May 4, 2016

Large Paleoeuropean DNA survey

An unprecedented survey of ancient DNA from Paleolithic Europe has been just published:

Qiaomei Fu et al., The genetic history of Ice Age Europe. Nature 2016. Pay per viewLINK [doi:10.1038/nature17993]

The supplemental materials (PDF) are freely accessible, as are the figures and tables (HTML). 

Quick highlights:
  1. Oldest Y-DNA R1b1 (and therefore R1b and R1) ever documented (Villabruna, Veneto, 14 Ka ago, Epigravettian cultural context). Also more Japan and La Braña related C1!
  2. Oldest mitochondrial DNA H (H7) may be in Gravettian Moravia, also oldest U6 may not be in Iberia or North Africa but in Gravettian Romania.
  3. Very important insights in autosomal DNA: a distinct Paleoeuropean population since Gravettian, two different late UP/Epipaleolithic populations. 
  4. Still very important gaps, notably SW France (the core of Paleolithic Europe) and most of Iberia. Also still missing West Asian sequences altogether, except for the rather anomalous Caucasus population and whatever may be inferred from Early European Farmers, whose ancestry was mostly (aprox. 3/4) West Asian.

A good synthesis of the scope and some of the findings of this study is in fig. 1:

(click to expand)


The survey confirms (supp. materials 4) that haplogroup I used to be the most common patrilineage in Paleolithic Europe. But it was not the only one:

The oldest ones (pre-Villabruna, c. 14 Ka BP) were largely C1:
  • Kostenki 14 (Russia, Gravettian): C1b
  • Goyet Q116-1 (France, Aurignacian): C1a
  • Vestonice 16 (Moravia, Gravettian): C1a2
Also in this oldest group (arbitrarily defined as pre-Villabruna), there was some I* or maybe pre-I (some markers are missing in many individuals), including: Pavlov 1 (Gravettian, Moravia), Paglicci 133 (Gravettian, South Italy), Hohle Fels 49 (Magdalenian, Swabia), Goyet Q2 (Magdalenian, France) and Bukhardtshohle (Magdalenian, Swabia). Notice that its prevalence and clarity as "I proper" increases after the LGM; the Gravettian ones seem to be pre-I rather than true I.

Other oldest lineages are BT* (Vestonice 15), CT* (Ciclovina 1, Kostenki 12, Vestonice 13), F* (Vestonice 43). Notice that in most cases not all the ideal SNP testing was performed, so it is still possible and even probable, I'd think, that BT* and CT* are actually F*.

In the more recent "post-Villabruna" group:

The revelation of the group is of course Villabruna, which carried R1b1

There are also two I* (Cuiry Les Chardaudres 1 and Berry Au Bac), one I2 (Rochedane) and one F* (Falkenstein).

I must also mention that previous studies found mostly I2 in Epipaleolithic samples, excepted La Braña, which carried C* (maybe some sort of C1 but unconfirmed). R1a1* was found in Karelia as well.

Synthesis: I and R1b1, the most common lineages of Europe West of the Elbe, only show up after the Last Glacial Maximum, at least as far as we know. I probably coalesced in the subcontinent, the issue of where R1b, the most common modern patrlineage of Western Europe, coalesced and how it expanded remains open but the Villabruna data point defines a terminus ante quem for this haplogroup, which MUST be older than 14,000 years necessarily, discarding some of the most outrageous recentist chronologies altogether. The great initial diversity of CT-derived lineages suffered bottlenecks with the LGM and probably also later, pruning most of them (although rare instances of some of those lines such as F* or C1 are still found among modern Europeans).

Mitochondrial DNA

Lots of interesting stuff in this issue of the matrilineages, but also some strange issues in the data that do raise eyebrows quite a bit. The full dataset is in the supplemental materials section 2. 

However they do not provide clear data on how the tests were performed, just a generic listing. This is very problematic, notably when they state that El Mirón is U5b, when Hervella (with more clear methodology) classified her as H just a year ago. Another similar issue is the apparent H7 (H7a1?) in Vestonice 14, which is first classified as "damaged" (based apparently on X-chr contamination, the CI for H7 is 0.9-1) and then listed as "U" in the extended table 1, with no reasoning whatsoever for the change. 

Rumor is already around about a mysterious H-hater "black hand" being at play here. I can't neither confirm nor reject it but I do think that the authors should explain themselves more clearly on this most important matter, which is beginning to be more than just annoying, fueling conspiracy theories and what-not.

Another interesting issue is a possible U6 in Muierii (Gravettian Romania, CI 0.88-0.97), labeled as "damaged" again and refurbished as mere amorphous "U". This is a very important issue and is directly related with the presence of mtDNA H in Paleolithic Europe and the origin of these lineages in North Africa. 

Northwestern Africa (not counting Cyrenaica) did not experience any sort of Upper Paleolithic (UP) until c. 22 Ka BP, when a new culture of very likely Iberian Solutrean affinity, the Iberomaurusian or Oranian expanded from Taforalt (Arif, North Morocco). In my understanding this is the most likely origin of mtDNA H (H*, H1, H3, H4 and H7) in North Africa and maybe also of mtDNA V, and also should be related to the bicontinental distribution of mtDNA U6 (in North Africa but also and quite diversely in Iberia) and the surely related distribution of Y-DNA E1b-M81. 

