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More North Iberian Epipaleolithic mtDNA (and first Epipaleolithic nuclear DNA)

29 Jun

[Scroll down for updates]

In this case two individuals (right) from La Braña-Arintero site in Valdelugueros (León province near the Asturian border), dated to 7000 years ago, borderline with Neolithic arrival but, according to the paper, still “Mesolithic” (i.e. Epipaleolithic).

The two individuals carried haplogroup U5b2c1 (I guess that they were relatives, maybe siblings). The mtDNA sequence was retrieved in full. 
It is worth mentioning that there have been other recent studies of Northern Iberian pre-Neolithic mtDNA:
Previously,  conference materials by Chandler, Sykes and Zilhao (2005) and by Kéfi (also 2005) had reported lots of likely mtDNA H and, less commonly, U5 and other lineages, in Epiplaeolithic Portugal and Late Upper Paleolithic (Oranian) Northern Morocco (Taforalt cave) respectively. Other studies in Upper Paleolithic Andalusia are also consistent with the presence of both main European grand lineages in the Iberian peninsula since Solutrean (U5 plus what?) and Magdalenian times (H with great likelihood).

Pre-Neolithic mtDNA lineages found in Northern Iberia to date (all quite unquestionable)

Update (revised): on the nuclear DNA sequences

Interestingly the study includes a large SNP sequence of the nuclear DNA of both individuals. When compared with several modern European populations (overloaded of Finnish and Tuscans, who hijack the analysis, the result is as follows:

Figure S3
PCA with 1KGPomni Chip Data (European Populations) and La Braña 1 (left) and La Braña 2 (right)
click to expand to original resolution (still not enough to discern Iberians by subpopulation easily)

As we can see the dimension 1 is hijacked by the Tuscan-Finnish duality, while the dimension 2 seems almost private, extending inside all populations with minor variations. This render the PCA essentially useless and meaningless. However it would seem that the La Braña individuals cluster best with some British and some of their creole cousins from Utah (CEU).

However when global tripolar comparison is made (after removing the noisy Finns), the result is:

Figure S2. PCA with the Shotgun Data from La Braña 1 (Left) and La Braña 2 (Right) and the Worldwide Data Set from 1,000 Genomes Project,

Interestingly the La Braña individuals not just cluster separately from Modern Europeans but they actually look “more Asian” than these. In fact, would we superimpose these PCA plots on any global one with more samples (which always takes an L shape with vortex at or near the European cluster) like this one (from Etyo Helix), the La Braña people would overlap Afghans and Gujaratis, roughly.

So it’s like the analysis performed is more perplexing than informative. Not really helpful. We can only hope that the sequences are soon released to the public domain so independent researchers can perform contrasting analysis. These PCAs alone are almost useless.

Update (Jun 29): details of the La Braña-Arintero findings:

Close-up of Braña 1 (source)

The cave was only excavated since 2006. Braña 1 was found in flexed position with ochre and a delimitation of the niche by rocks (but there is evidence that no earth was disposed on top of it). Braña 2 was found in non-anatomical disposal (possibly because of post burial alterations by water or people), at the bottom of a natural hole 4 m. deep, just beside the other one and with indications of being also a primary burial.

Braña 1 had no caries but erosion of some teeth in what is suggested to have been caused by the use of teeth tool. There is a serious injury in the upper jaw by piercing artifact (spear?), which healed.

Associated to Braña 2, there were found 24 perforated deer canines, possibly part of a necklace or other decoration originally.

The two burials are from almost exactly 7000 years ago. The ages are:

  • Braña 1: 6980±50 calBP (5990-5740 BP – raw C14)
  • Braña 2: 7030±50 calBP (6010-5800 BP – raw C14)

The assigning of the burials to ‘Mesolithic’ (Epipaleolithic) is based 100% on the datings and not on cultural elements (other than the deer canines) that are absent in this site. The ‘Mesolithic’ comparison dates from further North (Asturias) are from the 7th or 6th millennium uncalibrated but none of them is more recent than the ones from La Braña-Arintero (in fact they look as quite older):

  • El Espertín (Burón): 7080±40 BP and 7790±120 BP (not calibrated)
  • Los Canes: unspecified dates from the 6th millennium BP (not calibrated), where similar deer canine decorations were found also in burial context

    Refs.

    Julio Vidal et al., LOS HOMBRES MESOLÍTICOS DE LA BRAÑA-ARINTERO(VALDELUGUEROS, LEÓN): UN HALLAZGO FUNERARIO EXCEPCIONALEN LA VERTIENTE MERIDIONAL DE LA CORDILLERA CANTÁBRICA. 2008. ··> found at Academia.edu.

    Julio Vidal et al., LOS HOMBRES MESOLÍTICOS DE LA BRAÑA-ARINTERO (VALDELUGUEROS, LEÓN): EL HALLAZGO, SITUACIÓN, ASPECTOS ARQUEO-ANTROPOLÓGICOS, CRONOLOGÍA Y CONTEXTO CULTURAL ··> found at Academia.edu.

