February 15, 2013

Der Sarkissian's NE European ancient DNA formally published

This entry is a bit redundant because a previous version of this paper (presented as doctoral thesis) was already discussed in length months ago. Let us recall that this study provided the first confirmed (by coding region testing) mtDNA sequence belonging to haplogroup H in Northern Europe prior to the Neolithic*

Clio Der Sarkissian et al., Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe. PLoS Genetics, 2013. Open accessLINK [doi:10.1371/journal.pgen.1003296]


North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans.

As you may realize, the Sardinian sequences discussed also in the thesis are not part of this paper. Also the emphasis is on the presence of Oriental lineages (C*, C1, C5, D* and Z1a) in North-Eastern Europe prior to the Neolithic, which is, no doubt another element of interest.

Table 1. Results for mitochondrial DNA typing
Yuzhni Oleni Ostrov is in Karelia,Popovo in Northern Russia and Bol'shoy in Sápmi (Lapland)

As mentioned in the previous entry there is another (not shown) 13th century Sámi sample (Chalmny-Varre) which is totally modern in composition: dominated by haplogroup V7e and complemented by U5b1b1 and U5a1.

The simulations performed by the authors suggest that:

The model of genetic continuity between aUzPo and present-day Saami was found to fit the observed data better than the model of genetic continuity between aUzPo and present-day NEE.

The model also suggests that modern NE Europeans from the area (Russian, Finns and even to some extent Karelians and Volga-Ural peoples) are product of later migration from Central Europe, however they could not test this for the Saami because they could not find a plausible source population for them. 

This is maybe best visualized in figure 2:

Figure 2. Principal Component Analysis of mitochondrial haplogroup frequencies.

In this graph the Sámi look rather continuous with ancient locals but they show even more continuity with ancient Pitted Ware populations from the Baltic (aPWC, Chalcolithic semi-foragers with possible roots in Eastern European Neolithic) and related "foragers" from NE Poland and Lithuania (corresponding to various periods, even Chalcolithic in some cases), as well as more genuine pre-Neolithic hunter-gatherers from Germany (all them pooled as aHG).

It must be mentioned in any case that there is no single known case of haplogroup V in any pre-Neolithic sample (neither in Europe, nor anywhere else). And this one makes up the bulk of modern Sámi mtDNA pool.



* Other such strongly confirmed haplogroup H (mtDNA) sequences were also reported last year for Northern Iberia Paleolithic and Epipaleolithic remains. Many other Paleolithic sequences are suspect but have only been tested for the Hyper-Variable Region (HVS), which is often not conclusive for this haplogroup, causing in the recent past some people to (wrongly) reject the presence of this lineage, now the most common in Europe, before the Neolithic. Now we know that it did exist in both Northern and Southern Europe, although many questions remain on its commonality and history.


  1. "there is no single known case of haplogroup V in any pre-Neolithic sample (neither in Europe, nor anywhere else). And this one makes up the bulk of modern Sámi mtDNA pool."

    Just to connect the dots and provide context, haplogroup V (derived from HV0a and mtDNA dates, for all the issues with that methodology at 13,600 years BP) has a likely origin in Iberia or Northwest Africa, the other places where it is found in some frequency. Thus, the Saami likely is the merger of a Pitted Ware forager/fisher population and a forager/fisher population that migrated to the Saami region via an Atlantic coastal route in the vicinity of Iberia/NW Africa some time in early prehistory. It is found in the Saami, in Tunisan Berbers (16.3%), in Cantabrians (15%), and in the Basque (10.4%). A possible ancient DNA of hg HV or R0 from which it is derived (V is derived from HV which in turn derived from R0) was identified in Southern Italy ca. 24000 years ago, although routes to the Western Med. via either the Northern or Southern coast of the sea are plausible.