While it's easy to imagine mtDNA H (and maybe also V) migrating from Europe to North Africa in this context, less clear has been so far the issue of U6 origins: as U-derived lineage it must ultimately derive from the early UP populations of West Asia but then again the first UP in the region must have arrived from SW Europe in the Last Glacial Maximum (LGM) period. So something I've been wondering all this time, particularly since the crucial, rare and basal, U6c lineage was discovered to exist not just in Morocco but also in Andalusia, is if U6 actually arrived to NW Africa from Europe and not, as is often assumed, vice-versa. 

So you will understand how this issue of properly identifying ancient mtDNA H and U6 lineages is important not only for the understanding of the roots of Europeans but also for those of North Africans. There are interests at play here because many geneticists have made a personal issue of "molecular clock" age estimates (whose actual scientific, empirical, value is often close to zero but are "sold" as "scientific" instead) and also of exaggerating the West Asian Neolithic influence in Europe beyond reason, leading to true quasi-ideological "DNA wars" that are totally out of place. 

Please, let's be serious: there is no room for childish games on these matters, you guys and gals are grown ups with a PhD!

Otherwise a lot of U (as usual: U*, U5, U2), notable is U8c (CI 0.91-1 but declared "damaged" in spite of extremely low X-chr contamination), which, if confirmed, could offer clues about the origins of the rare Italo-Jordanian U8c (and indirectly about Basque U8a and the quite common but surely Neolithic haplogroup K). Also discarded are several samples that initially produced lineages under macro-haplogroup M, however Goyet Q116-1 was labeled as "pass" with this lineage. So there is Paleoeuropean M, or at least there was once upon a time, this one beyond any doubt.

Autosomal DNA

This last part is most interesting as well. As you can see in the figure 1 above, the authors described three Paleoeuropean clusters: blue (aka Vestonice), green (aka El Mirón, however El Mirón is actually green-red admixed) and red (aka Villabruna, equivalent to the WHG grouping seen in some recent studies). Black-marked samples are out of any group and the Siberian (Mal'ta) and Caucasus (Satsurbilia) clusters are not too relevant here. 

Annotated by me: in green approx. dates for reference, in gray approx. reconstruction of the ancestry of late Paleoeuropeans

First of all it is clear that all or most Paleoeuropeans form a unique macro-cluster (orange shaded) to the exclusion of the Mal'ta and Satsurbilia clusters and also of Early Neolithic Stuttgart (~3/4 West Asian). This macro-cluster is comparable in affinity to that of Han-Dai-Karitiana, so even the word "race" can be used. Some people have argued that "there was no Europe" back then, because the Bosporus was an isthmus, but from the genetic data it seems clear that Europe was more distinctive then than it is now, after the Neolithic massive admixture event that spanned from Europe to India with West Asian centrality. 

Then we see an older "Gravettian" or blue or Vestonice cluster, that is clearly pre-LGM and that does not include however peripheral Gravettians such as Mal'ta, Kostenki or Goyet Q53-1.

But the most interesting feature is that two different populations existed at the end of the Paleolithic period: the green one (El Mirón) is strictly Magdalenian and vanishes with the Epipaleolithic (at least for this sample, which has mayor gaps), instead the red one (Villabruna or WHG) was initially less common in Magdalenian and spans beyond its cultural borders into Epigravettian Italy too, however it becomes the only thing around in the Epipaleolithic, suggesting the expansion of a single population in that late period, maybe with the geometric microlithism which precedes in most areas the arrival of Neolithic and may well have expanded from France. 

Looking at the orange range of less obvious affinities, I tried to pinpoint tentative origins for those two populations. The green one relates best with GoyetQ116-1 (Aurignacian), while the red one does with GoyetQ53-1 (Gravettian). This is also somewhat apparent in the PCA and I tried to indicate it with the annotated arrows. 

Especial thanks for his insights to Jean Lohizun.


  1. R1b1 in that time period doesn't go against conventional age estimates at all. None of these haplogroups do, obviously excluding the contaminated "H".

    Hopefully an upcoming paper will use this aDNA data to refine the Y-DNA/mtDNA mutation rates even further.

    1. Lank, please consider my reply below to Alexander.

  2. Hey... I knew Fu et al would kick you back to life! ;.)

  3. "Damage" should not be understood as a denigration. It means postmortem degradation of the sort typifying ancient DNA (see here); restricting analyses to fragments exhibiting terminal deaminations thins the data but enhances confidence in authenticity. Significant discrepancies between damaged and non-damaged slices of aDNA data are evidence for modern contamination and a prompt to privilege the former.

    On Vestonice14 see Supp. Section 2, p. 18:

    In the case of mtDNA data, only Vestonice14 showed a change in haplogroup comparing damaged fragments to all fragments, suggesting mtDNA contamination. Further evidence of contamination in Vestonice14 comes from the fact that when we determine sex based on the proportion of Y chromosome fragments (Supplementary Information section 3), the sex for this individual switched from female when all fragments are analysed to male for damaged fragments only.