    Update (Jul 1):
    Even if I do not often see eye-to-eye with Dienekes, he is the one providing the first known independent analysis of the La Braña people. He has done so in two successive updates of the entry on these interesting, yet perplexing, sequences.
    As you may know, he uses two main sets of zombie components (deduced from his own analysis, sometimes a bit questionably but well…), which he calls K7 and K12. They are Eurocentric in concept, what is convenient for this purpose.
    K7 has three West Eurasian components that he labels West Asian, Southern and Atlantic-Baltic. Where Atlantic-Baltic is the main European component, being strongest towards the West and the North, the top population being Lithuanians and the 50% isocline going through the Tyrrhenian Sea, the Northern Appenines, the Greek-Bulgarian border and the ethnic border between Russians and others in the North Caucasus. In other words: Europeans are generally high in this component, with very few exceptions, all them Mediterranean or Caucasian.
    For the K7 analysis, Dienekes got:

    9.3% African and 90.7% Atlantic_Baltic

    No modern Europeans are so high in the Atlantic-Baltic component (Lithuanians are 84-88%) but more notably none have such high levels of (simplified) African component, the closest being modern Portuguese with 2.5%. In fact Portuguese-D are in Dienekes’ K7 analysis: 60% Atlantic-Baltic, 2.5% African and the rest belonging to components that we can safely consider Neolithic or post-Neolithic arrivals:
    • 30% Southern (i.e. Eastern Mediterranean South or Arabia)
    • 7% West Asian (i.e. Eastern Mediterranean North or Caucasus)
    • 1% South Asian
    After removal of these likely Neolithic-arrival components and apportioning, the “reformed” Portuguese sample would end up being 96% Atlantic-Baltic and 4% African, what leads me to think that some extra Atlantic-Baltic may also have arrived with the Neolithic-specific components, assuming that the La Braña pre-Neolithic substrate can be extrapolated to Portugal (what may be but is not necessarily the case).
    As for K12, it may shed even more light. According to Dienekes, the La Braña people produce:

    45% Atlantic_Med, 41.6% North_European, 10.3% East_African, 1% Sub_Saharan

    Basically the Atlantic-Baltic has split in two European subcomponents and the African one in two as well (with a tiny 3 points displacement from the European to the African components as these become more refined). Remember that they are zombies (pre-determined components) and not the product of any direct comparison with actual populations. However for this purpose it is probably the best thing to do initially.
    For reference the Atlantic-Mediterranean component is highest in SW Europe (Basques and Sardinians notably), while the North European is highest in NE Europe, in spite of the misleading name (former USSR, Finland). British (or the CEU HapMap sample or the Irish) are almost half-and-half for both components, just like the La Braña people, what explains why they cluster best with them… if we ignore the African part.
    Like the La Braña people, British also have c. 10% “other stuff”, in their case it is however the “Gedrosia” component, strongest in Pakistan and Caucasus and which is suspected to be informative of Indoeuropean (Kurgan) ancestry (along with uncertain amounts of the Northeastern, “North European”, component).
    But the big mystery is the  East African component, which is distinct from the North West African (Moorish or Berber) one, which we might all have expected on first look. This East African component is highest among the Sandawe (68%), Somali (69%), Ethiopians (55%) and that’s about it. North Africans have some but not at all at such levels and certainly not without the NW African or other components absent in the La Braña pair.
    This is extremely hard to explain because modern Portuguese’s African component is nearly all NW African (7.7%), with some minor Sub-Saharan (0.7%) and nearly no East African (0.1%). So the illusion maybe generated at K7 of these people’s genomes being explainable by means of revising modern Iberians… seems to collapse.
    So the results remain perplexing (I have received criticisms for using this and similar words but that’s the truth and if you look online, nobody seems to have good answers – it’s not just me).
    But the results are still informative. Regardless of whatever the East African component means (what obviously demands further analysis), it seems obvious now that both European-specific components (North European and Atlantic-Med in Dienekes’ slang) are pre-Neolithic.
    And that is important because it opposes the most common and simplistic Neolithic replacement  models. It would seem that, whatever the intra-European genetic shaking and re-scattering and the arrival of minority genetic components from the Neolithic onwards (mostly from West Asia), the bulk of European ancestry is Paleolithic European after all.

