May 04, 2015

Ancient mtDNA from Neolithic France

PLoS ONE 10(4): e0125521. doi:10.1371/journal.pone.0125521

When the Waves of European Neolithization Met: First Paleogenetic Evidence from Early Farmers in the Southern Paris Basin

Maïté Rivollat et al.

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.



Gioiello said...

"Gurgy is localized in the southern area of the Paris Basin, which lies at the westernmost part of the LBK cultural influence (S1 Fig and S2 Fig) [2,24]. The Gurgy necropolis shows a potential RRBP cultural tradition (clearly LBK derived) in terms of burial type, position or orientation (S1 File) [64]. However, some archaeologists have observed parallels with western Switzerland [34] and demonstrated cultural exchanges between Paris Basin populations and groups from southern France associated with Cardium and Chasséen cultures [27,28,30,65] [...]
We propose that the archaeological data and the paleogenetic results obtained on the Gurgy necropolis are consistent with the hypothesis that the Mediterranean cultural influence on the Paris Basin entails some gene flow, implying the northerly migration of Mediterranean farmers in the Paris Basin and admixture with farmer descendants of LBK populations from Central Europe. As proposed by Sidéra [29,69], exogamy between groups might explain the fusion of the material culture of both Central and southern Neolithic spheres in the Paris Basin and the mixture of southern/Central Europe farmer lineages observed in the Gurgy necropolis [...]
Consequently, farmer groups from the Late Neolithic period were formed from a mosaic of maternal lineages from diverse European origins, and this mixed constitution might explain the genetic similarity of these farmer groups to Gurgy [...]
PCA revealed genetic differentiation between modern populations from the Near East and those from Europe (S4 Fig) and high genetic homogeneity of modern European populations [...]
The map specifically reporting these shared informative haplotype frequencies shows interesting hotspots in Turkey and the Balkan Peninsula and along Danube Valley and the Mediterranean shores (S6 Fig). Thus, the geographic distribution of these informative haplotypes in modern European populations might reflect some aspects of alleged Gurgy group history, i.e., the scenario proposing that the group comprised an admixture between the descendants of the farmers from Danubian and Mediterranean expansion routes, who are the descendants of farmers from the Balkans and Anatolia [...]
However, we are fully aware that these data do not definitively prove admixture between farmers associated with both Neolithization routes and that the proposed admixture model must be tested under a robust analytical framework, such as the coalescent theory that would account for genetic drift and population demography within a gene genealogy".

Gioiello said...

GLN 276 Male Adult 2006 Yes A24, M2, M3, M4 RM1, RP2 10550G 11467G 12705C K 16093C 16224C 16234T K
GLN 276 C C A C T T T A T A C C A T G T G G C G A G G C T G K
L2* L3* M* C D N* A N1* N1a I W X R* R0* HV* H H H1(J1) H3 V B R9 J T U* U4 U5 K
2885 3594 10400 13263 5179 10873 4248 10238 13780 10034 3505 6371 12705 11719 14766 2706 7028 3010 6776 4580 8280 13928 12612 1888 11467 11332 13617 10550
Individual C/T T/C C/T A/G C/A C/T T/C T/C A/G T/C A/G C/T T/C A/G T/C G/A T/C G/A T/C G/A C/G G/C/A A/G G/A A/G C/T T/C A/G Hg

Very likely there already was a K1a1b1a believed "Jewish" with the mutation C16234T.

Gioiello said...

Of course this sample could be also K1a8a, having also 16093C, even though in the aDNA it could be due to a mutation post mortem:
DQ301816 Behar Haplogroup [K1a8] 20-JUN-2007
A73G A263G C295A 315.1C C497T A750G T1189C A1438G A1811G A2706G A3480G A4769G G5821A C7028T C7927G A8860G G9055A T9698C A10398G A10550G T11299C A11467G G11719A A12308G G12372A C14167T C14766T T14798C A15326G T15850G T16093C T16224C C16234T T16311C T16519C

eurologist said...