    Miscodings are of course not an unalloyed good, so various kinds of UDG treatment can be applied to repair them (including techniques that remove damage in the interiors of DNA molecules while letting it be at their ends, so that one can still computationally fish them out: see here).

    1. Alright, Alexander, fair enough. You seem a well informed guy, so can you explain why no markers are provided so we can revise the haplogroup assignation? This is a regular practice in mtDNA reporting, particularly ancient DNA. I just do not understand how a sequence can jump from H to U.

      Haak found years ago that there was one such case in which a U* ancient lineage could, most improbably, have all the HVS-I sequence back-mutated to appear CRS (otherwise normally H). And one might imagine that this is the case again (totally unclear without explicit mutations statement) but what is impossible and has never before happened is that H becomes U5b after revision, much less contradicting the RFLP markers tested by Hervella.

      So I think someone is totally manipulating the data set here, really. And that's something I don't like at all. Exceptional claims require exceptional clarity in the reporting and discussion, something that this study is missing regarding mtDNA.

    2. I'm in fact surprised that the study passed the peer review with these flaws, although on the other hand I presume the reviewers did not pay too much attention to mtDNA issues, valuing instead the important insights on other issues.

      "Just because it's published in Nature it does not mean it's wrong", they say. But my legitimate questions are not because it is "published in Nature" as such but because mtDNA is reported improperly, making claims that make no sense.

    3. The Vestonice14 mtDNA sequence is available on GenBank with id: KC521458. You can download the fasta file from GenBank and give it to the James Lick software available here: Then you can see it is a U5 sequence. A sequence can jump from H to U with contamination, but the researchers eliminated the contamination taking only the damaged fragments only because they are typical of ancient DNA.

    4. I'll look at it. In principle for mtDNA you don't need any software, just visually compare with the HRS at PhyloTree for the relevant markers (however it's possible that an insertion or deletion alters the positions, caution there because I already committed such an error before).

  4. So basically it appears that what we call WHG is essentially Middle Eastern if I understand this correctly.
    Maju, in a previous post you had linked to a post on Aggsblog contemplating the origins of the Central European Gravettian from the Middle East. I wonder if that would rather fit for the Epigravettian?

    1. To the first question: nope. I don't see any reason to think WHG is "essentially Middle Eastern". On the contrary: as I have argued in the autosomal section it appears that both the "red" (WHG) and "green" clusters both derive within a Europe-exclusive macro-cluster that excludes Paleosiberians (ANE), Paleocaucasians and also Paleolithic West Asians (inferred from Stuttgart). They are all local Paleoeuropeans, which must be considered as quite diverse but also clearly distinct from anything non-European. Only Karelia (Epipaleolithic) shows external influences from Siberia.

    2. To the second question: there is no single Epigravettian but several groups: at least one in Italy and another totally different one in Eastern Europe, no known connection between them other than both descending from the original pre-LGM Gravettian culture. Epigravettian is a catch-all term for various groups that evolved separately from Gravettian and did not go through the very dynamic Western post-LGM sequence of Solutrean, Magdalenaian and two successive Epipaleolithic (Epimagdalenian) layers.

      It's not something else: epi- means "after" and is used in the sense of "late derived development of..." All Epigravettian groups are derived from Gravettian, at least as far as archaeologists can tell.

      Instead archaeologists wouldn't be able to tell where the heck Solutrean comes from, other than tracking its oldest known manifestations to Aquitaine. With Magdalenian is a bit different because it does look like a second and quite refined Aurignacian but the link is mysterious, as Aurignacian had vanished many many millennia before, although now and then you read references to possible LGM "Epi-Aurignacian" intermediate links in either France or the Low Countries (very blurry issue).

      On the other hand Western Epipaleolithic cultures are all (except maybe the Hamburgian-Ahresburgian) Magdalenian-derived but, as we see here, the genetic connection of some of them with Magdalenian peoples is partial at best. Instead we see Magdalenian and Epigravettian peoples sharing genetics across the frozen Alps.

      So, how to explain? IDK with any certainty but maybe Epigravettian Italians crossed the Alps (via the Ligurian coast?) and adopted Western (Magdalenian) techno-culture, later on (after the Ice Age, which ended c. 10 Ka BP) replacing other Magdalenian peoples. But, while plausible, I would not dare to bet anything serious to this ad-hoc hypothesis I throw here.

  5. Maju.
    You don’t mention H13.
    To my interest (again thanks for reference in your previous post) I’ve notice that Kotias was H13. Which I Have only found alongside with an R1b in Yamnaya (I0370, Samara, Russia) and with a r1b Bell_Beaker_(I0112, Germany).

    Do you remember the crazy fixation I had with U4… well I then later, very earlier in research for thesis, changed fast to H2 (which is a parent clade for H1, H3 and H13!). So I am happy to see H13 in there and also Satsurblia (neighbour to Kotias) just clustering with r1b Villabruna as per Davidski new PCA.