    Update (Jul 1 – II):

    (From Dienekes’ blogfair use of copyrighted work)
    Dienekes is even providing us with a nice visual comparison (right), using his K12 zombies, of five prehistoric Europeans.
    Notice that the two so-called hunter-gatherers from Götland (an island off Sweden) are actually Neolithic hunter-gatherers at the best and Neolithic mixed-economy people most likely. They belong to the Pitted Ware culture, which is derived from the Neolithic of Ukraine and nearby parts of Russia: the Dniepr-Don culture. Derived from this, eventually some people with characteristic pottery, possibly some domestic animals such as pigs, but a largely gatherer economy (hunt and fish) spread towards the Baltic and in some cases crossed it towards Sweden.
    That would explain their high levels of NE European (aka North European) component.
    The South (or rather SW) Swedish farmer belonged instead to the Megalithic phenomenon and the Funnelbeaker (TRB) culture of Denmark and nearby areas. His affinities are mostly Sardo-Basque (Atlantic-Med), with a bit of Neolithic and NE European elements.
    The North Italian farmer (or rather Alpine pastoralist)  is the famous Ötzi “the iceman”. His affinities are also Sardo-Basque (to a lesser extent than the Nordic farmer) and also has a good deal of West Asian affinities (Caucasus and SW Asian) and even some North African affinities.
    Finally the Northwes Spanish hunter-gatherer is a combo of both La Braña genomes (very similar and quite incomplete), whose meaning (in my opinion always) I have discussed in the previous update section, a few lines above.

    Updates (Jul 3): strange ritual for ‘Mesolithic’ and some other DNA comparisons

    The latest zombie comparison (different set of zombies) by Dienekes (scroll for updates in the already provided link) is similar to the previous (i.e. c. 90% like modern Europeans, specifically NW ones without the “Neolithic” stuff) but instead of being anomalous towards Africa it is towards East Asia. Not sure what to think other than it seems to point to some unchartered component with deep roots.

    Maybe more interesting but still in the hmmmm zone is the comment at Diario de León[es] by Pablo Arias, Director of the Prehistoric Research Institute of Cantabria. Among other less important details,he argues that the burial or rather lack of it thereof (as the corpses were placed in the cave without earth covering, even if Braña 1 does display signs of intentional funerary disposition) is most anomalous, actually unique, among ‘Mesolithic’ burial practices which always included proper burial and not just disposition. My translation:

    Nevertheless, he details that there are some peculiarities making it unique: like the kind of necklace found along individual number 2 and very specially the characteristic of the funerary space: corpses deposited on the floor of a selected hypogeum. “From another point of view, La Braña-Arintero provides another evidence of the spectacular increase in the number of burials in the 7th millennium a.C. and that may relfect an intensification of the territoriality in these societies”.

    Pablo Arias precises that the more striking characteristic of the funerary context of La Braña-Arintero resides in the sepulchral space itself, detailing that it is an exclusively funerary site, with no link to settlements of that age. We see that a remote cavity, apparently not suited for habitation, and the corpses have been placed there in peculiar spaces, well delimited by natural space in the way of niches.

    And this, as he defends in the article, is a funerary behavior that has no clear precedents in other peninsular contexts and rather reminds to behaviors more common in later periods instead.

    And… what we just needed, so to say: Bushman affinities! In his latest comparison, using the DIY Harappa World calculator, Dienekes finds that the Braña composite is stubbornly >80% European (in this case 55% NE Euro and 27% Mediterranean) and some 17% (the highest figure so far!) non-European, mostly 7% Siberian and 6% Bushman (San).

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    149 responses to “More North Iberian Epipaleolithic mtDNA (and first Epipaleolithic nuclear DNA)

    1. ᧞eandertalerin

      June 28, 2012 at 9:54 pm

      Haven't they compared the mesolithics with Basques? It seemed to me they did. That's what I've read in Dienekes' blog:"In the latter PCA, where the origin of each Iberian sample is known, it is possible to see that the Mesolithic specimens are not related to modern Basques, contrary to what has been previously suggested in some recent studies"Yet I don't understand why they say these two speciments are more related to northern than to southern Europeans. Finns don't seem specially related to them.

       
    2. Heraus

      June 28, 2012 at 10:33 pm

      I don't see Basques being tested either …I don't get why Dienekes concludes modern-day Iberians (well, it's just about one ancient Asturo-Leonese sample) are not the descendants of Mesolithic Iberians : actually, the results are pretty consistent with what we know of the subsequent migrations affecting the Iberian peninsula (Med/West Asian migrations).I'll admit there's indeed a problem with the Admixture tests Dienekes is running with all those ancient people constantly appearing to be nearly fully "Atlantic/Baltic" as he labels the cluster bar that one individual from South Sweden which show a balance between the main two European components (quite similar to modern Basques in his tests) : Atlantic/Baltic and Med.Should that mean that indeed, in early Neolithic times, up to modern-day Basque lands were subject to Med migrations preceding West Asian ones (read : Anatolia then Balkans) ? I find it strange.

       
    3. pconroy

      June 28, 2012 at 10:37 pm

      @Neandertalerin,The 2 specimens are more related to Northern Europeans, as they are closest to the British, who are Northern European??What's not clear about that?

       
    4. ᧞eandertalerin

      June 28, 2012 at 10:49 pm

      @pconroy:In those graphs, I only see 3 northern european populations (two of them very closely related to each other) and 2 southern ones. Finns don't seem closer to the mesolithic individuals than Tuscans are. The closest are CEU/British, but northern europeans also include Germans, Latvians, Russians, Danish, etc. What's even more: CEU/Brits are closer to southern europeans than to the Finns, so I don't understand where does the division between northern and southern europeans come from.

