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]

Abstract

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.

23 comments:

  1. Very interesting indeed!

    My eldest daughter's maternal ancestry goes back to Northern France (Champagne district) and she is mtDNA H*

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  3. Indeed, there are 55 samples with mtDNA results on the S1 table on the following link: http://journals.plos.org/plosone/article/asset?unique&id=info:doi/10.1371/journal.pone.0125521.s009

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    1. You are right: when I count them linearly, without paying attention to the haplogroups, I get 55, but when I count the haplogroups separately, then I get only 51, why? Where's the stupid error I'm so obviously committing?

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    2. OK, I found them: I had not counted 2 K, 1 N1a and 1 U*. Corrected and thanks for the pressure.

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  4. Maju, Recent Allentoft et al. don't excite you?:).

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    1. Honestly, I only had time to read it shallowly yet. It's not a matter of this or that stuff exciting me, it's just that blogging, giving my opinion, discussing... does not excite me anymore as it used to.

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    2. Maju, You are getting depressed, well don't!! keep the fighting for truth on.....

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    3. Call it what you will. My opinion is that I'm just one among seven billion people and that many others could do the same task and if they are not up to the task, why should I be?

      Why should I be the one who is not all the time thinking selfishly: family, car, money, luxury expenditures. Where is my little cabin by the beach?

      I've been fighting "for truth", as you put it, since I was 15 or so. I'm now 47, time to retire very possibly.

      Anyhow, too much information banging my brain for any good. Overloaded.

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    4. Maju i suspect you are not doing it the right way otherwise you wouldn't face such frictional thoughts.
      Age is not the issue but attitude is, you can't compare yourself with others is matter of type every person is of different type though interested on the same subject(s) hence they express their interests differently...

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    5. I can compare myself with others, of course. It's not that we are all identical or anything like that but I'm not doing anything particularly notable either. Everyone is replaceable and everyone MUST be replaceable anyhow.

      There are several reasons for this: (1) if you "are many", you can't be killed or otherwise destroyed, the enemy, the cabal of liars is rendered powerless, (2) social progress depends of the very success of this fact: nothing is gained unless it is generalized, the teacher lives on through his/her pupils, (3) people has the right to give up, to get depressed, angry, sick or lose their mind (or even dead, as we all must); if what they are doing is really important someone else will take the position: not one but many - but we have to be humble enough to consider that maybe what we do is not that important after all.

      Age is indeed an issue. I have reached an age in which almost every single individual from the times I discuss in this blog was dead. People used to die at my age. In some countries that is still true today. Our closest biological relative, the chimpanzee, almost never live past 50, even in pampered conditions. We do: but it is unclear why we do live so long in clear decline. Also in my opinion this lengthy extension of human life hinders progress because old people have a hard time changing their mind and learning new stuff and progress needs of open minds: today our biology is backstabbing us, because if occasional elder wisdom was an asset in times past, today generalized elder stubbornness, clinging to obsolete values and ideas and very especially to power resorts, is a burden for the greatest part. There are many honorable exceptions but that's the general trend.

      Every single breakthrough scientist, every single revolutionary leader... did their job before their 50s, often in their 20s and 30s.

      My time is passing and I know it. I do realize that my mind can't keep up with all the information anymore, my body demands less time on the chair and before the PC, but very especially, I'm losing my curiosity, my very love for learning and even sharing (you grow grumpy and misanthropic too, particularly if you are of the kind of person for whom being with people, even if virtually so, is not a treat but mostly a burden).

      If Humankind wants nice things, Humankind will have to work them, to create them, to fight for them, and not just consume stuff mindlessly.

      There will be others, don't worry. I have absolutely no doubt: the processing power of the global cooperative mind is only growing as we speak. No single particular individual is irreplaceable, much less me.

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    6. Maju just do not give up and its not burden but your destiny....

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    7. Fuck destiny! No self-respecting being accepts destiny.

      As many other things through my life, I have even studied to great depth matters of "destiny" like Astrology, and I can tell you one thing: destiny is just a stupid cage worth only the effort to smash it to nothingness. Creativity and willpower, as well as consciousness and sensibility is our divinity, the so-called destiny is just another challenge and accepting it is only fit for cowards.

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    9. Destiny is made up by decisions or indecisions. If destiny would be as overwhelmingly dominant as you imagine it, we'd be robots and would never need to take any decision whatsoever. Our decisions would not matter at all and therefore all you could say would be totally pointless because the path would be strictly set, no matter what we decide or not decide.

      Anyhow people like me don't have focus nor patience: our destiny is not having it. Saturn in Aries if you want to analyze it in astrological terms. Let the people with Saturn in Taurus or whatever focus and be patient, we are just not that way: we are impulsive!

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  5. Maju, you can't just give up what you do so good its your destiny and that destiny is related to focus and patience, unless you are under the impression that you have known everything to know...

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  6. Maju, i understand you dilemma but i'm not talking about Astrology etc but your work!, you must keep doing it without thinking of the results, age, what you got and didn't etc etc, if you are not enjoying it anymore then you have lost your focus.

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    1. There is no "you must", that's for slaves.

      There is "you can", there is "you want" and there is "you will".

      It's not about results, it's about the tic-tac of life's clock, it's about things having their time, it's about moving on, it's particularly about being able and wanting.

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    2. Maju, so you are ''unable'' ok....

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  7. I've enjoyed your blog and respect your opinion. If you slow down or drop out, then thanks for what you have posted so far.

    This is a big study, bigger than the reich et. al one in my opinion. I think the fact it goes totally unmentioned by most sources shows the huge bias you have been struggling against so I do not blame you for growing weary.

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    1. I want to discuss it, just I don't seem to find time to even properly read it. I have made some comments at Bell Beaker Blogger's take on it though, notably re. lactase persistance, which is shockingly very low on this massive sample, an absence I attribute to the lack of Western European samples (both Chalcolithic Basque and Megalithic Swedish have much more than any of those, implying that the European LP allele must have expanded from West to East).

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  8. @Groggard That study of 101 is useless to read !
    because to much attention was given like before to the Yamnaya and the narritive that Yamnaya were coming out of some Steppe at Black or Caspian Sea and massively migrated to central Eur. to became BB . --- While in fact all the known data suggest that Yamnaya Y-Dna including one I2a who they now say was Catacomb, was derived from some Comb-Ware culture and no Steppe was even populated before Neolithic or regularly roamed by mesolthics cause the lived by the Rivers like at the Dnepr Rapids.
    in order to testify from where the Bavarian BB R1b-L51 were appearing or were in the mesolthic as still not splitted , Other Regions should been studied

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  9. You got what you asked for: http://forwhattheywereweare.blogspot.com/2015/06/alentoft-2015-more-ancient-dna-from.html

    There's a donation button on top left. Took me hours!

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