    1. Kotias' H13 is from another paper: not listed in the supplemental materials. H13 is, along with H8, your usual "Central Asian H", so not too relevant for Europe proper.

    2. right. Its just that is part of the table they provide.

  6. The paper itself you can read for free at Reich's webpage:

    I am also rather skeptical of the Middle Eastern origin thing, it is possible but there are really not enough samples, especially from Iberia and the Balkans.

  7. I wonder if the older Villabruna R1b sample is a better fit for the WHG type ancestry in Basques than later WHGs like Loschbour.

    1. The best fits for WHG ancestry in general, before this study, seemed to be the Epipaleolithic Hungarian KO1 and the Magdalenian Swiss Bichon, both are "red" as is Villabruna, but also others.

      Just naively relating Y-DNA to autosomal DNA is probably not going to do the trick, but each time I look at that map, I don't see dots: I see a huge blank area just at the core or Upper Paleolithic Europe (SW France). It's like studying a city on evidence from distant nearby suburbs, you know that there is some relation but you should also know that many things do not match 1:1.

    2. I agree. It is unfortunate that there were no samples from the Solutrean.

  8. BTW, Villabruna had the same Y DNA(R1b1) and mtDNA(U5b2) haplogroups as me :). The same lineages have been being thrown around in West Eurasia for 10,000s of years, so that'll happen.


    All the new Paleo-European mtDNA that has come in this year has in my mind has proven mtDNA H in modern Europe is not descended of Paleo-Europe. Therefore it's unlikely H1, H3, and V in North Africa are from Paleo Europe.

    The Magdalenian genomes from Spain and Germany clearly descended from the same ancestor. By 10,000 years ago it looks like they were replaced by their close relatives; WHG. Madalenian might not have many descendants in modern Europe at all. So, I don't see how they could be a source of mtDNA H.

    We need to forget about pre-Neolithic Europe and focus on Paleolithic Anatolia/Aegean/Near East as the place of origin of most European mtDNA. Pre-Neolithic ancestry is mostly replaced in mtDNA U5/U4/U2e(10-15%) and Y DNA I(popular before 3000-1000 BC expansion of R1b and R1a).

    "I wonder if the older Villabruna R1b sample is a better fit for the WHG type ancestry in Basques than later WHGs like Loschbour."

    Dude serisouly? You know better. R1b-P312 expanded 10,000 years after Mr. Villabruna died. It's a happy coincidence he belonged to a lineage that would one day dominate the region. The authors of this paper actually stated it as fact that R1b-L151 expanded in West Europe during the Bronze age, they didn't even leave room for debate.

    1. There are "green" and "red" Magdalenian samples and then there is El Mirón, which is about 50-50 intermediate between both groups. Red/WHG peoples were ALSO from Magdalenian culture. The only exception is Villabruna (the map has another Italian red dot, but that one is missing in the data altogether, so it feels like another error).

      Whether "red" migrated from France to Italy or viceversa we do not know but we do know that "red" (i.e. WHG) was present in France and Spain (El Mirón is both "red" and "green": admixed) in Magdalenian times.

      Now, after Magdalenian times, in the Epipaleolithic, probably in the context of Tardenoisian, called "geometric microlithism" in Iberia, there was a new expansion, once again from France. I cannot emphasize the importance of France in European paleohistory even if I'd sing the Marsellaise on top of the Eiffel Tower. France is also crucial re. Y-DNA R1b and may well be crucial re. H (from Gurgy to Paternabidea: early modern-like mtDNA pools, outside: chaos and confusion). We just won't know until we sample.

      Anyhow the mtDNA aspect of this study is awful. It's not even labeled as such but the content is all vagueness and unlikely unbacked claims.

    2. "Dude serisouly? You know better. R1b-P312 expanded 10,000 years after Mr. Villabruna died. It's a happy coincidence he belonged to a lineage that would one day dominate the region. The authors of this paper actually stated it as fact that R1b-L151 expanded in West Europe during the Bronze age, they didn't even leave room for debate."

      The timeline has narrowed, but the possible geographic range of a source has widened. Before,

      However, given the lighting-fast first wave of expansion R1b, I think R1b as an Indo-European marker, even among Basques, is more plausible. Consider this: if you move to an area, marry local women, and have sons who themselves move on to a new area, and marry local women, who have grandsons... and so on and so forth. The identity of the original R1b carrier could quickly become effectively lost, both culturally and genetically. I don't think it would be a stretch to think that in some areas - perhaps many areas - Vasconic locals assimilated an early wave of Indo-Europeans, rather than visa versa.

      The reverse could be true too though. A spread of R1b from some other source could have arrived into Eastern Europe and been assimilated by pre-IE speaking locals.

      We do know now that R1b was part of the Y-chromosome pool of WHG though. That means that any argument that Eastern Europe must be the source of R1b in Europe today, and that it must have arrived in EHGs directly from the East, is much less certain than it was.

