Ancient human genomes suggest three ancestral populations for present-day Europeans

Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Karola Kirsanow, Christos Economou, Ruth Bollongino, Qiaomei Fu, Kirsten Bos, Susanne Nordenfelt, Cesare de Filippo, Kay Prüfer, Susanna Sawyer, Cosimo Posth, Wolfgang Haak, Fredrik Hallgren, Elin Fornander, George Ayodo, Hamza A. Babiker, Elena Balanovska, Oleg Balanovsky, Haim Ben-Ami, Judit Bene, Fouad Berrada, Francesca Brisighelli, George B.J. Busby, Francesco Cali, Mikhail Churnosov, David E.C. Cole, Larissa Damba, Dominique Delsate, George van Driem, Stanislav Dryomov, Sardana A. Fedorova, Michael Francken, Irene Gallego Romero, Marina Gubina, Jean-Michel Guinet, Michael Hammer, Brenna Henn, Tor Helvig, Ugur Hodoglugil, Aashish R. Jha, Rick Kittles, Elza Khusnutdinova, Toomas Kivisild, Vaidutis Kučinskas, Rita Khusainova, Alena Kushniarevich, Leila Laredj, Sergey Litvinov, Robert W. Mahley, Béla Melegh, Ene Metspalu, Joanna Mountain, Thomas Nyambo, Ludmila Osipova, Jüri Parik, Fedor Platonov, Olga L. Posukh, Valentino Romano, Igor Rudan, Ruslan Ruizbakiev, Hovhannes Sahakyan, Antonio Salas, Elena B. Starikovskaya, Ayele Tarekegn, Draga Toncheva, Shahlo Turdikulova, Ingrida Uktveryte, Olga Utevska, Mikhail Voevoda, Joachim Wahl, Pierre Zalloua, Levon Yepiskoposyan, Tatijana Zemunik, Alan Cooper, Cristian Capelli, Mark G. Thomas, Sarah A. Tishkoff, Lalji Singh, Kumarasamy Thangaraj, Richard Villems, David Comas, Rem Sukernik, Mait Metspalu, Matthias Meyer, Evan E. Eichler, Joachim Burger, Montgomery Slatkin, Svante Pääbo, Janet Kelso, David Reich, Johannes Krause

Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.


12 thoughts on “Ancient human genomes suggest three ancestral populations for present-day Europeans

  1. I have been pondering this study quite a bit in the last days and first and foremost congratulations and thanks for a very interesting material.

    Said that, I have some caveats:

    1. I suspect (largely from the PCA fits) that Lochsbour is a quite poor representative of the WHG component, being the most distant of all WHG samples from present day Europeans (and by a lot). It would seem almost necessary to perform some control tests using other WHG samples such as Braña 2 or Skoglund, who fall much closer to present day Europeans.

    2. The concept of “Basal Eurasian” is getting many people confused. Per supp. fig. 10.1, it means nothing but West Eurasian (or West Asian) with an extra African affinity. In the paper it is briefly mentioned as a distinct ancestral population, however I understand that the best explanation is not a distinct widespread population but rather an African (Egyptian-like) founder effect in the earliest European Neolithic of Thessaly, still very obvious in the widespread presence of Y-DNA E1b-V13 (still dominant in Greece and Albania) and spotted in a Cardium Pottery population from L’Avellaner cave (Garrotxa, Catalonia), along with G2a.

    In my understanding this is best interpreted assuming a founder effect in Thessaly Neolithic, possibly after some sort of quasi-coastal migration from the Levant (which in turn has clear Mesolithic Egyptian influences), whose archaeological evidence remains elusive (actually we know near to nothing of the possible West Asian sources of Thessaly Neolithic).

    Another reason to believe that this “Basal Eurasian” artifact actually represents a mixed West Asian + North African population (with plausible partial origins in Palestine) is the fact that all three EEF samples fit best with Canarians, which are a mixed European-North African population. Add to that that the overall position tends more to the Southern Levant than to Anatolia or even the Northern Levant.

    Hope this notes are of some interest.

    • Angel found ‘negroid’ traits in Neolithic people from both Anatolia and Macedonia whilst Brace et all identified a ‘subsaharan’ strain in the Natufians of Palestine.

      Though the use of the word ‘negroid’ should not really be taken at face value, physical anthropologists have in the past picked up something racially ‘odd’ in parts of Europe and West Asia before certain earlier populations became overprinted.

      It seems intuitive to connect the ‘basal Eurasian’ mentioned in there paper with these oddities, or maybe with the non-Negroid, black Yemenis who resemble the Veddahs and might be of ancient origins.

      • I must say I’m not too happy about your speculative mixing of physical phenotype issues with my comment on the genetic one, Bones. None the less because one is quantitative measurable and the other really not, especially at these levels of dilution. Do Finns look Mongol? Mostly not at all, right? Well, half or their Y-DNA is from that area ultimately.