       
    5. pconroy

      June 28, 2012 at 11:25 pm

      When I think of Northern Europeans, I think of Irish, British, Scandinavians and Lithuanians. I exclude the Finns and Estonians are they are North East Europeans and quite different. The Slavs are more Eastern European then Northern. Much of Germany is Central Europe and is closer to Northern Italy than Northern Europe.

       
    6. Heraus

      June 28, 2012 at 11:31 pm

      I don't know how you guy can read that PCA plot, the vertical amplitude of Britons is too considerable to properly analyze something. It is not readable at all. Only Tuscans seem differentiated. The Mesolithic Iberian appears to be neutral on both axes.

       
    7. princenuadha

      June 29, 2012 at 12:05 am

      @maju I heard its in the "mini library".I have no idea what that means though.

       
    8. Maju

      June 29, 2012 at 12:26 am

      Lots of comments in so little time! :)I must say that, on second thought, the PCA is very much hijacked by specially the Finnish-Mediterranean duality (PC1) and the La Braña samples fall near the zero, what is not what I would expect from someone very different from modern Europeans as a whole, but rather someone quite average, even if not similar to the local populations maybe. But then in the continental comparison plot they fall apart, tending towards "India" (or where I'd expect to see West Asia, India and Central Asia in similar better sampled comparisons). So in the European only comparison, in spite of the Tuscan-Finnish hijacking of the plot, we can conclude that the individuals look quite average European, out of the Asian-influenced extremes that these two populations represent (influenced by West Asia in the TSI case and Siberia in the Finnish case). However in the global plot we are pushed to think that these people are somewhat "more Asian" than modern Europeans. I have got my hands on a copy and there's not much more that I can see other than in the Supp. Material there's a comparison with a more varied Iberian sample, including some Basques. The results are very similar and it's extremely difficult to discern which Iberian subsample is each because they are plotted all in yellow, which almost does not contrast against the white background. If you want a copy just email me: lialdamiz[at]gmail[dot]com

       
    9. Maju

      June 29, 2012 at 12:37 am

      If you heard that from Jean Manco, she means she has it in her "cloud" Google library, which she shares with a number of people.

       
    10. princenuadha

      June 29, 2012 at 3:34 am

      Yes.You knew where I got that from. Do you visit world families?

       
    11. Maju

      June 29, 2012 at 3:50 am

      No but from the words used I deduced… If you ask her she will surely agree to allow you access, I guess. It's nothing but her personal "cloud" collection of papers. I always forget to organize mine… 🙂

       
    12. Maju

      June 29, 2012 at 4:43 am

      Edited the nDNA part (the update) and bumped the entry (it may appear twice therefore in your RSS feeds).

       
    13. Etyopis

      June 29, 2012 at 3:39 pm

      Very interesting Maju, In the past they also found E-V13 in Iberia from 7,000 years ago, source: "Ancient DNA suggests the leading role played by men in the Neolithic dissemination", presuming this is around the same time frame, they had proposed the E-V13 as a 'Neolithic' lineage, yet the PCA on the autosomal DNA of these new specimen from about the same time frame does not look very close to where the 'traditional' place of where the Neolithic dispersion (at least one of them or the main one) is thought to have originated. Does this mean that this 7KYA is the transition time for Iberia? Can you shed some light on this?

       
    14. ᧞eandertalerin

      June 29, 2012 at 3:52 pm

      Is it possible that these two mesolithics are actually mixed with neolithics or are neolithics themselves? That'd explain why they're more East Asian than present day Europeans.If these mesolithics were descended from the first HAM that arrived in Europe about 40 Ka, I wouldn't expect them to be closer to E. Asians than the middle easterners who arrived there much later. Alternatively, maybe there were multiple waves of immigrants from Asia to Europe in the last 40.000 years, not just two or three.

       
    15. Maju

      June 29, 2012 at 4:10 pm

      Indeed, according to the latest calibrated dates, c. 7500-6500 BP was the Neolithic transition in SW Europe (including much of France AFAIK). See this entry.The oldest dates in Iberia and France for Neolithic (variants of Cardium Pottery) are all from around 7500, always in the coastal areas (excepted some anomalous dates from Aragon which are probably wrong in something – they appear to be slightly older than anything else). These individuals are certainly borderline, per the chronology, but I have no reason so far to think they would be Neolithic instead of Epipaleolithic.

       
    16. Etyopis

      June 29, 2012 at 4:13 pm

      It looks like the samples are closest to a hypothetical people that are a hybrid of British and finns from the PCA plots, PC1 looks like an North East to South/Western axis, separating the finns from other Euros, PC2 looks like a North West to South East Axis, separating British from Tuscan, so on PC1 this 7 KYA sample looks almost center but leaning more to the finns, while on PC2 looks leaning more to the British than the Tuscans.