  9. It is highly unlikely that those nice cave paintings in Europe were arts by the ancestors of Europeans, because most Paleo-cDNAs in northern Eurasia have much more affinity with East Asians and Amerindians. Thanks to cows, R1 in Europe finally got to expand a few thousand years ago, or R1 men would have been left behind by Bantu. One of O lines started to expand tens of thousands of years ago in Asia and one of Q lines had been lucky in America until some Europeans got lost, "found" America and saw the gold jewelry on Amerindians.

  10. It is astonishing how close that the "Mongoloid" race to Oases1 and Ustlshim. A program on History Channel estimates that Amerindians were one third of world population before they were decimated. Even if they were one quarter, add another quarter (minimum) of east Asians, the "Mongoloid" race were over half of human population before Amerindians were "found". Beside, East Asia has been crowded and Huns, Mongolians and Turks sure had spread their genes to the West. It makes no sense that the East was peopled last. Not "out of Africa", it is definitely "into Africa". How could San people separate from other people for 50 ky, but people left Africa into a new and vast land mass of multiple continents and never separated between populations for 50ky. Now, Africa is the only continent with more varieties of wild animals and there were many more just decades ago. Anyway, genetics will rewrite ancient history. The myth that dogs were domesticated in Middle East has been shattered by genetics.

    1. Oase scores "deep red" for all other samples. It's not close to anything else, probably because of their extra Neanderthal admixture. The PCA is misleading here: it creates a realistic "triangle" with the main three groups but then the rest are forced to fit in it and that's in many cases just an artifact.

    2. The megafauna in Africa is actually evidence for human origins there and not in Asia, though there may have been a somewhat circuitous path from that origin point with homo erectus up to today that includes Asia at some point. The megafauna in Africa survived because they evolved alongside humans, and evolved strategies to avoid being over hunted by us. The dodo, and many other species, were not so lucky.

      "It is astonishing how close that the "Mongoloid" race to Oases1 and Ustlshim."

      That shouldn't be terribly surprising for Ust Ishm - he was a fisherman in the Ob river basin, and that basin is closely linked to the Yenisei, Lena and Amur river basins, the latter of which drains into the Pacific. I don't think it's a stretch to see a connected population of fishers across Siberia eventually contributing to and drawing from early East Asian populations.

      That being said though, Ust Ishim was not so much closer to East Asians, so much as he was more distant from modern Europeans. Ust Ishim is closer to La Brana, Papuans, and pretty much everyone than to modern Europeans. That's likely due to ongoing gene flow between Africa and the Middle East which other populations did not experience.

    3. Dude, Primates were arboreal in SE-Asia when Dinos.reigned.
      Apes left asia when the Tethys Sea was tectonically up shifted and allowed Proconsul to set foot in south.Levant/Arabia

  11. It is funny how genetics has created more "centrism", such as Yism and the fragile ego of some men hanging dearly on their precious Y. R in Europe expanded quite late and is not that dominant anyway in whole Europe(less than 20% according to one source). Einstein had E. I am curious about a EDAR variant with strong association with East Asians and Amerindians and quite surprised about the sheer number of comments and some ludicrous speculations about its origin and any selective advantage. From my limited reading, it seems that it will take a while to untangle all the mysteries. There are probably over 100 genes involved in regulation and production of Melanin and one gene usually has multiple functions too. Humans were lucky to have not only survived the last interglacial but flourished, too successful(overpopulation). Anyway, people must have half brain to believe this gene was sexually selected for hair or smaller breasts or even more sweat glands (Africa and Indian subcontinent are hot too)when ancient people were not sure when the next meal would come while watching out for predators. This gene is important for fetal development too, but it was the hair and breasts got a lot of attention. If nothing else, it evolved East Asians one base pair away from Chimpanzees, but definitely more to it. Asians have less body odor and usually have dry ear wax (ABCB11 gene, reduced function) and they also have less body hair. Who knows, it might just offset some other genes with reduced functions. Some hairy people stink.

    1. This comment has been removed by the author.

  12. Human adaptation and population differentiation in the light of ancient genomes "Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation. [...]

  13. A new paper has come out on the U6* mtDNA carried by Muierii2. Open access. The mtDNA tree they come up with is bizarre, though.

    1. Most interesting, thank you. Why do you say the tree is "bizarre"? Because of the chronology? That and the position of U8b, which, for what I know, should form a clade with K versus U8a, are the only things that are a bit odd IMO but not any odder than most stuff we have to read on those matters with hyper-recentist chronologies that make no sense whatsoever.

  14. Not so much the chronology (I will have to dig into that more) as the branching. Maybe you can make some sense of it but I can't. The U section is may be okay but the rest of it makes me suspicious.

    X is made a sister branch to R3 (now R1b) within R. Specifically this is the X2b belonging to Hungarian Neolithic sample NE3 (I1499) and the R3 belonging to the Hungarian WHG KO1 (I1507). But as far as I can tell R1b and X2b share no mutations at all under the level of N.