    A best guess for time of this migration to the North would be post-LGM and perhaps in connection with the repopulation of Europe post-LGM or the Epipaleolithic wave of migration that preceded the Neolithic by a few thousand years or the Neolithic revolution's arrival itself. The range of Saami diversity in mtDNA V (which is a majority mtDNA haplogroup assignment for the Saami) suggests an mtDNA mutation rate based age of 7600 years BP - which would suggest a somewhat more recent migration to the North, right around the time that farming arrives in Iberia and Cantabria. Internal Saami U5b1 diversity suggests a common source 6,000 years BP, and the shared root of Berber and Saami U5b1 diversity suggests shared roots 9,000 years BP. Saami also have mtDNA Z in lesser amounts associated with Siberia and estimated by diversity and mutation rates to date to about 2700 years BP.

    There are three Y-DNA haplogroups that are predominant in the Saami (N1c followed closely by I1 followed distantly by R1a with a regionally limit distribution).

    The plausible suggestion is that a fairly small proto-Saami population with mtDNA Ub51a and V and with Y-DNA I1 migrates from SW Europe/NW Africa via an Atlantic route to Scandinavia in the late Epipaleolithic or early Iberian Neolithic. In the absence of any Mesolithic European ancient Y-DNA evidence, the presence of Y-DNA I1 as apparently the dominant pre-Uralic Y-DNA type in the Saami is that strongest evidence that Y-DNA I was an important Mesolithic Y-DNA haplogroup in much of West Eurasia and that Y-DNA had an ancient coincidence, at least in some regions, with mtDNA U5, which was by far the most common Mesolithic mtDNA haplogroup in West Eurasian mtDNA. The absence of mtDNA V in all but one Mesolithic ancient mtDNA sample of uncertain classification suggests that this probably arrived from West Asia or SW Europe sometime long after the initial Cro-Magnon colonization of Europe (quite plausible from the Berber side rather than the Iberian side of the Strait of Gibralter and merging into the proto-Saami population in a Cantabrian population descended from Cantabrian refugia ancestors only sometime long after the LGM).

    Then, the Saami acquire mtDNA Z and traces of D5 and U4, as well as Y-DNA N1c in a male dominated admixture giving rise to Saami ethnogenesis that has a strong demic component probably sometime in the first millenium BCE from linguistically Uralic Pitted Ware descendants from whom they also acquire their current Saami Uralic proto-language in a language shift that ended the use of their prior language.

    Later male dominated, probably linguistically Indo-European migrants from Central Europe to the region (perhaps proto-Russians) bring an introgression at modest levels of Y-DNA R1a, and mtDNA H into Saami genetics.

    1. This is the phylogeny of V: R→R0→HV→HV0→V

      The Gravettian Italian (Paglicci) R0-CRS was described as HV because it lacks the HVS-I marker that lead to R0a (T16362C) but for the same reason cannot be HV0 (T16298C) and therefore not V either.

      A different kind of test was performed in one of the two R0-CRS samples of Gravettian Apulia, demonstrating that it was not H. So I think that we are safe when we say it NOT either of the following HV subclades: HV0 (incl. V), HV1, HV2, HV4a, HV6, HV8, HV15, H1V17, HV12a, HV13 nor H. It could be one of the other modern ones or a variant now extinct. But in any case it is not within HV0 and therefore we can say with great certainty that it does not seem to have any particular relation to V.

      The first HV0 (plausibly V but could also be HV0a1, HV0a* or HV0*) known to science are:
      → Danubian Neolithic Germany (4600-3000 BCE): three individuals, different sites and chronologies (LBK)
      → Portuguese Neolithic (date not reported for each sample but say c. 5-4000 BCE): one individual
      → Chalcolithic Languedoc (3000 BCE): two maybe related individuals (post-Cardial context)

      Incidentally the area where most mtDNA V has been reported to date other than the very especial Sámi case is Catalonia, just south of Languedoc. At first it was said that it was a "Basque" clade but later studies watered down this claim a lot. IMO it looks very much a lineage of European Neolithic origins but the precise ultimate origin cannot be tracked with the data we have. Nothing obvious points specifically to Italy in any case, nor to Danubian Neolithic alone either.