       
    17. Maju

      June 29, 2012 at 4:13 pm

      I agree with your perplexity, Maria Llüisa. I have no good answers but naturally I am rather distrustful of the usefulness of the comparisons performed by the research team. The individuals are borderline with Neolithic but I have no specific reason to doubt that they belonged to a purely Epipaleolithic community.

       
    18. Etyopis

      June 29, 2012 at 4:15 pm

      I can't see the diagram at all it is very small, do you have a bigger picture? thanks

       
    19. Maju

      June 29, 2012 at 4:22 pm

      The closest individuals (in the European PCA) are some Utahns (CEU, blue triangles) in fact, but then in the global plot no modern European is close at all. Something most people don't seem to understand is that zero means nothing in a PCA, unless it is demonstrated by other data: zero is neutral as to the extremes of the selected PCs, so the La Braña people were neutral to PC1 (neither high nor low in the "Mediterranean vs. Finnish" axis, although slightly trending to the negative side, as we would expect from any pre-Neolithic peoples) and neutral also to PC2 – whatever it represents, to me it means nothing, specially with La Braña 2 – only in the left plot, La Braña 1, actually behaves as you suggest: Britain-TSI (what may again suggest slight non-Mediterraneanness, what is logical).In this case, I'd create zombies and run supervised Admixture on the samples in order to detect real affinities. Here we only see neutrality to the displayed European trends (PCs).

       
    20. Maju

      June 29, 2012 at 4:27 pm

      In a different example (for comparison): Indians, when in a global PCA, behave as non-African but relatively neutral in the West-East axis (tending to Europe but not too much). That's not because they are admixed or anything (they tend to cluster with truly admixed peoples like Uyghurs but no relation in fact) but because neither axis captures their "essence", so to say. This one only shows up in Eurasian-only PCA plots, when they define a whole axis, against which both European and Chinese are negative. That's why PCAs are often misleading… they can be useful but only when properly designed. And these are not. And the only thing this paper offers is PCAs…

       
    21. Maju

      June 29, 2012 at 4:38 pm

      No, sorry: I did all I could with the original image, namely marking the thousands with red bars. The explanations (and another chronology table, and link to the original PDF in Spanish) are in the original entry, which is the link I actually meant to post in the previous comment (my apologies).

       
    22. Etyopis

      June 29, 2012 at 4:55 pm

      Ah, I did not see the global plots, in that they would maybe be close to modern Chuvash type people?I agree that an intermediate appearance in a PCA plot does not necessarily indicate a mixing event between distinct populations A and B, it could just as well have been due to descent from a population that had common ancestry between populations A and B for instance, that is why I used 'hypothetical'

       
    23. Maju

      June 29, 2012 at 5:23 pm

      I had not seen the Chuvash over there but more like the nearby (in the plot) Sindhi than the Chuvash.Why? because in the PC1 they look "less Eurasian" (or "more African" if you wish) than any European or East Asian sample, a (false, illusory) tendency that does happen with Indian samples but not with truly admixed West-East Eurasian ones like Chuvash and the like. It's a tendency that it's just saying: I don't really fit well in this comparison: the reference points are confusing. I'm not saying that the La Braña people have actually any connection with Sindhis or anything, just that they display the same kind of neutralization tendencies in a simplified tripartite global polarity.More detailed comparisons are needed before we can say something more clear.

       
    24. Maju

      June 29, 2012 at 6:16 pm

      Very borderline in fact. I have just updated (again) with some further data of the findings and, while it looks somewhat reasonable that these are 'Mesolithic' findings, the evidence is at least a bit inconclusive, as nearly the only reason is the chronology, which the authors say is "unquestionably" 'Mesolithic' but is actually "unquestionably" borderline.

       
    25. Etyopis

      June 29, 2012 at 6:29 pm

      Yes, there is a slight African pull on PC1, I think your assessment is reasonable without having enough data, the first sample for instance is approximately 1/5 of the way from the center of Europeans to the center of East Asians on the Y Axis, while it is about 1/20 of the way between the center of Europeans and the center of the Africans (Luhya and Yoruba in this case) on the X axis, offsetting with these approximate coordinates I see on my PCA plot populations such as Makrani, Balochi, Brahui, Kalash and Pathan.

       
    26. Maju

      June 29, 2012 at 7:10 pm

      Indeed. But, IF the Braña people would truly have a West Asian or Indian tendency (as would seem from this simplistic comparison of global plots) then they would show up as more "Tuscan" in the European plot, because generally Mediterranean peoples with some apparent West Asian admixture (as is the case of Tuscans) tend to also have more of the "Pakistani" components (Balochi or whatever you call them).That does not happen at all. It's weird: the PCAs are more confusing than clarifying.