    The other very dubious thing is that Oase1 is put beside R (+X) clade with N1 outside it. But Oase1 was missing 2 diagnostic N mutations, 9540T and 8701A, which would mean he is pre-N. On this tree either Oase1 has back-mutated these two mutations or they have recurred in N1 and R both, which is very unparsimonious as far as I can tell. (9540 is unique to N in all of PhyloTree, 8701 is not so unstable either having back-mutated twice and recurred 5 times in total.)

    There are some little things but those are the ones that I really can't understand.

    1. It seems to me that they just used a bunch of sequences to "reinvent" the human mitogenomic tree, producing a lot of errors that is what shocks us. This kind of conflicts were common before PhyloTree was around: to our eyes they make no sense but to academics in their little scholastic and hierarchic bubble, looking at references from, say, 2001 and 2006, it may make sense, sort of.

      What is clear is that the tree is "naive" and does not attempt to fit in the standard PhyloTree one (almost infinitely more robust). That does not mean that the identification of the haplogroups is wrong, just that the tree they manage to make "unconstrainedly" is.

    2. In relation with this issue of U6, I was yesterday reminded of this 2015 study, which also suggests a deep chronology for U6 BOTH in Europe (Iberia) and North Africa, coincident with the Iberomaurusian or Oranian era. This may back a European ultimate origin for U6, as I consider in this entry, just that in Europe (other than Iberia) it did not survive the LGM, but in North Africa did. The main backing for this hypothesis are (a) the Muierii U6* and (b) the fact that there is no known Upper Paleolithic in NW Africa before the Iberomaurusian, this one looking derived from European cultures (Solutrean) rather than West Asian ones.

  15. I guess you are right, it is probably just a matter of too few samples.

    It's too bad there is still no Solutrean aDNA. Actually the only Palaeolithic sample from Iberia at all was the Magdalenian Red Lady of El Mirón, which is good but hardly enough. In fact she is the only useful sample from the entire Franco-Cantabrian refuge (there is the Gravettian LaRochette from Charente but that was too poor quality to analyze beyond being mitochondrial haplogroup M). There is still nothing from Mediterranean Spain, or the Lower Rhone, or Liguria. Those are pretty big puzzle pieces to be missing.

    What's the Solutrean aspect of the Iberomaurusian? To me it looks rather Epigravettian but I am not well-informed about the Solutrean.

    1. It does not make any sense that reference to Epigravettian: there was never such thing in Iberia, much less in Africa. What there was seemingly in South Iberia was a strong impact of Gravettian proper that later influenced the local Solutrean (sometimes Gravetto-Solutrean is used but maybe is a tad exaggerated).

      What matters is that the very concept of Iberomaurusian (nowadays also called "Oranian") was understood since the beginning, correctly it seems, to be derived from Iberian UP, hence the name: not the usual meaningless label but descriptive. Later there was an "anti-colonialist" current that interpreted that the culture had originated in NE Africa (and it was then when the term "Oranian" was introduced) but today it is very clear that the oldest sites are in the West, the oldest of all being Taforalt (> 21 Ka BP), so maybe "Taforaltian" would be an optimal name but is not in use.

      What is very clear is that the Iberomaurusian represents the first UP (blade tech or "mode 4") in the region and that its technique is similar to Solutrean, with double face fine retouch, although incorporating also the back-tipped element characteristic of Aterian, which seems to have been exported to Iberia in the late phases of the local Solutrean (i.e. our typical arrow point shape seems to have originated, at least in this part of the world, in this cultural mestizaje, being unknown before AFAIK).

      I mentioned but very briefly some of these issues in this entry on the Iberian Solutrean. My emphasis was in the synchronousness of Solutrean in Gorham's Cave (Gibraltar) and the formation of Iberomaurusian in Taforalt. I can't but notice that Taforalt is near Oujda and that there is a mysterious gap between Gibraltar and this cave, probably caused by lack of research, I presume, and this may well be because all that gap corresponds, almost exactly, to the old Spanish protectorate and it was in colonial times when much of the early research on these matters was done (apparently only by the French).

  16. so r1a farmers from middle east bring the wheat farming in india?
    r1b farmers from middle east bring the wheat farming in western europe?
    and o farmers from south china bring rice farming whit them
    i got it right?

    1. I replied with a "being overly simplistic, yes, but..." and some details, to your first question in the other thread you asked the same question:

      Regarding R1b and European Neolithic I don't think we have yet the clues to answer that. It's clear from ancient DNA that most early European Neolithic settlers (or likely descendants) were Y-DNA G2a and that the R1b found was rare and too upstream from the Western European lineages that are now most common by far. R1b is much older than R1a1, so we cannot so easily draw a parallel.

      To understand that we need to sample Atlantic Europe extensively, where there must have been peculiar founder effects in relation with Megalithism and Bell Beaker. We do not have enough Y-DNA but we do have enough mtDNA and the first modern-like mtDNA genetic pools are in Gurgy (Burgundy) and Paternabidea (Navarre), and R1b-S116 most likely expanded from somewhere between these two sites (or the wider area that includes both).

      Another possible candidate could be Portugal, where both archaeological phenomena had major centrality and probably true origins, and where some studies suggest that had a "hyper-modern" mtDNA pool (lots of H) in Neolithic times.