        I am talking of a diluted Egyptian-like (?) influence in Greece (surely after further dilution in West Asia, either Palestine or Anatolia or both), then diluted again as those Thessalian early farmers expanded through Europe. Yes, the E1b lineage almost certainly coalesced ultimately in Sudan or Ethiopia (not Nigeria) but (judging on mtDNA and nDNA), the amount of such Tropical African component in Europe is almost certaily too negligible to be detectable in phenotype.

        In Western Iberia there is a more (also very diluted but maybe not so much) direct Moroccan-like influence (main Y-DNA marker E1b-M81) of unknown origins (I have a couple of theories but too long to explain here) but all I have ever spotted in phenotypes is the occasional Berber look.

        As for Yemenis and other peninsular Arabs. In this case I do believe that there is a geunine “Basal Eurasian” (or earliest OoA remnant) element in that area, which has been often misinterpreted as Indian Ocean slave trade byproduct, when IMO most of it derives from much more ancient interactions with NE Africa, possibly even from the times of the original migration out-of-Africa (OoA). Similarly much of the L(xM,N) in NW Africa (~20-25%) is probably much older than the trans-Saharan slave trade and a genuine remnant of flows like those at the genesis of Aterian some 125 Ka ago (for example L3k or the unusual A0 and A1a yDNA lineages, shared at very low frequencies with West and Central Africa).

        But all this is a different story of what I was trying to convey above, which rather relates to the reconstructed history of E1b in North Africa and probably also to that of the Afroasiatic (linguistic family) genesis or expansion northwards. In Epipaleolithic (“Mesolithic”) times it is detectable some Egyptian or Nubian originated influence in both NW Africa (Capsian culture) and Palestine (Kebaran or at the very least its semi-desert subgroups, which would eventually lead to the Semitic genesis in the Circum-Arabian Pastoralist Complex or PPNC). All this almost certainly relates to the expansion of Northern Afroasiatic languages (Berber, Egyptian and Semitic).

        Apparently an offshoot of the Palestinian branch mysteriously (and almost certainly very diluted except in yDNA) arrived to Greece just in time (or maybe a bit earlier) to take part in the first European Neolithic in Thessaly. It’s very likely that this people did not even spoke Afroasiatic anymore but they did have notable amounts of E1b-V13, still apparent in Greece and Albania (and to quite less extent in other parts of Europe along the Neolithic expansion routes, both inland and coastal). Traces of this African affinity may still be detectable among EEFs, what should question the “Basal Eurasian” concept and replace it by the more likely correct minor African (Egyptian) influence in the Levant since Mesolithic times. But I honestly doubt you can spot it in modern looks, with the odd exception maybe.

      • I have only seen the frontal photo that comes in the study. To my eye it does have some archaic-looking features (notably the prominent browridge, a trait still present in some people of our species) but he must be a Homo sapiens, notably because a high quality genome has been obtained and analyzed (also in comparison with Neanderthals and Denisovans).

        However the archaic-like features, together with his positioning in the PCA as the most distant from modern Europeans of all the WHG samples, do suggest that he was somewhat anomalous, maybe in the sense of being very peripheral, inbred or whatever. Such marked browridge is not at all common in UP skulls of Europe at the very least, not more than today probably. Just search for images of Cro-Magnon, Chancelade, Taforalt or even the oldest of all known Europeans: Pestera cu Oase. None of them shows such a trait. I guess that the prominent browridge could have been more common in the Northern areas, at least judging by this rare head sculpture (→, which I believe is from Moravia. Some individuals in any case do show a strong brow bone and this may be relatively common in some regions (from memory I’d say that maybe parts of Latvia but unsure).

        On its own the brow bone cannot determine the species unlike quite probably does the chin prominence, which is exclusive of our species.

        I know that is not probably on the hands of the researchers (the French state has a very negative attitude towards genetic research) but I would love to see this same kind of analysis with sequences from Magdalenian (or Epipaleolithic) peoples from SW France, which I suspect should be closer to the actual source of WHG influence in modern Europeans. In absence of this, control tests with those WHG individuals who fall much closer to modern Europeans, such as Skoglund or La Braña 2, seem almost necessary IMO, because the WHG ancestry may well be much larger than what appears using Lochsbour as only reference.

    • No.

      The old hypothesis you mention is anyhow without merit as far as I can discern. The Magdalenian remains appear just typical West Eurasian.

      I don’t mean to predict anything. I just see in the very PCA graph of this study that Lochsbour is very much distant from modern Europeans, much more than any of the other WHG individuals. So that’s why I think that he may be very much not representative of the real WHG component. In general all the samples are from rather unusual contexts, so what I’d love is to have also some samples from more “central” ones, such as Magdalenian or Tardenois contexts, or maybe Italian, Moravian or Ukrainian late paleolithic, which may better represent the true WHG element (or maybe not but we can only know for sure with data).

      But I would be content if the same formal tests performed with Lochsbour would have been performed, for control reasons, with Braña 2 and/or Skoglund.

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