       
    27. Unknown

      June 30, 2012 at 4:21 am

      From an older post: "That alone should have put the Neolithic replacement theory to rest but, of course, faith is blind and irrational, and some seem to be grasping for the proverbial straws…"It's funny to observe how the same is now happening to the proponents of the Paleolithic Continuity theory. Why not just acknowledge the new evidence against your theory, and stop calling the paper confusing, perplexing, and unhelpful?

       
    28. Maju

      June 30, 2012 at 4:48 am

      I call the paper, or more precisely the "analysis" performed, whatever I deem appropriate. While the authors extracted nDNA from borderline Epipaleolithic-Neolithic individuals (the data is not as clear as we'd like in this matter) the main issue is how they compared with modern populations and that is quite sub-par.I await independent reanalysis and hope it is done as soon as possible.Whatever the case you can't say as Lalueza has been saying all around that this paper (without challenging methods and conclusions) demonstrates that the cave people of La Braña are not ancestors of modern Iberians, IF anything it'd suggest that: 1. Modern Iberians would be less directly related, maybe mixed with some other peoples.2. Modern Brits (and white Utahns) are their descendants (well, not really but one could easily construct that narrative, specially considering that there is some archaological evidence for Neolithic demic replacement in Britain (and later in Utah). Even accepting the narrative construed in the paper, which I find oddly confusing, there's a lot that does not make good sense and require further exploration. Only a pseudoscientist (someone who considers science as means to an end, instead of as the end itself) would argue against that. I don't think that this paper demonstrates much in either direction. On the other hand repeated finding of pre-Neolithic mtDNA H (in Iberia of all places!), that really challenges at least the most common narratives of the Neolithic Replacement hypothesis. Maybe if you can construct a model B… But I would not expect so much from someone who signs as "Unknown" (i.e. someone we all probably know).

       
    29. princenuadha

      July 1, 2012 at 6:34 am

      "Interestingly the La Braña individuals not just cluster separately from Modern Europeans but they actually look "more Asian" than these."Actually, dienekes was wrong about that. Brana is closer to Asians AND Africans. So… I guess that means the Europeans have been drifting further from the two.Maju, I got good news for you. Look at this: http://www.worldfamilies.net/forum/index.php?topic=10663.msg133689#msg133689"In terms of closeness it goes roughly NW Europeans>Western Scandinavians/Germans>Iberians>North Italians>Eastern Europeans>NorthEastern Europeans>Greeks and South Italians."-jeanLSince brana shares more with the west then maybe western meso lineages did survive.

       
    30. Maju

      July 1, 2012 at 3:32 pm

      I do not have a fully finished opinion, unlike so many others, relative to which news can be "good" or "bad"… but I would agree that the Dienekes' analysis (scroll down to updates) is interesting. According to that, in the K7 analysis, they are: "9.3% African and 90.7% Atlantic_Baltic". Atlantic-Baltic being a component that is very high among North Europeans but also among Basques (73%). And in the K12 analysis, they are: "45% Atlantic_Med, 41.6% North_European, 10.3% East_African, 1% Sub_Saharan". What, per the relevant ref. spreadsheet. The Atlantic-Mediterranean component is highest among Sardinians and Basques, clearly indicating that, if these ancient people are Epipaleolithic the AM component is as well (it was argued it being Neolithic). It is a widespread component through Western Europe (40-60% levels).The North European component is most dense today among Lithuanians in fact and rather than "Northerner" it is a Northeasterner European component, reaching levels above 50% (actually above 60% and even 70%) in NE Europe only (former European USSR, except Caucasus, and Finland). For reference the British are at 40-50% levels, while the French and Spanish are under 40% and under 30% respectively (Basques are under 20%, lower than Spaniards). The most intriguing feature is the "NE African" and "African" components, which I feel legitimate to suspect as of North African origin, very specially because the people of NW Iberia do have notable NW African (and other less clear African) Y-DNA and mtDNA lineages, whose origin in the Solutrean or Neolithic I could not clearly discern before now.Ref. K7 and K12 "zombies" according to Dienekes.The sequences are here. Now I wish I knew how to manipulate that stuff so it can be freely compared with a varied array of moderns in many many different comparisons, until we get a result. I'll try to learn but I promise nothing (those specialist programs don't have easy to learn tutorials).

       
    31. Maju

      July 1, 2012 at 5:44 pm

      Updated again with consideration of the Dienekes comparisons. The European components are overly normal and emphasizes that both the "North European" (Balto-Russo-Finnic) and the "SW European" (Sardo-Basque) components are equally pre-Neolithic, but the 11% "East African" (and not "NW African") is not.

       
    32. Maju

      July 1, 2012 at 5:45 pm

      I mean it's not "normal", not "not pre-Neolithic", what it seems to be indeed.