      So until we properly research the Atlantic coastal regions properly we won't know how exactly R1b-S116 and its Nordic "brother" R1b-U106 became so common. My opinion is that it has to do with very specifically Atlantic founder effects in the context of a very specific, distinct, innovative and sometimes quite powerful Atlantic Neolithic complex.

  17. thanks for insight
    while replacing hunter-gatherers with farmers is easily understood ,replacing farmers with other farmers is harder to grasp.
    beside war and genocide ,we could imagine that some farmers outcompete other farmers whit their superior farming tech (maybe a plough instead a stick,combined farming instead of slash and burn).
    zalmoxians out

    1. Well, in the areas surveyed in Europe, that happened indeed. Even before the Indoeuropean arrival we see a change in the genetic pool of farmers towards a greater fraction of paleoeuropean ancestry. And we also see that in the archaeo-cultural landscape, for example, in West Germany and nearby areas, Danubian Neolithic was replaced by Michelsberg culture (loosely part of the Funnelbeaker category) from North to South. That happened without doubt, what we do not understand yet well is what exactly implied because not much attention has been placed on these critical cultural layers.

      As for what was more important: plough or sword (so to say, there were no swords yet and maybe no ploughs either). That's hard to discern. A key factor in Germany specifically may have been that Danubian (LBK) expanded in the Neolithic climate optimum and receded afterwards, so maybe part of the key of the success of Michelsberg and related cultures was greater importance of cattle and less reliance on crops, or maybe it was soil exhaustion after centuries of slash and burn. I just can't say but IMO an economic element should be part of the explanation because even wars are won largely because of good logistics, i.e. better economy and management. Not the only factor but surely one to consider in the wider picture.

  18. Hello, on that PCA above Aurignacians are strongly ENA shifted, do think it's because they weren't fully differentiated yet? According to the newest research Villabruna Cluster was east eurasian admixed yet they are much further away from ENA on this PCA than Vestonice Cluster. Ust'-Ishim and Oase 1 cluster with south asian ASI tribals like Paniya, Pullinar and Kusunda. This makes sense but some Paniya and Kusanda individuals are even more australoid(closer to australian aborigenes) than Oase 1 despite the fact that Kusunda has mongoloid and Paniya has Neolithic Iranian admixture. Vestonice clusters with more generalized ASI admixed Indian samples which may suggest basal eurasian admixture in the Vestonice cluster. 35000 years old GoyetQ 116-1 is so close to these Burusho, Turkman and Nogai samples, why is that?
    That K13 tests shows that paleolithic Europeans already had WHG-like component yet were quite mixed which could be a sign of not complete differentation in ancients. On K13 they show Amerindian, Siberian, East Asian, South Asian/ASI and even something akin to Near Eastern and indeed some studies detected Basal Eurasian in Kostenki.
    Other puzzling observations is how far away Villabruna and El Miron clusters are from each. Did they both evolve from Vestonice Cluster or descended from different unsampled populations?
    Strange thing is that on the PCA above MA1 clusters towards East Asians,yet on the 3D PCA he is on the opposite side. MA1 is supposed to be ENA admixed.

    1. Let's understand one thing: sampling strategy matters A LOT and that means that, if I get four equally distant populations A, B, C and D, but with unequal figures (say n(A)=20, n(B)=15, n(C)=10 and n(D)=1), the resulting PCA will be about the larger populations only, with D (the most undersampled population) tending to either neutrality ("I'm neither this nor that") or negativeness ("I'm totally not what defines this PC axis in the positive value"). That allows for very weird false clusters and that's also why I hate-hate-hate too large and global samples: because they confuse things a lot. More focused and numerically balanced samples are much more interesting.

      Another thing: "Basal Eurasian" is something African-like (maybe even outright African, at least in part, although from North-NE areas which are not represented by Yorubas). "Basal Eurasian" is definitely not something South Asian and it is in fact defined by the literature as something that is in West Eurasians (in various amounts) but not in other Eurasians (South and East Asians or also Australasians).

      Finally it must be clear that population differentiation from others of the same origin (here ignoring possible admixture altogether for simplicity), such as the various Euriasian populations, is caused by two factors: (1) initially the founder effect or effects (they incorporate genetics from essentially a small subset of the original population and not from all the sub-groups and lineages), and later and gradually (2) endogamy-driven drift, which should be stronger the smaller the effective population is and the more time it spends in effective isolation.

      And finally admixture with "ghostly" populations such as Neanderthals, "Basal Eurasian", etc. pushes the results towards the root and in a PCA or low-resolution ADMIXTURE analysis towards the "others" catch-all category. That's why Oase-1 falsely clusters with East Asians above: because that's just the "others" category, the ones that the algorithm can only define as "not the main groups". Directly this is caused by both extreme antiquity (not enough drift had accumulated yet) and the Neanderthal admixture which is very strong in Oase 1.

      First things first, now let's see if I can answer some of your more specific questions.

    2. "on that PCA above Aurignacians are strongly ENA shifted, do think it's because they weren't fully differentiated yet?"

