions). 

Fig 4. Pairwise FST distances.

It is apparent in the above figure that FST distances of the Gurgy population are much shorter (hence probably more related) with late Neolithic and Chalcolithic populations of both Central and Southwestern Europe than with any population that pre-dated the abandonment of the necropolis. Among these however it is Karsdorf the one most closely related, reinforcing the notion of a mainly Danubian origin, albeit a bit peculiar one (Derenburg, Halberstadt and the average "PRE_Central_F" are not particularly close).

But the most interesting part is surely the much greater affinity to the populations after the 4000 BCE chronological divide, which is also the baseline of the expansion of the Megalithic phenomenon. This matter requires more detailed analysis but it does suggest that the Franco-Basque area could well have been important in the formation of Chalcolithic and therefore modern European populations in the Western half of the subcontinent. A vehicle for this demographic "reform" should have been Megalithism, no doubt.

But we do need more data, sure we do.