       
    33. terryt

      July 1, 2012 at 11:11 pm

      "But the big mystery is the East African component, which is distinct from the North West African (Moorish or Berber) one, which we might all have expected on first look. This East African component is highest among the Sandawe (68%), Somali (69%), Ethiopians (55%) and that's about it". But we do have East African Y-DNA through the Mediterranean. E1b1b1-M35 as a whole certainly looks East African in origin, and many of the E1b1b1a-V68 subgroups are also basically East African. In general E looks like an early traveller through the Mediterranean, presumably one of the first haplogroups to venture out into the wider Mediterranean islands.

       
    34. ᧞eandertalerin

      July 2, 2012 at 12:21 am

      Is it possible that this apparent East African admixture is a remnant of the OoA expansion from this region? I know it's odd, but supposedly these hunter-gatherers were closer in time and possible genetically too to the first HAM who left Africa.

       
    35. Maju

      July 2, 2012 at 1:23 am

      The components, zombies or otherwise, are affinity indicators. In this case, the sequence (or rather the composite of both sequences) is forced to align with a limited number of pre-selected components. The strange thing is that it chooses East Africa and not whatever else, and this is roughly consistent with its anomalous position in the global PCA plot. But what does it represent? Indeed it may be a residue of something that existed in the past and not anymore. But then East Africa is not more similar to the past than any other component (or should not be), so… perplex.More analysis is needed.

       
    36. Maju

      July 2, 2012 at 1:28 am

      Not likely to be the same thing, specially when that lineage has been found among Neolithic and not Epipaleolithic populations. But who knows?That would make better sense, IMO, IF the La Braña people would be a Neolithic people and not Epipaleolithic. They are borderline by chronology but we have no reason to think they were Neolithic, much less in such a peripheral mountain zone – so early.

       
    37. Andrew Oh-Willeke

      July 2, 2012 at 4:21 am

      The geographic spread in the H v. U5 ancient DNA map is suggestive of the notion of H as a possible Epipaleolithic expansion with a colony that is pushing U5 slightly inland.Autosomal affinity of last to adopt farming and herding Northern Europeans with Mesolithic Iberians makes plenty of sense.I'm not convinced that Dienkes k=7 or k=12 zombies have the resolution needed for the task, which may be more complicated especially in ancient DNA sets.I also wouldn't be surprised if the "East African" affinity really reflects a much more wide ranging Mesolithic hunter-gather component that has been suppressed by post-LGM hunter-gatherer demographic expansion out of the Near East, as well as Neolithic and post-Neolithic population expansions, to which extant African hunter-gatherers are a best fit even if not a very good fit. Founder effects could also have greatly reduced post-LGM autosomal diversity among European hunter-gatherers who repopulated Europe over a fairly short time frame relative to the initial modern human population of Europe.

       
    38. Maju

      July 2, 2012 at 5:17 am

      But what happens with all the likely (and in some cases as certain as it can be) H in Portugal and Morocco? What about nearly unmistakable H17'27 in Gravettian Sunghir? What about the possible other H (R-CRS) in UP Britain? I think that there's too much speculation on this matter and that most likely H has been part of the UP genetic scene of Europe (and, maybe since Oranian, also North African and probably also of West Asia to some extent) since Gravettian or older times, more or less the same as U variants (mostly U5 and U4 but also some U*-CRS, now very rare, and U2 in at least one case). However it is possible that some very common haplogroups like H1 and H3 expanded later, within intra-European Neolithic flows like Megalithism. For example the only pre-Neolithic H1 (H1b specifically) known is from Portugal, precisely where the Megalithic phenomenon was conceived and developed before its rather quick expansion though Atlantic Europe in the 4th and 3rd millennia BCE. H1 would fit very well with Megalithism, IMO.

       
    39. Andrew Oh-Willeke

      July 2, 2012 at 7:08 pm

      "But what happens with all the likely (and in some cases as certain as it can be) H in Portugal and Morocco? What about nearly unmistakable H17'27 in Gravettian Sunghir? What about the possible other H (R-CRS) in UP Britain"It looks like there may have been population turnover in North Africa (from archaeology) ca. 16,000 BP. So, seeing H as an expansion out of the Middle East on both sides of the Mediterranean following the LGM but before the Neolithic, rather than out of the Iberian refugium, may be the best fit to the data. The dearth of H in Upper Paleolithic Northern Europe or at very old dates elsewhere, during which times and places U is predominant, suggests a less ancient H in Europe.H1 and H3 expansion during megalithism has merit.

       
    40. Andrew Oh-Willeke

      July 2, 2012 at 7:12 pm

      You'd expect more Y-DNA A and B than you see, and also I agree with Maju that most of the E1b1b1 in Europe looks young and is in the upper branches of the phylogeny. Also, the African DNA in Europe has a SW v. SE split, with the SW having an affinity for Morocco and the SE having an affinity for NE Africa. So, a strong East African component in Iberia is very out of tune with modern populations.