      Yes, absolutely. Just that I would not call them "ENA-shifted" but root-shifted, something that both populations tend to at different degrees. Basically negative PC1 approximates the Eurasian root or the non-(Paleo)-European root, to be a bit more precise. Back-question: what does the N in "ENA" stands for, I know it means "East Asians", so why that "N"?

      "According to the newest research Villabruna Cluster was east eurasian admixed"...

      Must reply with a question: what is "the newest research", Davidski's 3D PCA? If so, it will be loaded with the issues I have stated in the previous comment, particularly the problem of way-too-large and way-too-global samples. Said that, I don't see them any significantly drifted, just slightly so against "modern and Neolithic Europeans" (left X axis) and that should be understood as "not modern nor Neolithic enough". They are very close anyhow, what should be read as "mostly like modern or Neolithic Europeans" and "mostly not like others".

      "yet they are much further away from ENA on this PCA than Vestonice Cluster."

      That's because Davidski introduces a lot of other populations, which rearrange the PCA almost completely. Excluding the Z axis, which I find extremely hard to read, what Davidski's graph produces is a West-East polarity (modern or also Neolithic in Europe) in the X axis and an East Asian specific polarity in the Y axis that is totally irrelevant for European analysis.

      "Ust'-Ishim and Oase 1 cluster with south asian ASI tribals like Paniya, Pullinar and Kusunda."

      A clear case of false cluster of "others" which say "we are not this nor that, we don't fit in the categories", in this case neither modern/Neol. Europeans nor East Asians. They just tend somewhat to "not Europe", what should not be read as "somewhat East Asian" (unless proven by other more serious means, not the case).

      "some Paniya and Kusanda individuals are even more australoid (closer to australian aborigenes) than Oase 1"

      From a genetic point of view that's a false claim. There's no relatedness between Indians and Australian Aborigines other than generic Eurasianness (or Asianness, after all Europe is just a peninsula of Asia).

      In any case both Oase and Ust Ishim have major Neanderthal admixture, which will in all cases pull them towards the root or the "others" category.

      "35000 years old GoyetQ 116-1 is so close to these Burusho, Turkman and Nogai samples, why is that?"

      Because it is 35,000 years old, that's why. It tends to the root which is also the "others" category in such a poorly planned PCA.

    3. "Other puzzling observations is how far away Villabruna and El Miron clusters are from each."

      Forget the PCAs and look at Fu's fig. 3a above (heatmap): they are actually not too distant: their members relate to each other at orange colors, what indicates some affiliation or relatedness (not too intense, that would be yellow-green-white, but not extremely distant either, that is red). In fig. 3b they are numerous enough to forge their own polarity opposite to each others in the vertical axis and relative to which all others align in that dimension (mostly towards neutrality: neither one nor the other). In David's PCA they appear as more or less modern-European-like (Villabruna are similar to modern and Neolithic Europeans, El Miron group not quite).

      "That K13 tests shows that paleolithic Europeans already had WHG-like component yet were quite mixed which could be a sign of not complete differentation in ancients."

      Exactly: they haven't yet experienced the whole process of drift towards the "black" component, that's why they appear falsely "admixed".

      ... "how far away Villabruna and El Miron clusters are from each. Did they both evolve from Vestonice Cluster or descended from different unsampled populations?"

      Can't say for sure, but my impression (always on Fu's data) is that the Villabruna cluster is a bit more like Vestonice (i.e. "more Gravettian"), while the El Mirón cluster seem to have both ancestries: Gravettian (slightly weaker than the Villabruna group) and Aurignacian (they are clearly affiliated to Goyet 116-1).

      Considering Davidski's graph, it would seem as if the Gravettian ancestry made it more strongly to modern Europeans than the Aurignacian one, and that's probably because of the Villabruna group, which seems to dominate since Epipaleolithic (still balanced in the Late UP proper). It's like something happened in the Late Magdalenian or so that altered the genetics of Paleoeuropeans in favor of "Villabrunanness" (greater Gravettian ancestry) and against "Mironness" (more balanced Aurignacian-Gravettian ancestry). Strange and unexpected before this paper but interesting anyhow.

      " on the PCA above MA1 clusters towards East Asians,yet on the 3D PCA he is on the opposite side. MA1 is supposed to be ENA admixed."

      Another mirage. Ma1 is in essence a West Eurasian peculiar branch that is most directly related to the main patrilineal ancestry of Native Americans (Y-DNA Q1, much more weakly to mtDNA X2, both of which can be tracked via Siberia from a West Asian most likely origin, also archaeologically). For all the hype Ma1/"ANE" has, it does have one main merit often overlooked: demonstrating Standford's "Solutrean hypothesis" utterly false.

      But AFAIK Ma1 does not have any obvious East Asian admixture, even if minor "ANE" was indeed scattered in North China and surroundings (with instances of Q1-dominated populations known to have still existed in the Neolithic of Gansu). Ust Ishim could have true or direct ancient East Asian ancestry but that's another thing and also a very isolated individual with all kinds of peculiarities, which doesn't seem to have left any legacy, right?)


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