This is good work and seems to substantiate the theory of admixture between Mediterranean and Danubian Neolithic in the Paris Basin.

While these two groups likely spoke languages from +- unrelated families (Levantine/ S-C Anatolian vs. NW Anatolian/ Balkan), the common and shared admixture with HGs indicates that language and cultural barriers weren't all that steep and difficult to overcome.

Fig. S6 is interesting - it seems to indicate that the East has largely been overrun with different mtDNA since the early Neolithic (i.e., not just with males).

Unknown said...

I really wished they had not pooled the data from the different populations for Figure 1. I would have liked to look at the diversity.

PreHG is populations older than 4000 BCE that are deemed to be Hunter Gatherers. Most but not all are from the far north. Some samples are very old, others are very young and I find the labelling of these as PreHG cynical. Of the 5 PreHG with mitochondrial haplogroups ALL are considered to be H3/H1/H. The only U they mention in any of the groups was in the Gurgy samples, which is surprising (and unlikely).

For some reason the results for Post-HG (30 samples) are left out of the final paper.

Basically the paper says that the Neolithic French look like a mixture of southerners and northerners. Quelle surprise.

cosasdehombres said...

Why not to do a complete mithocondrial analysis? At this time is a must, not a choice. And more, they could not make a Y-DNA, because of the bad qualities of the material? Cause otherwise, if it´s only a "we prefer to save the money" it´s a pain. As I suppose they have access to those individuals -and the rest of the genetic community will not have this access. We need to replace those mtDNA only (and worst mtdna partial!) with mtDNA, YDNA and autosomal. The techonology and costs are affordable

Unknown said...
This comment has been removed by the author.
Gioiello said...

A pearl. "Only three samples sharing a haplotype (K characterized by a 16,224C mutation) [...]", p.6. Has anyone said them that T16224C is one of the three fundamental mutations in HVRI of hg. K*? What have they to teach me about mtDNA?
Of course I agree with whom said above that only an FMS could permit to link these samples of aDNA with modern ones. It doesn't seem to me that there is evidence from these data of the two supposed routes of migration from Middle East to Europe, which seems better an idée recu than a demonstrated one. As to what I said above, only an FMS could say if the K sample may be linked with the K1a1b1a of to-day, if 16093C is a mutation due to methylation or if it continues the mutation present in hg. K from its origin, if the very rare mutation in 10873T is real or due to contamination with the hg. N samples present there, and if it could be a sample of K1a8 o K1a8a and if it is linked to the Middle Eastern samples or the demonstration that the Ashkenazi samples of K1a8 of to-day have an European origin.

Alexandros said...

Very interesting data (as with all aDNA data), but unfortunately the authors did not make the best of what they had in hand.

A major issue I see is the lack of comparison with the Near Eastern Neolithic farmer haplotypes from Fernandez et al 2014 (DOI: 10.1371/journal.pgen.1004401). If you want to investigate Neolithic farmer migrations into Europe, you really need some comparisons with the source population!

Another issue is the seemingly unrefined comparison between the Neolithic French haplotypes and modern population haplotypes (especially modern Near Eastern populations). The authors decided to clump populations together, which may make some sense, however they are losing useful information on shared haplotype analysis, since their meta-population groups are quite broad.
The authors also seem somewhat uncertain on how to group some populations. For example, the Cypriots are at some point grouped with Southeastern Europeans, like Cretans, mainland Greeks and other Balkanic populations (Table S5), they are later group as 'Turkey-Kurdistan-Cyprus' (Table S7) and finally at Table S11 as 'Syria-Jordan-Palestine-Cyprus'. Why not study Cypriots and other surrounding populations separately?? If anything, these are the places where agriculture first appeared and studying these populations separately may give some insight into the source locations of the spread of agriculture into central Europe.

A minor but important issue, the labels in the PCA plot in Suppl Fig S4 are so huge, that makes it a struggle to make any sense of the data.

Overall a useful study, especially the raw data!