      Its presence in Africa (especially in Tunisian Berbers but also in some other corners, sometimes remote if my memory is correct) however suggest a SW Europe-NW Africa connection, which should not be later than Neolithic because of the general genetic landscape differences - i.e. North Africa has a sizable bloc of mtDNA, mostly H, linked to SW Europe but in the Y-DNA side of the equation it looks mostly NE African (middle and lower Nile area) what implies to my eyes gender biased replacement from that region that should be of Epipaleolithic or Neolithic age. This suggests that V was present in parts of Europe and (by extension) NW Africa before Neolithic. But it's not totally impossible that it arrived from West Asia (or the Balcans?) to both regions with Neolithic, being (if so) more related in "history" to lineages like K, T, etc. than to its relative H.

      As for the last part of your comment (tentative reconstruction of the origins of Sámi genetic pool), it looks OK to me (except that we can't say for sure at this point that Y-DNA I was important in the "Mesolithic" in Europe - that remains conjectural IMO). I also remain cautious re. your interpretation of Oriental mtDNA among Sámi because it's likely that each historical subpopulation had their own rather distinct genetic pool that was gradually homogenized by strong drift (the Sámi are just some 130,000 now and they were surely many less in the past), so it's very possible that N1c, etc. were already there since very long ago.

    2. Something not often discussed: Y-DNA haplgroup I is related to J (both are IJ http://en.wikipedia.org/wiki/Haplogroup_IJ_%28Y-DNA%29), so maybe IJ was the primary "Europoid" haplogroup at some point.

      If this was an early proto-Europoid haplogroup, then maybe the R's came in with later Asiatic migrations (squeezing out IJ as the dominant N. European haplogroup). R shows up some odd places, like North America (http://en.wikipedia.org/wiki/Haplogroup_R-M173_%28Y-DNA%29).

    3. I have no reason whatsoever to imagine that I is older that R1b in Europe, especially West of the Rhine. The first Y-DNA I documented (Languedoc) is from Neolithic with other Neolithic Y-DNA (E1b, G2a) and mt DNA lineages as companions. However it probably originated in other parts of Europe (Eastern/SE Europe).

      The same that West Asia (or any other place) is not an homogeneous bloc (with diverse lineages like J1, J2, G, R1b, R1a, etc), Europe was not either a single piece and we can well imagine various waves or several lineages sharing wave and scattering with some randomness first. The assumption of one lineage = one people is unrealistic. Only an extreme founder effect with only one effective founder or extreme drift (long time no see anyone not a cousin) do that. Of course these happened here and there but even in the most remote areas going through obligate arctic bottlenecks (Native Americans, for example) you see more than just one founder lineage and the founding of the West Eurasian population was not so extreme for sure.

      As for R1 in North America the default conclusion is recent admixture. But if you can reasonably prove otherwise...

    4. http://en.wikipedia.org/wiki/Y-DNA_haplogroups_in_indigenous_peoples_of_the_Americas

      R1 reaches 79% in North America. If this is supposedly all European introgression, where is the French I, E1b, and J?

      Reich 2012 tested some of these populations for "Reconstructing the origin of Native American populations."

    5. "where is the French I, E1b, and J?"

      In "others" surely, sometimes reaching as much as 30%.

      There was some talk in the past on some rare apparent R(xR1) and also on Mongolian R but I have never read any continuity on those studies. All I can say is that why it's not impossible that some other "Western" lineages made it to America via Beringia, it remains to be demonstrated and the general attitude among population geneticists is to treat them as recent admixture from Europe, which is probably correct at least for the bulk of it, and even remove them from illustrative graphs and such (because they attribute it to very recent arrival in the context of the Modern Age).

      "Reich 2012 tested some of these populations for "Reconstructing the origin of Native American populations.""

      And? Do you have a link or at least title, doi...?

  2. http://www.ncbi.nlm.nih.gov/pubmed/22801491

    No data have been released.


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