       
    41. Maju

      July 2, 2012 at 7:55 pm

      There's no such thing a an "Iberian refugium". Sometimes, not too knowledgeable authors use such name but they actually mean the Franco-Cantabrian region, which is only marginally "Iberian" and mostly Occitan/Aquitanian/South French. Around the LGM however the true "Iberian province" of the Southern peninsula, became less marginal than usual and probably fed North Africa with fresh blood in the context of the (Gravettizing) Solutrean and its transmediterranean closely related counterpart: the Oranian (or Iberomaurusian) culture. This was c. 20 Ka ago (not c. 16 Ka. ago)I have NO IDEA how can you fit, in archaeological terms your most strange idea of an "expansion out of the Middle East on both sides of the Mediterranean following the LGM but before the Neolithic". That has ZERO archaeological support. Following the LGM, i.e. in the late UP, (South) Iberia lost again its relevance and Middle-West Europe (the Rhine) gained it again instead. But all the post-LGM process happen in or around France and have NO connections with West Asia (aka "the Middle East"). IF anything there could be flows TOWARDS West Asia, suggested by some scatter of Franco-Cantabrian-like rock art in Turkey and Egypt or some Eastern-European-like Gravettian influences in the Epipaleolithic of the Zagros. But all those are not well researched, so the connections are at best speculative (but would be Europe > West Asia and not the other way around in any case). I strongly suggest that you re-read Bocquet-Appel's excellent paper on European archaeological demography (and in general improve your knowledge of European, West Asian and North African archaeology before you go around throwing weird ideas without any archaeological foundation). I sincerely hope that your take on superstrings is more solid because what you're throwing here is indefensible from an archaeological viewpoint, what makes me doubt of your opinions on other matters where my knowledge is admittedly less solid.

       
    42. dalouh

      July 3, 2012 at 6:54 am

      hi Majuthere is another update from Dienekes.."UPDATE III: In terms of the euro7 calculator, the results are: 89.6% Northwestern, 1.6% Southeastern, and 8.7% Far_Asian."

       
    43. Maju

      July 3, 2012 at 10:17 am

      Closest to such apportions would be Irish or a range of modern Celtic/Germanic peoples – what is consistent with all we have seen so far. But the c. 10% East Asian (wasn't it African?) is still very perplexing.I'd run a set of unsupervised Admixture comparisons if I could figure out how to insert a sequence and make up for the low coverage.

       
    44. Maju

      July 3, 2012 at 1:30 pm

      Updated again to include, among other stuff, the comment of Pedro Arias, a Cantabrian high-profile professor who argues that the funerary disposition of La Braña is anomalous for "Mesolithic" contexts, where true burial was the norm.

       
    45. Maju

      July 3, 2012 at 1:31 pm

      Correction: Pablo Arias, not "Pedro".

       
    46. ᧞eandertalerin

      July 4, 2012 at 12:37 am

      Bushmen!?!?!? That's crazy! Maybe there was a migration of Bushmen to the Iberia peninsula about 50 Ka? In any case, some other admixture-experiments have yielded about 2% of East african admixture (or whatever) in Spaniards.

       
    47. Maju

      July 4, 2012 at 1:31 am

      I think it was you who suggested earlier it might mean some kind of generic Homo gibberish, maybe (who knows!) even Neanderthal remnants? The compass seems to be pointing to the root of either the Homo sapiens tree or at least the Eurasian root but it finds no correct reference so it wobbles. So maybe there is a 15-20% of really different ancestry from modern Europeans… and any other modern humans, at least their main components. At this point, I'd compare by pairs or small groups with every other population and not anymore use zombies. I doubt these can say anything else. It's very possible that the La Braña composite may produce its own distinct component and there the interesting thing may be to compare with others by means of Fst distances and such. The composites do not seem able to tell anything else.

       
    48. Marnie

      July 4, 2012 at 3:23 am

      Had a quick look at Dienekes' post on how the Braña sample "components" broke out with Dienekes calculator, and the HarappaWorld and MDLP5 calculators. Based on the differing results, I'd say that apart from a clearly consistent apportioning of the sample to Paleo Mediterranean and Western European components, the rest is noise.However, it is notable that the MDLP5 calculator picks up a 16% East Eurasian component while HarappaWorld picks up a 6.7% Siberian component. In any case, below the 10% level, I'd say these calculators are just hunting through noise. Not to say that there couldn't be something interesting going on, but you'd need more samples to even begin to figure it out.

       
    49. Maju

      July 4, 2012 at 3:36 am

      But the noise is almost as consistent as the rest. If you want my bet an ancient OoA component now lost (seldom detected except maybe in the Slovenian HGDP sample). I pondered Neanderthal admixture (now lost or heavily diluted) but then it should not point to Africa, even in the wobble. We need a non-supervised Admixture series. But if you're waiting for me to do it first… it'll take a while because it implies reading and experimenting with technical gibberish… a major effort.

       
    50. Marnie

      July 4, 2012 at 6:56 am

      "We need a non-supervixed Admixture series"Haven't looked closely at this, but perhaps more Braña samples or a more detailed SNP sequencing of these samples will be published. "But the noise is almost as consistent as the rest"What do you mean?

       

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